September 2011 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: dan: Tool help updates.
by Bitbucket 21 Sep '11

21 Sep '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/ce13c0d3a3d7/ changeset: ce13c0d3a3d7 user: dan date: 2011-09-21 10:11:07 summary: Tool help updates. affected #: 134 files (-1 bytes) --- a/tools/annotation_profiler/annotation_profiler.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/annotation_profiler/annotation_profiler.xml Wed Sep 21 04:11:07 2011 -0400 @@ -132,5 +132,11 @@ **TIP:** non-redundant (nr) refers to the set of intervals that remains after the intervals provided have been merged to resolve overlaps +------ + +**Citation** + +If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* + </help></tool> --- a/tools/emboss_5/emboss_antigenic.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_antigenic.xml Wed Sep 21 04:11:07 2011 -0400 @@ -44,6 +44,13 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/antigenic.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/antigenic.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_backtranseq.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_backtranseq.xml Wed Sep 21 04:11:07 2011 -0400 @@ -215,6 +215,12 @@ You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/backtranseq.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/backtranseq.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> --- a/tools/emboss_5/emboss_banana.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_banana.xml Wed Sep 21 04:11:07 2011 -0400 @@ -19,6 +19,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/banana.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/banana.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_biosed.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_biosed.xml Wed Sep 21 04:11:07 2011 -0400 @@ -1,7 +1,7 @@ <tool id="EMBOSS: biosed4" name="biosed" version="5.0.0"><description>Replace or delete sequence sections</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>biosed -sequence $input1 -outseq $out_file1 -target $target -replace $replace -osformat2 $out_format1 -auto</command> + <command>biosed -sequence $input1 -outseq $out_file1 -target "$target" -replace "$replace" -osformat2 "$out_format1" -auto</command><inputs><param format="fasta" name="input1" type="data"><label>On query</label> @@ -68,6 +68,12 @@ You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/biosed.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/biosed.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> --- a/tools/emboss_5/emboss_btwisted.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_btwisted.xml Wed Sep 21 04:11:07 2011 -0400 @@ -19,6 +19,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/btwisted.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/btwisted.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_cai.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_cai.xml Wed Sep 21 04:11:07 2011 -0400 @@ -180,6 +180,12 @@ You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/cai.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/cai.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> --- a/tools/emboss_5/emboss_cai_custom.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_cai_custom.xml Wed Sep 21 04:11:07 2011 -0400 @@ -22,6 +22,12 @@ You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/cai_custom.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/cai_custom.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> --- a/tools/emboss_5/emboss_chaos.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_chaos.xml Wed Sep 21 04:11:07 2011 -0400 @@ -18,6 +18,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/chaos.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/chaos.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_charge.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_charge.xml Wed Sep 21 04:11:07 2011 -0400 @@ -30,6 +30,12 @@ You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/charge.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/charge.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> --- a/tools/emboss_5/emboss_checktrans.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_checktrans.xml Wed Sep 21 04:11:07 2011 -0400 @@ -82,6 +82,12 @@ You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/checktrans.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/checktrans.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> --- a/tools/emboss_5/emboss_chips.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_chips.xml Wed Sep 21 04:11:07 2011 -0400 @@ -25,6 +25,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/chips.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/chips.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_cirdna.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_cirdna.xml Wed Sep 21 04:11:07 2011 -0400 @@ -18,6 +18,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/cirdna.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/cirdna.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_codcmp.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_codcmp.xml Wed Sep 21 04:11:07 2011 -0400 @@ -325,6 +325,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/codcmp.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/codcmp.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_coderet.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_coderet.xml Wed Sep 21 04:11:07 2011 -0400 @@ -68,6 +68,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/coderet.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/coderet.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> --- a/tools/emboss_5/emboss_compseq.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_compseq.xml Wed Sep 21 04:11:07 2011 -0400 @@ -37,6 +37,12 @@ You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/compseq.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/compseq.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> --- a/tools/emboss_5/emboss_cpgplot.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_cpgplot.xml Wed Sep 21 04:11:07 2011 -0400 @@ -28,6 +28,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/cpgplot.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/cpgplot.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_cpgreport.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_cpgreport.xml Wed Sep 21 04:11:07 2011 -0400 @@ -44,6 +44,12 @@ You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/cpgreport.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/cpgreport.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> --- a/tools/emboss_5/emboss_cusp.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_cusp.xml Wed Sep 21 04:11:07 2011 -0400 @@ -25,6 +25,12 @@ You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/cusp.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/cusp.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> --- a/tools/emboss_5/emboss_cutseq.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_cutseq.xml Wed Sep 21 04:11:07 2011 -0400 @@ -67,6 +67,12 @@ You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/cutseq.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/cutseq.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> --- a/tools/emboss_5/emboss_dan.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_dan.xml Wed Sep 21 04:11:07 2011 -0400 @@ -79,6 +79,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/dan.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/dan.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_degapseq.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_degapseq.xml Wed Sep 21 04:11:07 2011 -0400 @@ -53,6 +53,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/degapseq.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/degapseq.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_descseq.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_descseq.xml Wed Sep 21 04:11:07 2011 -0400 @@ -67,6 +67,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/descseq.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/descseq.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_diffseq.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_diffseq.xml Wed Sep 21 04:11:07 2011 -0400 @@ -59,6 +59,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/diffseq.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/diffseq.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_digest.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_digest.xml Wed Sep 21 04:11:07 2011 -0400 @@ -60,6 +60,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/digest.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/digest.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_dotmatcher.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_dotmatcher.xml Wed Sep 21 04:11:07 2011 -0400 @@ -24,6 +24,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/dotmatcher.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/dotmatcher.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_dotpath.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_dotpath.xml Wed Sep 21 04:11:07 2011 -0400 @@ -31,6 +31,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/dotpath.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/dotpath.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_dottup.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_dottup.xml Wed Sep 21 04:11:07 2011 -0400 @@ -25,6 +25,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/dottup.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/dottup.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_dreg.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_dreg.xml Wed Sep 21 04:11:07 2011 -0400 @@ -17,6 +17,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/dreg.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/dreg.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_einverted.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_einverted.xml Wed Sep 21 04:11:07 2011 -0400 @@ -45,6 +45,12 @@ You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/einverted.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/einverted.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> --- a/tools/emboss_5/emboss_epestfind.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_epestfind.xml Wed Sep 21 04:11:07 2011 -0400 @@ -60,6 +60,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/epestfind.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/epestfind.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_equicktandem.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_equicktandem.xml Wed Sep 21 04:11:07 2011 -0400 @@ -55,6 +55,12 @@ You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/equicktandem.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/equicktandem.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> --- a/tools/emboss_5/emboss_est2genome.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_est2genome.xml Wed Sep 21 04:11:07 2011 -0400 @@ -98,6 +98,12 @@ You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/est2genome.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/est2genome.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> --- a/tools/emboss_5/emboss_etandem.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_etandem.xml Wed Sep 21 04:11:07 2011 -0400 @@ -71,7 +71,13 @@ You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/etandem.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/etandem.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> --- a/tools/emboss_5/emboss_extractfeat.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_extractfeat.xml Wed Sep 21 04:11:07 2011 -0400 @@ -92,5 +92,11 @@ You can view the original documentation here_. .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/extractfeat.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_extractseq.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_extractseq.xml Wed Sep 21 04:11:07 2011 -0400 @@ -63,6 +63,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/extractseq.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/extractseq.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_freak.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_freak.xml Wed Sep 21 04:11:07 2011 -0400 @@ -31,6 +31,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/freak.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/freak.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_fuzznuc.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_fuzznuc.xml Wed Sep 21 04:11:07 2011 -0400 @@ -70,6 +70,12 @@ You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/fuzznuc.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/fuzznuc.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> --- a/tools/emboss_5/emboss_fuzzpro.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_fuzzpro.xml Wed Sep 21 04:11:07 2011 -0400 @@ -39,6 +39,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/fuzzpro.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/fuzzpro.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_fuzztran.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_fuzztran.xml Wed Sep 21 04:11:07 2011 -0400 @@ -90,6 +90,12 @@ You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/fuzztran.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/fuzztran.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> --- a/tools/emboss_5/emboss_garnier.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_garnier.xml Wed Sep 21 04:11:07 2011 -0400 @@ -53,6 +53,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/garnier.html + .. _here: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/garnier.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_geecee.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_geecee.xml Wed Sep 21 04:11:07 2011 -0400 @@ -19,6 +19,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/geecee.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/geecee.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_getorf.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_getorf.xml Wed Sep 21 04:11:07 2011 -0400 @@ -124,6 +124,12 @@ You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/getorf.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/getorf.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> --- a/tools/emboss_5/emboss_helixturnhelix.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_helixturnhelix.xml Wed Sep 21 04:11:07 2011 -0400 @@ -58,6 +58,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/helixturnhelix.h… + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/helixturnhelix.h… + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_hmoment.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_hmoment.xml Wed Sep 21 04:11:07 2011 -0400 @@ -27,6 +27,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/hmoment.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/hmoment.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_iep.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_iep.xml Wed Sep 21 04:11:07 2011 -0400 @@ -33,6 +33,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/iep.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/iep.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_infoseq.