commit/galaxy-central: dan: Tool help updates.
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.ht... + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/helixturnhelix.ht... + +------ + +**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.
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