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_infoseq.xml Wed Sep 21 04:11:07 2011 -0400 @@ -71,6 +71,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/infoseq.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/infoseq.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_isochore.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_isochore.xml Wed Sep 21 04:11:07 2011 -0400 @@ -78,5 +78,11 @@ .. image:: ./static/emboss_icons/isochore.png +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + </help></tool> --- a/tools/emboss_5/emboss_lindna.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_lindna.xml Wed Sep 21 04:11:07 2011 -0400 @@ -94,6 +94,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/lindna.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/lindna.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_marscan.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_marscan.xml Wed Sep 21 04:11:07 2011 -0400 @@ -40,6 +40,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/marscan.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/marscan.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_maskfeat.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_maskfeat.xml Wed Sep 21 04:11:07 2011 -0400 @@ -67,6 +67,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/maskfeat.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/maskfeat.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_maskseq.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_maskseq.xml Wed Sep 21 04:11:07 2011 -0400 @@ -67,6 +67,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/maskseq.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/maskseq.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_matcher.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_matcher.xml Wed Sep 21 04:11:07 2011 -0400 @@ -52,6 +52,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/matcher.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/matcher.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_megamerger.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_megamerger.xml Wed Sep 21 04:11:07 2011 -0400 @@ -58,6 +58,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/megamerger.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/megamerger.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_merger.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_merger.xml Wed Sep 21 04:11:07 2011 -0400 @@ -71,6 +71,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/merger.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/merger.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_msbar.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_msbar.xml Wed Sep 21 04:11:07 2011 -0400 @@ -112,6 +112,12 @@ You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/msbar.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/msbar.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> --- a/tools/emboss_5/emboss_needle.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_needle.xml Wed Sep 21 04:11:07 2011 -0400 @@ -121,6 +121,12 @@ #--------------------------------------- #--------------------------------------- - + + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> --- a/tools/emboss_5/emboss_newcpgreport.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_newcpgreport.xml Wed Sep 21 04:11:07 2011 -0400 @@ -39,6 +39,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/newcpgreport.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/newcpgreport.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_newcpgseek.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_newcpgseek.xml Wed Sep 21 04:11:07 2011 -0400 @@ -30,6 +30,12 @@ You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/newcpgseek.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/newcpgseek.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> --- a/tools/emboss_5/emboss_newseq.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_newseq.xml Wed Sep 21 04:11:07 2011 -0400 @@ -67,6 +67,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/newseq.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/newseq.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_noreturn.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_noreturn.xml Wed Sep 21 04:11:07 2011 -0400 @@ -26,6 +26,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/noreturn.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/noreturn.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_notseq.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_notseq.xml Wed Sep 21 04:11:07 2011 -0400 @@ -64,6 +64,12 @@ You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/notseq.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/notseq.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> --- a/tools/emboss_5/emboss_nthseq.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_nthseq.xml Wed Sep 21 04:11:07 2011 -0400 @@ -64,6 +64,12 @@ You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/nthseq.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/nthseq.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> --- a/tools/emboss_5/emboss_octanol.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_octanol.xml Wed Sep 21 04:11:07 2011 -0400 @@ -34,5 +34,11 @@ You can view the original documentation here_. .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/octanol.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_oddcomp.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_oddcomp.xml Wed Sep 21 04:11:07 2011 -0400 @@ -35,6 +35,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/oddcomp.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/oddcomp.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_palindrome.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_palindrome.xml Wed Sep 21 04:11:07 2011 -0400 @@ -48,6 +48,12 @@ You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/palindrome.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/palindrome.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> --- a/tools/emboss_5/emboss_pasteseq.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_pasteseq.xml Wed Sep 21 04:11:07 2011 -0400 @@ -68,6 +68,12 @@ You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/pasteseq.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/pasteseq.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> --- a/tools/emboss_5/emboss_patmatdb.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_patmatdb.xml Wed Sep 21 04:11:07 2011 -0400 @@ -44,6 +44,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/patmatdb.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/patmatdb.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_pepcoil.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_pepcoil.xml Wed Sep 21 04:11:07 2011 -0400 @@ -41,6 +41,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/pepcoil.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/pepcoil.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_pepinfo.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_pepinfo.xml Wed Sep 21 04:11:07 2011 -0400 @@ -23,6 +23,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/pepinfo.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/pepinfo.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_pepnet.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_pepnet.xml Wed Sep 21 04:11:07 2011 -0400 @@ -28,6 +28,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/pepnet.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/pepnet.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_pepstats.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_pepstats.xml Wed Sep 21 04:11:07 2011 -0400 @@ -25,6 +25,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/pepstats.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/pepstats.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_pepwheel.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_pepwheel.xml Wed Sep 21 04:11:07 2011 -0400 @@ -40,6 +40,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/pepwheel.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/pepwheel.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_pepwindow.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_pepwindow.xml Wed Sep 21 04:11:07 2011 -0400 @@ -17,6 +17,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/pepwindow.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/pepwindow.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_pepwindowall.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_pepwindowall.xml Wed Sep 21 04:11:07 2011 -0400 @@ -17,6 +17,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/pepwindowall.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/pepwindowall.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_plotcon.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_plotcon.xml Wed Sep 21 04:11:07 2011 -0400 @@ -17,6 +17,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/plotcon.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/plotcon.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_plotorf.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_plotorf.xml Wed Sep 21 04:11:07 2011 -0400 @@ -35,6 +35,12 @@ You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/plotorf.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/plotorf.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> --- a/tools/emboss_5/emboss_polydot.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_polydot.xml Wed Sep 21 04:11:07 2011 -0400 @@ -43,6 +43,12 @@ You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/polydot.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/polydot.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> --- a/tools/emboss_5/emboss_preg.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_preg.xml Wed Sep 21 04:11:07 2011 -0400 @@ -16,6 +16,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/preg.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/preg.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_prettyplot.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_prettyplot.xml Wed Sep 21 04:11:07 2011 -0400 @@ -108,6 +108,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/prettyplot.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/prettyplot.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_prettyseq.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_prettyseq.xml Wed Sep 21 04:11:07 2011 -0400 @@ -48,6 +48,12 @@ You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/prettyseq.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/prettyseq.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> --- a/tools/emboss_5/emboss_primersearch.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_primersearch.xml Wed Sep 21 04:11:07 2011 -0400 @@ -28,6 +28,12 @@ You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/primersearch.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/primersearch.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> --- a/tools/emboss_5/emboss_revseq.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_revseq.xml Wed Sep 21 04:11:07 2011 -0400 @@ -72,6 +72,12 @@ You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/revseq.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/revseq.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> --- a/tools/emboss_5/emboss_seqmatchall.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_seqmatchall.xml Wed Sep 21 04:11:07 2011 -0400 @@ -49,6 +49,12 @@ You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/seqmatchall.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/seqmatchall.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> --- a/tools/emboss_5/emboss_seqret.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_seqret.xml Wed Sep 21 04:11:07 2011 -0400 @@ -65,6 +65,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/seqret.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/seqret.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_showfeat.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_showfeat.xml Wed Sep 21 04:11:07 2011 -0400 @@ -118,6 +118,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/showfeat.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/showfeat.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_shuffleseq.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_shuffleseq.xml Wed Sep 21 04:11:07 2011 -0400 @@ -57,6 +57,12 @@ You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/shuffleseq.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/shuffleseq.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> --- a/tools/emboss_5/emboss_sigcleave.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_sigcleave.xml Wed Sep 21 04:11:07 2011 -0400 @@ -50,6 +50,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/sigcleave.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/sigcleave.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_sirna.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_sirna.xml Wed Sep 21 04:11:07 2011 -0400 @@ -113,6 +113,12 @@ You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/sirna.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/sirna.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> --- a/tools/emboss_5/emboss_sixpack.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_sixpack.xml Wed Sep 21 04:11:07 2011 -0400 @@ -157,6 +157,12 @@ You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/sixpack.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/sixpack.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> --- a/tools/emboss_5/emboss_skipseq.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_skipseq.xml Wed Sep 21 04:11:07 2011 -0400 @@ -54,6 +54,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/skipseq.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/skipseq.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_splitter.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_splitter.xml Wed Sep 21 04:11:07 2011 -0400 @@ -74,6 +74,12 @@ You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/splitter.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/splitter.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> --- a/tools/emboss_5/emboss_supermatcher.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_supermatcher.xml Wed Sep 21 04:11:07 2011 -0400 @@ -59,6 +59,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/supermatcher.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/supermatcher.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> --- a/tools/emboss_5/emboss_syco.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_syco.xml Wed Sep 21 04:11:07 2011 -0400 @@ -192,6 +192,12 @@ You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/syco.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/syco.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> --- a/tools/emboss_5/emboss_tcode.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_tcode.xml Wed Sep 21 04:11:07 2011 -0400 @@ -39,6 +39,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/tcode.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/tcode.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_textsearch.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_textsearch.xml Wed Sep 21 04:11:07 2011 -0400 @@ -53,6 +53,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/textsearch.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/textsearch.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_tmap.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_tmap.xml Wed Sep 21 04:11:07 2011 -0400 @@ -34,6 +34,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/tmap.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/tmap.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_tranalign.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_tranalign.xml Wed Sep 21 04:11:07 2011 -0400 @@ -79,6 +79,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/tranalign.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/tranalign.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> --- a/tools/emboss_5/emboss_transeq.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_transeq.xml Wed Sep 21 04:11:07 2011 -0400 @@ -117,6 +117,12 @@ You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/transeq.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/transeq.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> --- a/tools/emboss_5/emboss_trimest.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_trimest.xml Wed Sep 21 04:11:07 2011 -0400 @@ -87,6 +87,12 @@ You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/trimest.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/trimest.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> --- a/tools/emboss_5/emboss_trimseq.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_trimseq.xml Wed Sep 21 04:11:07 2011 -0400 @@ -92,6 +92,12 @@ You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/trimseq.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/trimseq.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> --- a/tools/emboss_5/emboss_twofeat.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_twofeat.xml Wed Sep 21 04:11:07 2011 -0400 @@ -125,6 +125,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/twofeat.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/twofeat.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file --- a/tools/emboss_5/emboss_union.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_union.xml Wed Sep 21 04:11:07 2011 -0400 @@ -60,6 +60,12 @@ You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/union.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/union.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> --- a/tools/emboss_5/emboss_vectorstrip.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_vectorstrip.xml Wed Sep 21 04:11:07 2011 -0400 @@ -77,6 +77,12 @@ <help> You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/vectorstrip.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/vectorstrip.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> --- a/tools/emboss_5/emboss_water.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_water.xml Wed Sep 21 04:11:07 2011 -0400 @@ -61,6 +61,12 @@ You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/water.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/water.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> --- a/tools/emboss_5/emboss_wobble.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_wobble.xml Wed Sep 21 04:11:07 2011 -0400 @@ -35,6 +35,12 @@ You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/wobble.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/wobble.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> --- a/tools/emboss_5/emboss_wordcount.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_wordcount.xml Wed Sep 21 04:11:07 2011 -0400 @@ -30,6 +30,12 @@ You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/wordcount.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/wordcount.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> --- a/tools/emboss_5/emboss_wordmatch.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/emboss_5/emboss_wordmatch.xml Wed Sep 21 04:11:07 2011 -0400 @@ -69,6 +69,12 @@ You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/wordmatch.html + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/wordmatch.html + +------ + +**Citation** + +If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> --- a/tools/encode/gencode_partition.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/encode/gencode_partition.xml Wed Sep 21 04:11:07 2011 -0400 @@ -35,5 +35,11 @@ **Note:** Features overlapping more than one partition will take the identity of the lower-numbered partition. +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + </help></tool> \ No newline at end of file --- a/tools/encode/random_intervals.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/encode/random_intervals.xml Wed Sep 21 04:11:07 2011 -0400 @@ -54,5 +54,11 @@ **Regions to use** options * Bounding region of interest based on the dataset build. +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + </help></tool> \ No newline at end of file --- a/tools/evolution/mutate_snp_codon.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/evolution/mutate_snp_codon.xml Wed Sep 21 04:11:07 2011 -0400 @@ -56,5 +56,12 @@ chr1 59373 59376 NM_001005484 0 + ACA ACA Thr ACA 614523 15.11 0 2162384 0.284187729839 585 chr1 59373 59374 rs2691305 0 - A A C/T genomic single unknown 0 0 unknown exact 3 GCA chr1 59412 59415 NM_001005484 0 + GCG GCG Ala GCG 299495 7.37 0 2820741 0.106176001271 585 chr1 59414 59415 rs2531266 0 + G G C/G genomic single by-submitter 0 0 unknown exact 3 GCC chr1 59412 59415 NM_001005484 0 + GCG GCG Ala GCG 299495 7.37 0 2820741 0.106176001271 585 chr1 59414 59415 rs55874132 0 + G G C/G genomic single unknown 0 0 coding-synon exact 1 GCC + +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ + </help></tool> --- a/tools/gatk/analyze_covariates.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/gatk/analyze_covariates.xml Wed Sep 21 04:11:07 2011 -0400 @@ -96,5 +96,7 @@ For the underlying tool, please cite `DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011 May;43(5):491-8. <http://www.ncbi.nlm.nih.gov/pubmed/21478889>`_ +If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* + </help></tool> --- a/tools/gatk/count_covariates.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/gatk/count_covariates.xml Wed Sep 21 04:11:07 2011 -0400 @@ -431,5 +431,7 @@ For the underlying tool, please cite `DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011 May;43(5):491-8. <http://www.ncbi.nlm.nih.gov/pubmed/21478889>`_ +If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* + </help></tool> --- a/tools/gatk/indel_realigner.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/gatk/indel_realigner.xml Wed Sep 21 04:11:07 2011 -0400 @@ -347,5 +347,7 @@ For the underlying tool, please cite `DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011 May;43(5):491-8. <http://www.ncbi.nlm.nih.gov/pubmed/21478889>`_ +If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* + </help></tool> --- a/tools/gatk/realigner_target_creator.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/gatk/realigner_target_creator.xml Wed Sep 21 04:11:07 2011 -0400 @@ -301,5 +301,7 @@ For the underlying tool, please cite `DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011 May;43(5):491-8. <http://www.ncbi.nlm.nih.gov/pubmed/21478889>`_ +If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* + </help></tool> --- a/tools/gatk/table_recalibration.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/gatk/table_recalibration.xml Wed Sep 21 04:11:07 2011 -0400 @@ -399,5 +399,7 @@ For the underlying tool, please cite `DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011 May;43(5):491-8. <http://www.ncbi.nlm.nih.gov/pubmed/21478889>`_ +If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* + </help></tool> --- a/tools/gatk/unified_genotyper.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/gatk/unified_genotyper.xml Wed Sep 21 04:11:07 2011 -0400 @@ -420,5 +420,7 @@ For the underlying tool, please cite `DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011 May;43(5):491-8. <http://www.ncbi.nlm.nih.gov/pubmed/21478889>`_ +If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* + </help></tool> --- a/tools/gatk/variant_annotator.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/gatk/variant_annotator.xml Wed Sep 21 04:11:07 2011 -0400 @@ -412,5 +412,7 @@ For the underlying tool, please cite `DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011 May;43(5):491-8. <http://www.ncbi.nlm.nih.gov/pubmed/21478889>`_ +If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* + </help></tool> --- a/tools/gatk/variant_apply_recalibration.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/gatk/variant_apply_recalibration.xml Wed Sep 21 04:11:07 2011 -0400 @@ -273,5 +273,7 @@ For the underlying tool, please cite `DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011 May;43(5):491-8. <http://www.ncbi.nlm.nih.gov/pubmed/21478889>`_ +If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* + </help></tool> --- a/tools/gatk/variant_combine.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/gatk/variant_combine.xml Wed Sep 21 04:11:07 2011 -0400 @@ -306,6 +306,7 @@ For the underlying tool, please cite `DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011 May;43(5):491-8. <http://www.ncbi.nlm.nih.gov/pubmed/21478889>`_ +If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* </help></tool> --- a/tools/gatk/variant_eval.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/gatk/variant_eval.xml Wed Sep 21 04:11:07 2011 -0400 @@ -420,5 +420,7 @@ For the underlying tool, please cite `DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011 May;43(5):491-8. <http://www.ncbi.nlm.nih.gov/pubmed/21478889>`_ +If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* + </help></tool> --- a/tools/gatk/variant_filtration.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/gatk/variant_filtration.xml Wed Sep 21 04:11:07 2011 -0400 @@ -334,5 +334,7 @@ For the underlying tool, please cite `DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011 May;43(5):491-8. <http://www.ncbi.nlm.nih.gov/pubmed/21478889>`_ +If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* + </help></tool> --- a/tools/gatk/variant_recalibrator.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/gatk/variant_recalibrator.xml Wed Sep 21 04:11:07 2011 -0400 @@ -556,5 +556,7 @@ For the underlying tool, please cite `DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011 May;43(5):491-8. <http://www.ncbi.nlm.nih.gov/pubmed/21478889>`_ +If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* + </help></tool> --- a/tools/gatk/variants_validate.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/gatk/variants_validate.xml Wed Sep 21 04:11:07 2011 -0400 @@ -278,5 +278,7 @@ For the underlying tool, please cite `DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011 May;43(5):491-8. <http://www.ncbi.nlm.nih.gov/pubmed/21478889>`_ +If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* + </help></tool> --- a/tools/genetrack/genetrack_indexer.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/genetrack/genetrack_indexer.xml Wed Sep 21 04:11:07 2011 -0400 @@ -49,6 +49,12 @@ When shifting the averaging process in GeneTrack is able correct for longer or shorter than expected fragment sizes as long as the errors are reasonably random. +------ + +**Citation** + +If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* + </help></tool> --- a/tools/genetrack/genetrack_peak_prediction.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/genetrack/genetrack_peak_prediction.xml Wed Sep 21 04:11:07 2011 -0400 @@ -54,6 +54,12 @@ - **Prediction method** the function used to average nearby values +------ + +**Citation** + +If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* + </help></tool> --- a/tools/maf/vcf_to_maf_customtrack.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/maf/vcf_to_maf_customtrack.xml Wed Sep 21 04:11:07 2011 -0400 @@ -121,6 +121,11 @@ s CHB+JPT_1.5 0 1 + 1 *------ s CHB+JPT_2.5 0 7 + 7 *GGA*** +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ </help></tool> --- a/tools/meme/fimo.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/meme/fimo.xml Wed Sep 21 04:11:07 2011 -0400 @@ -223,6 +223,13 @@ For detailed information on FIMO, click here_. To view the license_. +------ + +**Citation** + +If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* + + .. _here: http://meme.nbcr.net/meme/fimo-intro.html .. _license: http://meme.nbcr.net/meme/COPYRIGHT.html --- a/tools/meme/meme.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/meme/meme.xml Wed Sep 21 04:11:07 2011 -0400 @@ -340,6 +340,12 @@ For detailed information on MEME, click here_. To view the license_. +------ + +**Citation** + +If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* + .. _here: http://meme.nbcr.net/meme/meme-intro.html .. _license: http://meme.nbcr.net/meme/COPYRIGHT.html --- a/tools/peak_calling/ccat_2_wrapper.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/peak_calling/ccat_2_wrapper.xml Wed Sep 21 04:11:07 2011 -0400 @@ -119,5 +119,12 @@ This tool allows ChIP-seq peak/region calling using CCAT. View the original CCAT documentation: http://cmb.gis.a-star.edu.sg/ChIPSeq/paperCCAT.htm. + +------ + +**Citation** + +If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* + </help></tool> --- a/tools/peak_calling/ccat_wrapper.py Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/peak_calling/ccat_wrapper.py Wed Sep 21 04:11:07 2011 -0400 @@ -25,6 +25,7 @@ tmp_dir = tempfile.mkdtemp() try: + assert os.path.exists( chrom_info_file ), "The required chromosome length file does not exist." proc = subprocess.Popen( args="%s %s > %s" % ( CCAT_BINARY, " ".join( map( lambda x: "'%s'" % x, [ input_tag_file, input_control_file, chrom_info_file, input_config_file, project_name ] ) ), output_log_file ), shell=True, cwd=tmp_dir ) proc.wait() if proc.returncode: --- a/tools/peak_calling/ccat_wrapper.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/peak_calling/ccat_wrapper.xml Wed Sep 21 04:11:07 2011 -0400 @@ -135,5 +135,12 @@ This tool allows ChIP-seq peak/region calling using CCAT. View the original CCAT documentation: http://cmb.gis.a-star.edu.sg/ChIPSeq/paperCCAT.htm. + +------ + +**Citation** + +If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* + </help></tool> --- a/tools/peak_calling/macs_wrapper.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/peak_calling/macs_wrapper.xml Wed Sep 21 04:11:07 2011 -0400 @@ -226,5 +226,12 @@ Depending upon selected options, 2 to 6 history items will be created; the first output will be a standard BED file and the last will be an HTML report containing links to download additional files generated by MACS. Up to two each of wig and interval files can be optionally created; the interval files are parsed from the xls output. View the original MACS documentation: http://liulab.dfci.harvard.edu/MACS/00README.html. + +------ + +**Citation** + +If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* + </help></tool> --- a/tools/peak_calling/sicer_wrapper.xml Tue Sep 20 11:31:23 2011 -0400 +++ b/tools/peak_calling/sicer_wrapper.xml Wed Sep 21 04:11:07 2011 -0400 @@ -172,5 +172,7 @@ For the underlying tool, please cite `Zang C, Schones DE, Zeng C, Cui K, Zhao K, Peng W. A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics. 2009 Aug 1;25(15):1952-8. <http://www.ncbi.nlm.nih.gov/pubmed/19505939>`_ +If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* + </help></tool> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Clearer message when converting fasta for custom builds.
by Bitbucket 20 Sep '11

20 Sep '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/ed73683806af/ changeset: ed73683806af user: jgoecks date: 2011-09-20 17:31:23 summary: Clearer message when converting fasta for custom builds. affected #: 1 file (-1 bytes) --- a/templates/user/dbkeys.mako Tue Sep 20 11:20:13 2011 -0400 +++ b/templates/user/dbkeys.mako Tue Sep 20 11:31:23 2011 -0400 @@ -104,7 +104,7 @@ % if 'count' in dct: ${dct['count']} % else: - working + ? % endif </td><td><form action="dbkeys" method="post"><input type="hidden" name="key" value="${key}" /><input type="submit" name="delete" value="Delete" /></form></td> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by Bitbucket 20 Sep '11

20 Sep '11

2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/3342e9df3cd2/ changeset: 3342e9df3cd2 user: jgoecks date: 2011-09-20 17:19:44 summary: Use fasta HDAs to specify custom builds. Do automatic conversions from fasta to 2bit and len; also, do conversion from len to linecount so that chrom/contig count is available. Finally, refactor 'compute fasta length' code out of tools and into converters. affected #: 10 files (-1 bytes) --- a/datatypes_conf.xml.sample Tue Sep 20 10:45:23 2011 -0400 +++ b/datatypes_conf.xml.sample Tue Sep 20 11:19:44 2011 -0400 @@ -135,6 +135,7 @@ <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true"/><datatype extension="twobit" type="galaxy.datatypes.binary:TwoBit" mimetype="application/octet-stream" display_in_upload="true"/><datatype extension="txt" type="galaxy.datatypes.data:Text" display_in_upload="true"/> + <datatype extension="linecount" type="galaxy.datatypes.data:LineCount" display_in_upload="false"/><datatype extension="memexml" type="galaxy.datatypes.xml:MEMEXml" mimetype="application/xml" display_in_upload="true"/><datatype extension="cisml" type="galaxy.datatypes.xml:CisML" mimetype="application/xml" display_in_upload="true"/><datatype extension="blastxml" type="galaxy.datatypes.xml:BlastXml" mimetype="application/xml" display_in_upload="true"/> --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/datatypes/converters/fasta_to_2bit.xml Tue Sep 20 11:19:44 2011 -0400 @@ -0,0 +1,13 @@ +<tool id="CONVERTER_fasta_to_2bit" name="Convert FASTA to 2bit" version="1.0.0"> +  +  + <command>faToTwoBit $input $output</command> + <inputs> + <param name="input" type="data" format="fasta" label="Fasta file"/> + </inputs> + <outputs> + <data name="output" format="twobit"/> + </outputs> + <help> + </help> +</tool> --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/datatypes/converters/fasta_to_len.py Tue Sep 20 11:19:44 2011 -0400 @@ -0,0 +1,48 @@ +#!/usr/bin/env python +""" +Input: fasta, int +Output: tabular +Return titles with lengths of corresponding seq +""" + +import sys, os + +assert sys.version_info[:2] >= ( 2, 4 ) + +def compute_fasta_length( fasta_file, out_file, keep_first_char ): + + infile = fasta_file + out = open( out_file, 'w') + keep_first_char = int( keep_first_char ) + + fasta_title = '' + seq_len = 0 + + # number of char to keep in the title + if keep_first_char == 0: + keep_first_char = None + else: + keep_first_char += 1 + + first_entry = True + + for line in open( infile ): + line = line.strip() + if not line or line.startswith( '#' ): + continue + if line[0] == '>': + if first_entry == False: + out.write( "%s\t%d\n" % ( fasta_title[ 1:keep_first_char ], seq_len ) ) + else: + first_entry = False + fasta_title = line + seq_len = 0 + else: + seq_len += len(line) + + # last fasta-entry + out.write( "%s\t%d\n" % ( fasta_title[ 1:keep_first_char ], seq_len ) ) + out.close() + +if __name__ == "__main__" : + compute_fasta_length( sys.argv[1], sys.argv[2], sys.argv[3] ) \ No newline at end of file --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/datatypes/converters/fasta_to_len.xml Tue Sep 20 11:19:44 2011 -0400 @@ -0,0 +1,13 @@ +<tool id="CONVERTER_fasta_to_len" name="Convert FASTA to len file" version="1.0.0"> +  +  + <command interpreter="python">fasta_to_len.py $input $output 0</command> + <inputs> + <param name="input" type="data" format="fasta" label="Fasta file"/> + </inputs> + <outputs> + <data name="output" format="len"/> + </outputs> + <help> + </help> +</tool> --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/datatypes/converters/len_to_linecount.xml Tue Sep 20 11:19:44 2011 -0400 @@ -0,0 +1,13 @@ +<tool id="CONVERTER_len_to_linecount" name="Convert Len file to Linecount" version="1.0.0"> +  +  + <command>wc -l $input | awk '{print $1}' > $output </command> + <inputs> + <param name="input" type="data" format="len" label="Fasta file"/> + </inputs> + <outputs> + <data name="output" format="linecount"/> + </outputs> + <help> + </help> +</tool> --- a/lib/galaxy/datatypes/data.py Tue Sep 20 10:45:23 2011 -0400 +++ b/lib/galaxy/datatypes/data.py Tue Sep 20 11:19:44 2011 -0400 @@ -446,6 +446,13 @@ dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk' +class LineCount( Text ): + """ + Dataset contains a single line with a single integer that denotes the + line count for a related dataset. Used for custom builds. + """ + pass + class Newick( Text ): pass --- a/lib/galaxy/web/controllers/user.py Tue Sep 20 10:45:23 2011 -0400 +++ b/lib/galaxy/web/controllers/user.py Tue Sep 20 11:19:44 2011 -0400 @@ -1165,6 +1165,9 @@ @web.expose @web.require_login() def dbkeys( self, trans, **kwds ): + # + # Process arguments and add/delete build. + # user = trans.user message = None lines_skipped = 0 @@ -1178,57 +1181,79 @@ else: dbkeys = from_json_string(user.preferences['dbkeys']) if 'delete' in kwds: + # Delete a build. key = kwds.get('key', '') if key and key in dbkeys: del dbkeys[key] elif 'add' in kwds: - name = kwds.get('name', '') - key = kwds.get('key', '') - len_file = kwds.get('len_file', None) - if getattr(len_file, "file", None): # Check if it's a FieldStorage object - len_text = len_file.file.read() - else: - len_text = kwds.get('len_text', '') - if not name or not key or not len_text: + # Add new custom build. + name = kwds.get('name', '') + key = kwds.get('key', '') + dataset_id = kwds.get('dataset_id', '') + if not name or not key or not dataset_id: message = "You must specify values for all the fields." elif key in dbkeys: message = "There is already a custom build with that key. Delete it first if you want to replace it." else: - # Create new len file - new_len = trans.app.model.HistoryDatasetAssociation( extension="len", create_dataset=True, sa_session=trans.sa_session ) - trans.sa_session.add( new_len ) - new_len.name = name - new_len.visible = False - new_len.state = trans.app.model.Job.states.OK - new_len.info = "custom build .len file" - trans.sa_session.flush() - counter = 0 - f = open(new_len.file_name, "w") - # LEN files have format: - # <chrom_name><tab><chrom_length> - for line in len_text.split("\n"): - lst = line.strip().rsplit(None, 1) # Splits at the last whitespace in the line - if not lst or len(lst) < 2: - lines_skipped += 1 - continue - chrom, length = lst[0], lst[1] - try: - length = int(length) - except ValueError: - lines_skipped += 1 - continue - counter += 1 - f.write("%s\t%s\n" % (chrom, length)) - f.close() - dbkeys[key] = { "name": name, "len": new_len.id, "count": counter } + dataset_id = trans.security.decode_id( dataset_id ) + dbkeys[key] = { "name": name, "fasta": dataset_id } + # Save builds. + # TODO: use database table to save builds. user.preferences['dbkeys'] = to_json_string(dbkeys) trans.sa_session.flush() + + # + # Display custom builds page. + # + + # Add chrom/contig count to dbkeys dict. + updated = False + for key, attributes in dbkeys.items(): + if 'count' in attributes: + # Already have count, so do nothing. + continue + + # Get len file. + fasta_dataset = trans.app.model.HistoryDatasetAssociation.get( attributes[ 'fasta' ] ) + len_dataset = fasta_dataset.get_converted_dataset( trans, "len" ) + # HACK: need to request dataset again b/c get_converted_dataset() + # doesn't return dataset (as it probably should). + len_dataset = fasta_dataset.get_converted_dataset( trans, "len" ) + if len_dataset.state == trans.app.model.Job.states.ERROR: + # Can't use len dataset. + continue + + # Get chrom count file. + # NOTE: this conversion doesn't work well with set_metadata_externally=False + # because the conversion occurs before metadata can be set; the + # dataset is marked as deleted and a subsequent conversion is run. + chrom_count_dataset = len_dataset.get_converted_dataset( trans, "linecount" ) + if not chrom_count_dataset or chrom_count_dataset.state != trans.app.model.Job.states.OK: + # No valid linecount dataset. + continue + else: + # Set chrom count. + chrom_count = int( open( chrom_count_dataset.file_name ).readline() ) + attributes[ 'count' ] = chrom_count + updated = True + + if updated: + user.preferences['dbkeys'] = to_json_string(dbkeys) + trans.sa_session.flush() + + + # Potential genome data for custom builds is limited to fasta datasets in current history for now. + fasta_hdas = trans.sa_session.query( model.HistoryDatasetAssociation ) \ + .filter_by( history=trans.history, extension="fasta", deleted=False ) \ + .order_by( model.HistoryDatasetAssociation.hid.desc() ) + return trans.fill_template( 'user/dbkeys.mako', user=user, dbkeys=dbkeys, message=message, installed_len_files=self.installed_len_files, lines_skipped=lines_skipped, + fasta_hdas=fasta_hdas, use_panels=kwds.get( 'use_panels', None ) ) @web.expose @web.require_login() --- a/templates/user/dbkeys.mako Tue Sep 20 10:45:23 2011 -0400 +++ b/templates/user/dbkeys.mako Tue Sep 20 11:19:44 2011 -0400 @@ -103,6 +103,8 @@ ## </pre> % if 'count' in dct: ${dct['count']} + % else: + working % endif </td><td><form action="dbkeys" method="post"><input type="hidden" name="key" value="${key}" /><input type="submit" name="delete" value="Delete" /></form></td> @@ -133,10 +135,12 @@ <input type="text" id="key" name="key" /></div><div class="form-row"> - <label for="len_file">Upload .len file:</label> - <input type="file" id="len_file" name="len_file" /><br /> - <label for="len_text">Or enter/paste length info below:</label> - <textarea id="len_text" name="len_text" cols="30" rows="8"></textarea> + <label for="len_file">Build Genome:</label> + <select name="dataset_id"> + %for dataset in fasta_hdas: + <option value="${trans.security.encode_id( dataset.id )}">${dataset.hid}: ${dataset.name}</option> + %endfor + </select></div><div class="form-row"><input type="submit" name="add" value="Submit"/></div> --- a/tools/fasta_tools/fasta_compute_length.py Tue Sep 20 10:45:23 2011 -0400 +++ b/tools/fasta_tools/fasta_compute_length.py Tue Sep 20 11:19:44 2011 -0400 @@ -1,47 +1,9 @@ #!/usr/bin/env python """ -Input: fasta, int -Output: tabular -Return titles with lengths of corresponding seq +Uses fasta_to_len converter code. """ -import sys, os +import sys +from galaxy.datatypes.converters.fasta_to_len import compute_fasta_length -assert sys.version_info[:2] >= ( 2, 4 ) - -def __main__(): - - infile = sys.argv[1] - out = open( sys.argv[2], 'w') - keep_first_char = int( sys.argv[3] ) - - fasta_title = '' - seq_len = 0 - - # number of char to keep in the title - if keep_first_char == 0: - keep_first_char = None - else: - keep_first_char += 1 - - first_entry = True - - for line in open( infile ): - line = line.strip() - if not line or line.startswith( '#' ): - continue - if line[0] == '>': - if first_entry == False: - out.write( "%s\t%d\n" % ( fasta_title[ 1:keep_first_char ], seq_len ) ) - else: - first_entry = False - fasta_title = line - seq_len = 0 - else: - seq_len += len(line) - - # last fasta-entry - out.write( "%s\t%d\n" % ( fasta_title[ 1:keep_first_char ], seq_len ) ) - out.close() - -if __name__ == "__main__" : __main__() \ No newline at end of file +compute_fasta_length( sys.argv[1], sys.argv[2], sys.argv[3]) \ No newline at end of file http://bitbucket.org/galaxy/galaxy-central/changeset/e21eb7138be8/ changeset: e21eb7138be8 user: jgoecks date: 2011-09-20 17:20:13 summary: Merge affected #: 2 files (-1 bytes) --- a/lib/galaxy/web/base/controller.py Tue Sep 20 11:19:44 2011 -0400 +++ b/lib/galaxy/web/base/controller.py Tue Sep 20 11:20:13 2011 -0400 @@ -2751,9 +2751,7 @@ def browse_tool_shed( self, trans, **kwd ): tool_shed_url = kwd[ 'tool_shed_url' ] galaxy_url = trans.request.host - # Set the galayurl cookie so we can get back here from the remote tool shed. - trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' ) - url = '%s/repository/browse_downloadable_repositories?webapp=community' % ( tool_shed_url ) + url = '%s/repository/browse_downloadable_repositories?galaxy_url=%s&webapp=community' % ( tool_shed_url, galaxy_url ) return trans.response.send_redirect( url ) @web.expose @web.require_admin --- a/lib/galaxy/webapps/community/controllers/repository.py Tue Sep 20 11:19:44 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Tue Sep 20 11:20:13 2011 -0400 @@ -262,6 +262,11 @@ return self.category_list_grid( trans, **kwd ) @web.expose def browse_downloadable_repositories( self, trans, **kwd ): + # Set the toolshedgalaxyurl cookie so we can get back + # to the calling local Galaxy instance. + galaxy_url = kwd.get( 'galaxy_url', None ) + if galaxy_url: + trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' ) repository_id = kwd.get( 'id', None ) if 'operation' in kwd: operation = kwd[ 'operation' ].lower() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Tweak tool shed cookie handling.
by Bitbucket 20 Sep '11

20 Sep '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/29e9f87731ec/ changeset: 29e9f87731ec user: greg date: 2011-09-20 17:17:27 summary: Tweak tool shed cookie handling. affected #: 2 files (-1 bytes) --- a/lib/galaxy/web/base/controller.py Tue Sep 20 10:45:23 2011 -0400 +++ b/lib/galaxy/web/base/controller.py Tue Sep 20 11:17:27 2011 -0400 @@ -2751,9 +2751,7 @@ def browse_tool_shed( self, trans, **kwd ): tool_shed_url = kwd[ 'tool_shed_url' ] galaxy_url = trans.request.host - # Set the galayurl cookie so we can get back here from the remote tool shed. - trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' ) - url = '%s/repository/browse_downloadable_repositories?webapp=community' % ( tool_shed_url ) + url = '%s/repository/browse_downloadable_repositories?galaxy_url=%s&webapp=community' % ( tool_shed_url, galaxy_url ) return trans.response.send_redirect( url ) @web.expose @web.require_admin --- a/lib/galaxy/webapps/community/controllers/repository.py Tue Sep 20 10:45:23 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Tue Sep 20 11:17:27 2011 -0400 @@ -262,6 +262,11 @@ return self.category_list_grid( trans, **kwd ) @web.expose def browse_downloadable_repositories( self, trans, **kwd ): + # Set the toolshedgalaxyurl cookie so we can get back + # to the calling local Galaxy instance. + galaxy_url = kwd.get( 'galaxy_url', None ) + if galaxy_url: + trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' ) repository_id = kwd.get( 'id', None ) if 'operation' in kwd: operation = kwd[ 'operation' ].lower() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fix for bug introduced in the last change set.
by Bitbucket 20 Sep '11

20 Sep '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/af1aaff959c4/ changeset: af1aaff959c4 user: greg date: 2011-09-20 16:45:23 summary: Fix for bug introduced in the last change set. affected #: 1 file (-1 bytes) --- a/lib/galaxy/webapps/community/controllers/repository.py Tue Sep 20 10:38:30 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Tue Sep 20 10:45:23 2011 -0400 @@ -1254,7 +1254,6 @@ action='preview_tools_in_changeset', repository_id=repository_id, changeset_revision=changeset_revision, - galaxy_url=galaxy_url, message=message, status='error' ) ) return trans.response.send_redirect( web.url_for( controller='repository', Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Add baseline support for using Fabric scripts for automatically installing tool dependencies on a local Galaxy instance when repositories are installed from a Galaxy tool shed, and persist the url to the local Galaxy instance in a cookie named toolshedgalaxyurl when installing a tool shed repository to a local Galaxy instance.
by Bitbucket 20 Sep '11

20 Sep '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/b13ab23c7d8e/ changeset: b13ab23c7d8e user: greg date: 2011-09-20 16:38:30 summary: Add baseline support for using Fabric scripts for automatically installing tool dependencies on a local Galaxy instance when repositories are installed from a Galaxy tool shed, and persist the url to the local Galaxy instance in a cookie named toolshedgalaxyurl when installing a tool shed repository to a local Galaxy instance. affected #: 12 files (-1 bytes) --- a/lib/galaxy/config.py Mon Sep 19 16:07:53 2011 -0400 +++ b/lib/galaxy/config.py Tue Sep 20 10:38:30 2011 -0400 @@ -119,9 +119,12 @@ self.ftp_upload_site = kwargs.get( 'ftp_upload_site', None ) self.allow_library_path_paste = kwargs.get( 'allow_library_path_paste', False ) self.disable_library_comptypes = kwargs.get( 'disable_library_comptypes', '' ).lower().split( ',' ) - # Location for dependencies + # Location for tool dependencies. if 'tool_dependency_dir' in kwargs: self.tool_dependency_dir = resolve_path( kwargs.get( "tool_dependency_dir" ), self.root ) + # Setting the following flag to true will ultimately cause tool dependencies + # to be located in the shell environment and used by the job that is executing + # the tool. self.use_tool_dependencies = True else: self.tool_dependency_dir = None --- a/lib/galaxy/datatypes/assembly.py Mon Sep 19 16:07:53 2011 -0400 +++ b/lib/galaxy/datatypes/assembly.py Tue Sep 20 10:38:30 2011 -0400 @@ -143,7 +143,6 @@ def __init__( self, **kwd ): Html.__init__( self, **kwd ) - log.debug( "Velvet log info %s" % 'JJ __init__') self.add_composite_file( 'Sequences', mimetype = 'text/html', description = 'Sequences', substitute_name_with_metadata = None, is_binary = False ) self.add_composite_file( 'Roadmaps', mimetype = 'text/html', description = 'Roadmaps', substitute_name_with_metadata = None, is_binary = False ) self.add_composite_file( 'Log', mimetype = 'text/html', description = 'Log', optional = 'True', substitute_name_with_metadata = None, is_binary = False ) --- a/lib/galaxy/tools/__init__.py Mon Sep 19 16:07:53 2011 -0400 +++ b/lib/galaxy/tools/__init__.py Tue Sep 20 10:38:30 2011 -0400 @@ -227,12 +227,11 @@ id = self.app.security.decode_id( workflow_id ) stored = self.app.model.context.query( self.app.model.StoredWorkflow ).get( id ) return stored.latest_workflow - def init_dependency_manager( self ): - self.dependency_manager = None if self.app.config.use_tool_dependencies: self.dependency_manager = DependencyManager( [ self.app.config.tool_dependency_dir ] ) - + else: + self.dependency_manager = None @property def sa_session( self ): """ @@ -341,12 +340,17 @@ """ Represents an external requirement that must be available for the tool to run (for example, a program, package, or library). Requirements can - optionally assert a specific version + optionally assert a specific version, or reference a command to execute a + fabric script. If fabric is used, the type is 'fabfile' and the version + attribute is not used since the fabric script includes all necessary + information for automatic dependency installation. """ - def __init__( self ): - self.name = None - self.type = None - self.version = None + def __init__( self, name=None, type=None, version=None, fabfile=None, method=None ): + self.name = name + self.type = type + self.version = version + self.fabfile = fabfile + self.method = method class Tool: """ @@ -882,10 +886,21 @@ self.requirements """ for requirement_elem in requirements_elem.findall( 'requirement' ): - requirement = ToolRequirement() - requirement.name = util.xml_text( requirement_elem ) - requirement.type = requirement_elem.get( "type", "package" ) - requirement.version = requirement_elem.get( "version" ) + name = util.xml_text( requirement_elem ) + type = requirement_elem.get( "type", "package" ) + if type == 'fabfile': + # The fabric script will include all necessary information for + # automatically installing the tool dependencies. + fabfile = requirement_elem.get( "fabfile" ) + method = requirement_elem.get( "method" ) + version = None + else: + # For backward compatibility, requirements tag sets should not require the + # use of a fabric script. + version = requirement_elem.get( "version" ) + fabfile = None + method = None + requirement = ToolRequirement( name=name, type=type, version=version, fabfile=fabfile, method=method ) self.requirements.append( requirement ) def check_workflow_compatible( self ): --- a/lib/galaxy/tools/deps/__init__.py Mon Sep 19 16:07:53 2011 -0400 +++ b/lib/galaxy/tools/deps/__init__.py Tue Sep 20 10:38:30 2011 -0400 @@ -18,11 +18,10 @@ and should each contain a file 'env.sh' which can be sourced to make the dependency available in the current shell environment. """ - def __init__( self, base_paths=[] ): """ - Create a new dependency manager looking for packages under the - paths listed in `base_paths`. + Create a new dependency manager looking for packages under the paths listed + in `base_paths`. The default base path is app.config.tool_dependency_dir. """ self.base_paths = [] for base_path in base_paths: @@ -31,19 +30,17 @@ if not os.path.isdir( base_path ): log.warn( "Path '%s' is not directory, ignoring", base_path ) self.base_paths.append( os.path.abspath( base_path ) ) - def find_dep( self, name, version=None ): """ Attempt to find a dependency named `name` at version `version`. If version is None, return the "default" version as determined using a symbolic link (if found). Returns a triple of: - env_script, base_path, real_version + env_script, base_path, real_version """ if version is None: return self._find_dep_default( name ) else: return self._find_dep_versioned( name, version ) - def _find_dep_versioned( self, name, version ): for base_path in self.base_paths: path = os.path.join( base_path, name, version ) @@ -52,7 +49,6 @@ return script, path, version else: return None, None, None - def _find_dep_default( self, name ): version = None for base_path in self.base_paths: @@ -65,5 +61,3 @@ return script, real_path, real_version else: return None, None, None - - --- a/lib/galaxy/web/base/controller.py Mon Sep 19 16:07:53 2011 -0400 +++ b/lib/galaxy/web/base/controller.py Tue Sep 20 10:38:30 2011 -0400 @@ -2749,10 +2749,11 @@ @web.expose @web.require_admin def browse_tool_shed( self, trans, **kwd ): - tool_shed_name = kwd[ 'tool_shed_name' ] tool_shed_url = kwd[ 'tool_shed_url' ] galaxy_url = trans.request.host - url = '%s/repository/browse_downloadable_repositories?tool_shed_name=%s&galaxy_url=%s&webapp=community' % ( tool_shed_url, tool_shed_name, galaxy_url ) + # Set the galayurl cookie so we can get back here from the remote tool shed. + trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' ) + url = '%s/repository/browse_downloadable_repositories?webapp=community' % ( tool_shed_url ) return trans.response.send_redirect( url ) @web.expose @web.require_admin @@ -2784,8 +2785,8 @@ status = 'error' else: os.makedirs( clone_dir ) + log.debug( 'Cloning %s...' % repository_clone_url ) cmd = 'hg clone %s' % repository_clone_url - log.debug( 'Cloning: %s' % repository_clone_url ) tmp_name = tempfile.NamedTemporaryFile().name tmp_stderr = open( tmp_name, 'wb' ) os.chdir( clone_dir ) @@ -2795,7 +2796,7 @@ tmp_stderr.close() if returncode == 0: repo_files_dir = os.path.join( clone_dir, repository_name ) - log.debug( 'Updating cloned repository to revision: %s' % changeset_revision ) + log.debug( 'Updating cloned repository to revision "%s"...' % changeset_revision ) cmd = 'hg update -r %s' % changeset_revision tmp_name = tempfile.NamedTemporaryFile().name tmp_stderr = open( tmp_name, 'wb' ) @@ -2831,6 +2832,39 @@ # We have an inavlid .xml file, so not a tool config. log.debug( "Ignoring invalid tool config (%s). Error: %s" % ( str( relative_path ), str( e ) ) ) if repository_tools_tups: + # Look at each tool to see if it includes a "requirement" that refers to + # a fabric script. For those that do, execute the fabric script to install + # tool dependencies. + for repository_tools_tup in repository_tools_tups: + tup_path, repository_tool = repository_tools_tup + for requirement in repository_tool.requirements: + if requirement.type == 'fabfile': + log.debug( 'Executing fabric script to install dependencies for tool "%s"...' % repository_tool.name ) + fabfile = requirement.fabfile + method = requirement.method + # Find the relative path to the fabfile. + relative_fabfile_path = None + for root, dirs, files in os.walk( repo_files_dir ): + for name in files: + if name == fabfile: + relative_fabfile_path = os.path.join( root, name ) + break + if relative_fabfile_path: + # cmd will look something like: fab -f fabfile.py install_bowtie + cmd = 'fab -f %s %s' % ( relative_fabfile_path, method ) + tmp_name = tempfile.NamedTemporaryFile().name + tmp_stderr = open( tmp_name, 'wb' ) + os.chdir( repo_files_dir ) + proc = subprocess.Popen( cmd, shell=True, stderr=tmp_stderr.fileno() ) + returncode = proc.wait() + os.chdir( current_working_dir ) + tmp_stderr.close() + if returncode != 0: + # TODO: do something more here than logging the problem. + tmp_stderr = open( tmp_name, 'rb' ) + error = tmp_stderr.read() + tmp_stderr.close() + log.debug( 'Problem installing dependencies for tool "%s"\n%s' % ( repository_tool.name, error ) ) # Generate an in-memory tool conf section that includes the new tools. new_tool_section = self.__generate_tool_panel_section( repository_name, repository_clone_url, --- a/lib/galaxy/webapps/community/controllers/common.py Mon Sep 19 16:07:53 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/common.py Tue Sep 20 10:38:30 2011 -0400 @@ -171,9 +171,21 @@ repository = get_repository( trans, id ) tool_requirements = [] for tr in tool.requirements: - requirement_dict = dict( name=tr.name, - type=tr.type, - version=tr.version ) + name=tr.name + type=tr.type + if type == 'fabfile': + version = None + fabfile = tr.fabfile + method = tr.method + else: + version = tr.version + fabfile = None + method = None + requirement_dict = dict( name=name, + type=type, + version=version, + fabfile=fabfile, + method=method ) tool_requirements.append( requirement_dict ) tool_tests = [] if tool.tests: @@ -335,13 +347,17 @@ trans.sa_session.flush() else: message = "Changeset revision '%s' includes no tools or exported workflows for which metadata can be set." % str( changeset_revision ) - status = "done" + status = "error" else: # change_set is None message = "Repository does not include changeset revision '%s'." % str( changeset_revision ) status = 'error' if invalid_files: - message = "Metadata cannot be defined for change set revision '%s'. Correct the following problems and reset metadata.<br/>" % str( changeset_revision ) + if metadata_dict: + message = "Metadata was defined for some items in change set revision '%s'. " % str( changeset_revision ) + message += "If the following files are Galaxy tool configs or exported Galaxy workflows, correct the problems and reset metadata.<br/>" + else: + message = "Metadata cannot be defined for change set revision '%s'. Correct the following problems and reset metadata.<br/>" % str( changeset_revision ) for itc_tup in invalid_files: tool_file = itc_tup[0] exception_msg = itc_tup[1] @@ -527,7 +543,7 @@ ToolClass = Tool return ToolClass( config_file, root, trans.app ) return None -def build_changeset_revision_select_field( trans, repository, selected_value=None, add_id_to_name=True, galaxy_url=None ): +def build_changeset_revision_select_field( trans, repository, selected_value=None, add_id_to_name=True ): """ Build a SelectField whose options are the changeset_revision strings of all downloadable_revisions of the received repository. @@ -541,15 +557,9 @@ options.append( ( revision_label, changeset_revision ) ) refresh_on_change_values.append( changeset_revision ) if add_id_to_name: - if galaxy_url: - name = '%s_changeset_revision_%d' % ( galaxy_url, repository.id ) - else: - name = 'changeset_revision_%d' % repository.id + name = 'changeset_revision_%d' % repository.id else: - if galaxy_url: - name = '%s_changeset_revision' % galaxy_url - else: - name = 'changeset_revision' + name = 'changeset_revision' select_field = SelectField( name=name, refresh_on_change=True, refresh_on_change_values=refresh_on_change_values ) --- a/lib/galaxy/webapps/community/controllers/repository.py Mon Sep 19 16:07:53 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Tue Sep 20 10:38:30 2011 -0400 @@ -122,7 +122,6 @@ return 'yes' return '' # Grid definition - galaxy_url = None title = "Repositories" model_class = model.Repository template='/webapps/community/repository/grid.mako' @@ -192,12 +191,11 @@ Display a SelectField whose options are the changeset_revision strings of all downloadable_revisions of this repository. """ - select_field = build_changeset_revision_select_field( trans, - repository, - galaxy_url=grid.galaxy_url ) + select_field = build_changeset_revision_select_field( trans, repository ) if len( select_field.options ) > 1: return select_field.get_html() return repository.revision + title = "Downloadable repositories" columns = [ RepositoryListGrid.NameColumn( "Name", key="name", @@ -264,9 +262,7 @@ return self.category_list_grid( trans, **kwd ) @web.expose def browse_downloadable_repositories( self, trans, **kwd ): - tool_shed_name = kwd.get( 'tool_shed_name', None ) repository_id = kwd.get( 'id', None ) - galaxy_url = kwd.get( 'galaxy_url', None ) if 'operation' in kwd: operation = kwd[ 'operation' ].lower() if operation == "preview_tools_in_changeset": @@ -274,8 +270,7 @@ return trans.response.send_redirect( web.url_for( controller='repository', action='preview_tools_in_changeset', repository_id=repository_id, - changeset_revision=repository.tip, - galaxy_url=galaxy_url ) ) + changeset_revision=repository.tip ) ) # The changeset_revision_select_field in the RepositoryListGrid performs a refresh_on_change # which sends in request parameters like changeset_revison_1, changeset_revision_2, etc. One @@ -292,31 +287,10 @@ return trans.response.send_redirect( web.url_for( controller='repository', action='preview_tools_in_changeset', repository_id=trans.security.encode_id( repository.id ), - changeset_revision=v, - galaxy_url=galaxy_url ) ) - elif k.find( changset_revision_str ) > 0: - # Keys look like: 'localhost:8763_changeset_revision_3' and values: '4ef2cf631604'. - items = k.split( '_%s' % changset_revision_str ) - galaxy_url = items[0] - repository_id = trans.security.encode_id( int( items[1] ) ) - repository = get_repository( trans, repository_id ) - if repository.tip != v: - return trans.response.send_redirect( web.url_for( controller='repository', - action='preview_tools_in_changeset', - repository_id=trans.security.encode_id( repository.id ), - changeset_revision=v, - galaxy_url=galaxy_url ) ) - - if tool_shed_name: - title = "%s downloadable repositories" % tool_shed_name - else: - title = "Downloadable repositories" - self.downloadable_repository_list_grid.title = title - self.downloadable_repository_list_grid.galaxy_url = galaxy_url + changeset_revision=v ) ) url_args = dict( action='browse_downloadable_repositories', operation='preview_tools_in_changeset', - repository_id=repository_id, - galaxy_url=galaxy_url ) + repository_id=repository_id ) self.downloadable_repository_list_grid.operations = [ grids.GridOperation( "Preview and install tools", url_args=url_args, allow_multiple=False, @@ -329,7 +303,6 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - galaxy_url = util.restore_text( params.get( 'galaxy_url', '' ) ) repository = get_repository( trans, repository_id ) changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) ) repository_metadata = get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) @@ -348,7 +321,6 @@ revision_label=revision_label, changeset_revision_select_field=changeset_revision_select_field, metadata=metadata, - galaxy_url=galaxy_url, display_for_install=True, message=message, status=status ) @@ -357,7 +329,7 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - galaxy_url = util.restore_text( params.get( 'galaxy_url', '' ) ) + galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' ) repository = get_repository( trans, repository_id ) changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) ) # Redirect back to local Galaxy to perform install. @@ -1232,7 +1204,6 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - galaxy_url = util.restore_text( params.get( 'galaxy_url', '' ) ) display_for_install = util.string_as_bool( params.get( 'display_for_install', False ) ) repository = get_repository( trans, repository_id ) repo = hg.repository( get_configured_ui(), repository.repo_path ) @@ -1274,7 +1245,6 @@ tool_state=tool_state, is_malicious=is_malicious, display_for_install=display_for_install, - galaxy_url=galaxy_url, message=message, status=status ) except Exception, e: --- a/templates/admin/select_tool_panel_section.mako Mon Sep 19 16:07:53 2011 -0400 +++ b/templates/admin/select_tool_panel_section.mako Tue Sep 20 10:38:30 2011 -0400 @@ -16,7 +16,7 @@ or concerns. </div><br/> -<div class="errormessage"> +<div class="warningmessage"> Installation may take a while, depending upon the size of the repository contents. Wait until a message is displayed in your browser after clicking the <b>Install</b> button below. </div> --- a/templates/webapps/community/repository/common.mako Mon Sep 19 16:07:53 2011 -0400 +++ b/templates/webapps/community/repository/common.mako Tue Sep 20 10:38:30 2011 -0400 @@ -83,7 +83,7 @@ hg clone <a href="${clone_str}">${clone_str}</a></%def> -<%def name="render_repository_tools_and_workflows( metadata, can_set_metadata=False, display_for_install=False, galaxy_url=None )"> +<%def name="render_repository_tools_and_workflows( metadata, can_set_metadata=False, display_for_install=False )"> %if metadata or can_set_metadata: <p/><div class="toolForm"> @@ -111,12 +111,12 @@ <tr><td><div style="float: left; margin-left: 1px;" class="menubutton split popup" id="tool-${tool_dict[ 'id' ].replace( ' ', '_' )}-popup"> - <a class="view-info" href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_dict[ 'tool_config' ], changeset_revision=changeset_revision, display_for_install=display_for_install, galaxy_url=galaxy_url )}"> + <a class="view-info" href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_dict[ 'tool_config' ], changeset_revision=changeset_revision, display_for_install=display_for_install )}"> ${tool_dict[ 'name' ]} </a></div><div popupmenu="tool-${tool_dict[ 'id' ].replace( ' ', '_' )}-popup"> - <a class="action-button" href="${h.url_for( controller='repository', action='view_tool_metadata', repository_id=trans.security.encode_id( repository.id ), changeset_revision=changeset_revision, tool_id=tool_dict[ 'id' ], display_for_install=display_for_install, galaxy_url=galaxy_url )}">View tool metadata</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_tool_metadata', repository_id=trans.security.encode_id( repository.id ), changeset_revision=changeset_revision, tool_id=tool_dict[ 'id' ], display_for_install=display_for_install )}">View tool metadata</a></div></td><td>${tool_dict[ 'description' ]}</td> --- a/templates/webapps/community/repository/preview_tools_in_changeset.mako Mon Sep 19 16:07:53 2011 -0400 +++ b/templates/webapps/community/repository/preview_tools_in_changeset.mako Tue Sep 20 10:38:30 2011 -0400 @@ -64,7 +64,7 @@ <br/><br/><ul class="manage-table-actions"> - <a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp='community', changeset_revision=changeset_revision, galaxy_url=galaxy_url )}">Install to local Galaxy</a> + <a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp='community', changeset_revision=changeset_revision )}">Install to local Galaxy</a></ul> %if message: @@ -75,7 +75,7 @@ <div class="toolFormTitle">Repository ${repository.name}</div><div class="toolFormBody"> %if len( changeset_revision_select_field.options ) > 1: - <form name="change_revision" id="change_revision" action="${h.url_for( controller='repository', action='preview_tools_in_changeset', repository_id=trans.security.encode_id( repository.id ), galaxy_url=galaxy_url )}" method="post" > + <form name="change_revision" id="change_revision" action="${h.url_for( controller='repository', action='preview_tools_in_changeset', repository_id=trans.security.encode_id( repository.id ) )}" method="post" ><div class="form-row"><% if changeset_revision == repository.tip: @@ -98,4 +98,4 @@ </div></div><p/> -${render_repository_tools_and_workflows( metadata, display_for_install=display_for_install, galaxy_url=galaxy_url )} +${render_repository_tools_and_workflows( metadata, display_for_install=display_for_install )} --- a/templates/webapps/community/repository/tool_form.mako Mon Sep 19 16:07:53 2011 -0400 +++ b/templates/webapps/community/repository/tool_form.mako Tue Sep 20 10:38:30 2011 -0400 @@ -111,7 +111,7 @@ <br/><br/><ul class="manage-table-actions"> %if display_for_install: - <a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp='community', changeset_revision=changeset_revision, galaxy_url=galaxy_url )}">Install to local Galaxy</a> + <a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp='community', changeset_revision=changeset_revision )}">Install to local Galaxy</a> %else: %if is_new: <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> --- a/templates/webapps/galaxy/admin/index.mako Mon Sep 19 16:07:53 2011 -0400 +++ b/templates/webapps/galaxy/admin/index.mako Tue Sep 20 10:38:30 2011 -0400 @@ -70,7 +70,7 @@ <div class="toolSectionBody"><div class="toolSectionBg"> %for name, url in trans.app.tool_shed_registry.tool_sheds.items(): - <div class="toolTitle"><a href="${h.url_for( controller='admin', action='browse_tool_shed', tool_shed_name=name, tool_shed_url=url )}" target="galaxy_main">${name}</a></div> + <div class="toolTitle"><a href="${h.url_for( controller='admin', action='browse_tool_shed', tool_shed_url=url )}" target="galaxy_main">${name}</a></div> %endfor </div></div> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Trackster: (a) remove child tracks, which are replaced with track groups and (b) preserve and restore track ordering, which was broken in 732ad7ebde0c.
by Bitbucket 19 Sep '11

19 Sep '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/a76e32124ad8/ changeset: a76e32124ad8 user: jgoecks date: 2011-09-19 22:07:53 summary: Trackster: (a) remove child tracks, which are replaced with track groups and (b) preserve and restore track ordering, which was broken in 732ad7ebde0c. affected #: 5 files (-1 bytes) --- a/lib/galaxy/web/base/controller.py Mon Sep 19 11:59:09 2011 -0400 +++ b/lib/galaxy/web/base/controller.py Mon Sep 19 16:07:53 2011 -0400 @@ -195,8 +195,7 @@ "dataset_id": trans.security.encode_id( dataset.id ), "prefs": prefs, "filters": track_data_provider.get_filters(), - "tool": get_tool_def( trans, dataset ), - "is_child": t.get('is_child', False) + "tool": get_tool_def( trans, dataset ) } ) config = { "title": visualization.title, "vis_id": trans.security.encode_id( visualization.id ), --- a/lib/galaxy/web/controllers/tracks.py Mon Sep 19 11:59:09 2011 -0400 +++ b/lib/galaxy/web/controllers/tracks.py Mon Sep 19 16:07:53 2011 -0400 @@ -573,8 +573,7 @@ "hda_ldda": track.get('hda_ldda', "hda"), "name": track['name'], "track_type": track['track_type'], - "prefs": track['prefs'], - "is_child": track.get('is_child', False) + "prefs": track['prefs'] } ) bookmarks = decoded_payload[ 'bookmarks' ] vis_rev.config = { "tracks": tracks, "bookmarks": bookmarks } --- a/static/scripts/trackster.js Mon Sep 19 11:59:09 2011 -0400 +++ b/static/scripts/trackster.js Mon Sep 19 16:07:53 2011 -0400 @@ -723,6 +723,22 @@ $(window).trigger("resize"); this.update_intro_div(); }, + /** JSONify view. */ + to_json: function() { + var + view = this, + jsonified_drawables = []; + this.viewport_container.children(".track,.group").each(function() { + // Get object ID. + var id = $(this).attr("id"); + id = parseInt( id.slice(id.lastIndexOf("_") + 1) ); + + // JSONify drawable. + jsonified_drawables.push(view.tracks[id].to_json()); + }); + + return jsonified_drawables; + }, /** Show or hide intro div depending on view state. */ update_intro_div: function() { if (this.num_tracks === 0) { @@ -2030,35 +2046,8 @@ this.tool = (tool_dict !== undefined && obj_length(tool_dict) > 0 ? new Tool(this, tool_dict) : undefined); this.is_overview = false; - // - // TODO: Right now there is only the notion of a parent track and multiple child tracks. However, - // a more general notion of a 'track group' is probably needed and can be easily created using - // the code already in place for parent/child tracks. The view would then manage track groups, and - // each track group could be managed on its own. - // - this.parent_track = parent_track; - this.child_tracks = []; - if (track.hidden) { return; } - - // - // If track has parent: - // -replace drag handle with child-track icon button; (TODO: eventually, we'll want to be able - // to make a set of child tracks dragable.) - // -remove tool b/c child tracks cannot have tools. - // - if (this.parent_track) { - this.header_div.find(".draghandle").removeClass('draghandle').addClass('child-track-icon').addClass('icon-button'); - this.parent_element.addClass("child-track"); - this.tool = undefined; - } - - // - // Child tracks container setup. - // - track.child_tracks_container = $("<div/>").addClass("child-tracks-container").hide(); - track.container_div.append(track.child_tracks_container); - + // // Create filters div. // @@ -2103,6 +2092,18 @@ }; extend(TiledTrack.prototype, Track.prototype, { /** + * Convert track to JSON object. + */ + to_json: function() { + return { + "track_type": this.get_type(), + "name": this.name, + "hda_ldda": this.hda_ldda, + "dataset_id": this.dataset_id, + "prefs": this.prefs + }; + }, + /** * Change track's mode. */ change_mode: function(name) { @@ -2208,19 +2209,10 @@ // // Remove option. // - - // Need to either remove track from view or from parent. - var parent_obj = view; - var no_tracks_fn = function() { $("#no-tracks").show(); }; - if (this.parent_track) { - // Track is child track. - parent_obj = this.parent_track; - no_tracks_fn = function() {}; - } track_dropdown.Remove = function() { - parent_obj.remove_track(track); + view.remove_track(track); if (parent_obj.num_tracks === 0) { - no_tracks_fn(); + $("#no-tracks").show(); } }; @@ -2331,10 +2323,6 @@ if (all_tiles_drawn) { track.postdraw_actions(drawn_tiles, width, w_scale, clear_after); } - // Draw child tracks. - for (var i = 0; i < this.child_tracks.length; i++) { - this.child_tracks[i].request_draw(force, clear_after); - } }, /** * Actions to be taken after draw has been completed. Draw is completed when all tiles have been @@ -2511,26 +2499,6 @@ region = (chrom !== undefined && low !== undefined && high !== undefined ? chrom + ":" + low + "-" + high : "all"); return " - region=[" + region + "], parameters=[" + track.tool.get_param_values().join(", ") + "]"; - }, - /** - * Add a child track to this track. - */ - add_track: function(child_track) { - child_track.track_id = this.track_id + "_" + this.child_tracks.length; - child_track.container_div.attr('id', 'track_' + child_track.track_id); - this.child_tracks_container.append(child_track.container_div); - moveable( child_track.container_div, '.child-track-icon' ); - if (!$(this.child_tracks_container).is(":visible")) { - this.child_tracks_container.show(); - } - this.child_tracks.push(child_track); - this.view.has_changes = true; - }, - /** - * Remove a child track from this track. - */ - remove_track: function(child_track) { - child_track.container_div.fadeOut('slow', function() { $(this).remove(); }); } }); --- a/static/scripts/trackster_ui.js Mon Sep 19 11:59:09 2011 -0400 +++ b/static/scripts/trackster_ui.js Mon Sep 19 16:07:53 2011 -0400 @@ -39,8 +39,7 @@ var track_from_dict = function(track_dict) { return new addable_track_types[track_dict.track_type]( track_dict.name, view, track_dict.hda_ldda, track_dict.dataset_id, - track_dict.prefs, track_dict.filters, track_dict.tool - /* TODO: ( track_dict.is_child ? parent_track : undefined */ ); + track_dict.prefs, track_dict.filters, track_dict.tool); }; /** @@ -57,7 +56,6 @@ var track_config, track, parent_track, parent_obj; for (var i = 0; i < tracks_config.length; i++) { track_config = tracks_config[i]; - // TODO: set parent for child track: track = track_from_dict(track_config); parent_obj = view; if (track_config.is_child) { --- a/templates/tracks/browser.mako Mon Sep 19 11:59:09 2011 -0400 +++ b/templates/tracks/browser.mako Mon Sep 19 16:07:53 2011 -0400 @@ -205,24 +205,8 @@ // Show saving dialog box show_modal("Saving...", "<img src='${h.url_for('/static/images/yui/rel_interstitial_loading.gif')}'/>"); - // TODO: make save into its own function. - // Save tracks. - var saved_tracks = [], tracks; - for (var i = 0; i < view.tracks.length; i++) { - track = view.tracks[i]; - - // Add track. - saved_tracks.push({ - "track_type": track.get_type(), - "name": track.name, - "hda_ldda": track.hda_ldda, - "dataset_id": track.dataset_id, - "prefs": track.prefs, - // TODO: remove parent-child relationships in favor of a group. - "is_child": false - }); - }; + var saved_tracks = view.to_json(); // Save bookmarks. var bookmarks = []; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Trackster: enable tools that produce BED output to be used in visual analytics framework. Enable cluster tool in Trackster.
by Bitbucket 19 Sep '11

19 Sep '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/af6ed2f06f35/ changeset: af6ed2f06f35 user: jgoecks date: 2011-09-19 17:59:09 summary: Trackster: enable tools that produce BED output to be used in visual analytics framework. Enable cluster tool in Trackster. affected #: 3 files (-1 bytes) --- a/lib/galaxy/visualization/tracks/data_providers.py Mon Sep 19 10:24:11 2011 -0400 +++ b/lib/galaxy/visualization/tracks/data_providers.py Mon Sep 19 11:59:09 2011 -0400 @@ -135,6 +135,88 @@ { 'name' : attrs[ 'name' ], 'type' : column_types[viz_col_index], \ 'index' : attrs[ 'index' ] } ) return filters + +class BedDataProvider( TracksDataProvider ): + """ + Abstract class that processes BED data from text format to payload format. + + Payload format: [ uid (offset), start, end, name, strand, thick_start, thick_end, blocks ] + """ + + def get_iterator( self, chrom, start, end ): + raise "Unimplemented Method" + + def get_data( self, chrom, start, end, start_val=0, max_vals=None, **kwargs ): + iterator = self.get_iterator( chrom, start, end ) + return self.process_data( iterator, start_val, max_vals, **kwargs ) + + def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): + """ + Provides + """ + # Build data to return. Payload format is: + # [ <guid/offset>, <start>, <end>, <name>, <score>, <strand>, <thick_start>, + # <thick_end>, <blocks> ] + # + # First three entries are mandatory, others are optional. + # + filter_cols = from_json_string( kwargs.get( "filter_cols", "[]" ) ) + no_detail = ( "no_detail" in kwargs ) + rval = [] + message = None + for count, line in enumerate( iterator ): + if count < start_val: + continue + if max_vals and count-start_val >= max_vals: + message = ERROR_MAX_VALS % ( max_vals, "features" ) + break + # TODO: can we use column metadata to fill out payload? + # TODO: use function to set payload data + + feature = line.split() + length = len(feature) + # Unique id is just a hash of the line + payload = [ hash(line), int(feature[1]), int(feature[2]) ] + + if no_detail: + rval.append( payload ) + continue + + # Simpler way to add stuff, but type casting is not done. + # Name, score, strand, thick start, thick end. + #end = min( len( feature ), 8 ) + #payload.extend( feature[ 3:end ] ) + + # Name, strand, thick start, thick end. + if length >= 4: + payload.append(feature[3]) + if length >= 6: + payload.append(feature[5]) + if length >= 8: + payload.append(int(feature[6])) + payload.append(int(feature[7])) + + # Blocks. + if length >= 12: + block_sizes = [ int(n) for n in feature[10].split(',') if n != ''] + block_starts = [ int(n) for n in feature[11].split(',') if n != '' ] + blocks = zip( block_sizes, block_starts ) + payload.append( [ ( int(feature[1]) + block[1], int(feature[1]) + block[1] + block[0] ) for block in blocks ] ) + + # Score (filter data) + if length >= 5 and filter_cols and filter_cols[0] == "Score": + payload.append( float(feature[4]) ) + + rval.append( payload ) + + return { 'data': rval, 'message': message } + + def write_data_to_file( self, chrom, start, end, filename ): + iterator = self.get_iterator( chrom, start, end ) + out = open( filename, "w" ) + for line in iterator: + out.write( "%s\n" % line ) + out.close() class SummaryTreeDataProvider( TracksDataProvider ): """ @@ -573,78 +655,7 @@ results.append( payload ) return { 'data': results, 'message': message } - -class BedDataProvider( TabixDataProvider ): - """ - Payload format: [ uid (offset), start, end, name, strand, thick_start, thick_end, blocks ] - """ - - def process_data( self, iterator, start_val=0, max_vals=sys.maxint, **kwargs ): - # - # Build data to return. Payload format is: - # [ <guid/offset>, <start>, <end>, <name>, <score>, <strand>, <thick_start>, - # <thick_end>, <blocks> ] - # - # First three entries are mandatory, others are optional. - # - filter_cols = from_json_string( kwargs.get( "filter_cols", "[]" ) ) - no_detail = ( "no_detail" in kwargs ) - rval = [] - message = None - for count, line in enumerate( iterator ): - if count < start_val: - continue - if count-start_val >= max_vals: - message = ERROR_MAX_VALS % ( max_vals, "features" ) - break - # TODO: can we use column metadata to fill out payload? - # TODO: use function to set payload data - - feature = line.split() - length = len(feature) - # Unique id is just a hash of the line - payload = [ hash(line), int(feature[1]), int(feature[2]) ] - - if no_detail: - rval.append( payload ) - continue - - # Simpler way to add stuff, but type casting is not done. - # Name, score, strand, thick start, thick end. - #end = min( len( feature ), 8 ) - #payload.extend( feature[ 3:end ] ) - - # Name, strand, thick start, thick end. - if length >= 4: - payload.append(feature[3]) - if length >= 6: - payload.append(feature[5]) - if length >= 8: - payload.append(int(feature[6])) - payload.append(int(feature[7])) - - # Blocks. - if length >= 12: - block_sizes = [ int(n) for n in feature[10].split(',') if n != ''] - block_starts = [ int(n) for n in feature[11].split(',') if n != '' ] - blocks = zip( block_sizes, block_starts ) - payload.append( [ ( int(feature[1]) + block[1], int(feature[1]) + block[1] + block[0] ) for block in blocks ] ) - - # Score (filter data) - if length >= 5 and filter_cols and filter_cols[0] == "Score": - payload.append( float(feature[4]) ) - rval.append( payload ) - - return { 'data': rval, 'message': message } - - def write_data_to_file( self, chrom, start, end, filename ): - iterator = self.get_iterator( chrom, start, end ) - out = open( filename, "w" ) - for line in iterator: - out.write( "%s\n" % line ) - out.close() - class VcfDataProvider( TabixDataProvider ): """ VCF data provider for the Galaxy track browser. @@ -685,7 +696,7 @@ Provide data from GFF file. NOTE: this data provider does not use indices, and hence will be very slow - for large datasets. + for large datasets. """ def get_data( self, chrom, start, end, start_val=0, max_vals=sys.maxint, **kwargs ): start, end = int( start ), int( end ) @@ -710,6 +721,30 @@ offset += feature.raw_size return { 'data': results, 'message': message } + +class BedTabixDataProvider( TabixDataProvider, BedDataProvider ): + """ + Provides data from a BED file indexed via tabix. + """ + pass + +class RawBedDataProvider( BedDataProvider ): + """ + Provide data from BED file. + + NOTE: this data provider does not use indices, and hence will be very slow + for large datasets. + """ + + def get_iterator( self, chrom, start, end ): + def line_filter_iter(): + for line in open( self.original_dataset.file_name ): + feature = line.split() + feature_chrom, feature_start, feature_end = feature[ 0:3 ] + if feature_chrom != chrom or feature_start > end or feature_end < start: + continue + yield line + return line_filter_iter() # # Helper methods. @@ -719,7 +754,7 @@ # type. First key is converted dataset type; if result is another dict, second key # is original dataset type. TODO: This needs to be more flexible. dataset_type_name_to_data_provider = { - "tabix": { Vcf: VcfDataProvider, Bed: BedDataProvider, "default" : TabixDataProvider }, + "tabix": { Vcf: VcfDataProvider, Bed: BedTabixDataProvider, "default" : TabixDataProvider }, "interval_index": IntervalIndexDataProvider, "bai": BamDataProvider, "summary_tree": SummaryTreeDataProvider, --- a/lib/galaxy/web/controllers/tracks.py Mon Sep 19 10:24:11 2011 -0400 +++ b/lib/galaxy/web/controllers/tracks.py Mon Sep 19 11:59:09 2011 -0400 @@ -397,7 +397,7 @@ def raw_data( self, trans, dataset_id, chrom, low, high, **kwargs ): """ Uses original (raw) dataset to return data. This method is useful - when the dataset is not yet indexed and hence using /data would + when the dataset is not yet indexed and hence using data would be slow because indexes need to be created. """ @@ -409,10 +409,15 @@ # Return data. data = None + # TODO: for raw data requests, map dataset type to provider using dict in data_providers.py if isinstance( dataset.datatype, Gff ): data = GFFDataProvider( original_dataset=dataset ).get_data( chrom, low, high, **kwargs ) data[ 'dataset_type' ] = 'interval_index' data[ 'extra_info' ] = None + if isinstance( dataset.datatype, Bed ): + data = RawBedDataProvider( original_dataset=dataset ).get_data( chrom, low, high, **kwargs ) + data[ 'dataset_type' ] = 'interval_index' + data[ 'extra_info' ] = None return data @web.json --- a/tools/new_operations/cluster.xml Mon Sep 19 10:24:11 2011 -0400 +++ b/tools/new_operations/cluster.xml Mon Sep 19 11:59:09 2011 -0400 @@ -1,5 +1,6 @@ <tool id="gops_cluster_1" name="Cluster"><description>the intervals of a dataset</description> + <trackster_conf/><command interpreter="python">gops_cluster.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -d $distance -m $minregions -o $returntype</command><inputs><param format="interval" name="input1" type="data"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Improve sorting and filtering in 'add to browser' grid.
by Bitbucket 19 Sep '11

19 Sep '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/b3eaa7291f56/ changeset: b3eaa7291f56 user: jgoecks date: 2011-09-19 16:24:11 summary: Improve sorting and filtering in 'add to browser' grid. affected #: 1 file (-1 bytes) --- a/lib/galaxy/web/controllers/tracks.py Mon Sep 19 08:49:00 2011 -0400 +++ b/lib/galaxy/web/controllers/tracks.py Mon Sep 19 10:24:11 2011 -0400 @@ -148,17 +148,17 @@ template = "/tracks/add_to_viz.mako" async_template = "/page/select_items_grid_async.mako" model_class = model.Visualization - default_filter = { "deleted" : "False" , "shared" : "All" } - default_sort_key = "title" + default_sort_key = "-update_time" use_async = True use_paging = False columns = [ grids.TextColumn( "Title", key="title", model_class=model.Visualization, filterable="standard" ), - grids.TextColumn( "Dbkey", key="dbkey", model_class=model.Visualization ) + grids.TextColumn( "Dbkey", key="dbkey", model_class=model.Visualization ), + grids.GridColumn( "Last Updated", key="update_time", format=time_ago ) ] def build_initial_query( self, trans, **kwargs ): - return trans.sa_session.query( self.model_class ) + return trans.sa_session.query( self.model_class ).filter( self.model_class.deleted == False ) def apply_query_filter( self, trans, query, **kwargs ): return query.filter( self.model_class.user_id == trans.user.id ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Trackster: reinstate width for tool panel that was inadverntently removed in dbc0cf838411.
by Bitbucket 19 Sep '11

19 Sep '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/3fe0b1d568a1/ changeset: 3fe0b1d568a1 user: jgoecks date: 2011-09-19 14:49:00 summary: Trackster: reinstate width for tool panel that was inadverntently removed in dbc0cf838411. affected #: 2 files (-1 bytes) --- a/static/june_2007_style/blue/trackster.css Mon Sep 19 07:22:23 2011 -0400 +++ b/static/june_2007_style/blue/trackster.css Mon Sep 19 08:49:00 2011 -0400 @@ -42,6 +42,7 @@ .nav-labeltrack{border-top:solid #999 1px;border-bottom:solid #333 1px;} input{font:10px verdana;} .dynamic-tool,.filters{margin-left:0.25em;padding-bottom:0.5em;} +.dynamic-tool{width:410px;} .filters>.sliders,.display-controls{float:left;margin:1em;} .sliders{width:410px;} .display-controls{border-left:solid 2px #DDDDDD;padding-left:1em} --- a/static/june_2007_style/trackster.css.tmpl Mon Sep 19 07:22:23 2011 -0400 +++ b/static/june_2007_style/trackster.css.tmpl Mon Sep 19 08:49:00 2011 -0400 @@ -246,6 +246,9 @@ margin-left: 0.25em; padding-bottom:0.5em; } +.dynamic-tool { + width:410px; +} .filters > .sliders, .display-controls { float: left; margin: 1em; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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