1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/663a2a57ed4d/
changeset: 663a2a57ed4d
user: dan
date: 2011-11-16 16:40:55
summary: Add information for UCSC data to annotation profiler.
affected #: 1 file
diff -r 26e928ede562caaaebcbe56b172b84e88a639a2e -r 663a2a57ed4db4303661f3771c518b7611f9c85f tools/annotation_profiler/annotation_profiler.xml
--- a/tools/annotation_profiler/annotation_profiler.xml
+++ b/tools/annotation_profiler/annotation_profiler.xml
@@ -136,6 +136,8 @@
**Citation**
+For the underlying data, please see http://genome.ucsc.edu/cite.html for the proper citation.
+
If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
</help>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/26e928ede562/
changeset: 26e928ede562
user: dan
date: 2011-11-16 15:50:34
summary: Add EMBOSS citation to EMBOSS tools.
affected #: 107 files
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_antigenic.xml
--- a/tools/emboss_5/emboss_antigenic.xml
+++ b/tools/emboss_5/emboss_antigenic.xml
@@ -48,8 +48,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_backtranseq.xml
--- a/tools/emboss_5/emboss_backtranseq.xml
+++ b/tools/emboss_5/emboss_backtranseq.xml
@@ -219,8 +219,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_banana.xml
--- a/tools/emboss_5/emboss_banana.xml
+++ b/tools/emboss_5/emboss_banana.xml
@@ -23,8 +23,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_biosed.xml
--- a/tools/emboss_5/emboss_biosed.xml
+++ b/tools/emboss_5/emboss_biosed.xml
@@ -72,8 +72,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_btwisted.xml
--- a/tools/emboss_5/emboss_btwisted.xml
+++ b/tools/emboss_5/emboss_btwisted.xml
@@ -23,8 +23,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_cai.xml
--- a/tools/emboss_5/emboss_cai.xml
+++ b/tools/emboss_5/emboss_cai.xml
@@ -184,8 +184,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_cai_custom.xml
--- a/tools/emboss_5/emboss_cai_custom.xml
+++ b/tools/emboss_5/emboss_cai_custom.xml
@@ -26,8 +26,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_chaos.xml
--- a/tools/emboss_5/emboss_chaos.xml
+++ b/tools/emboss_5/emboss_chaos.xml
@@ -22,8 +22,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_charge.xml
--- a/tools/emboss_5/emboss_charge.xml
+++ b/tools/emboss_5/emboss_charge.xml
@@ -34,8 +34,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_checktrans.xml
--- a/tools/emboss_5/emboss_checktrans.xml
+++ b/tools/emboss_5/emboss_checktrans.xml
@@ -86,8 +86,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_chips.xml
--- a/tools/emboss_5/emboss_chips.xml
+++ b/tools/emboss_5/emboss_chips.xml
@@ -29,8 +29,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_cirdna.xml
--- a/tools/emboss_5/emboss_cirdna.xml
+++ b/tools/emboss_5/emboss_cirdna.xml
@@ -22,8 +22,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_codcmp.xml
--- a/tools/emboss_5/emboss_codcmp.xml
+++ b/tools/emboss_5/emboss_codcmp.xml
@@ -329,8 +329,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_coderet.xml
--- a/tools/emboss_5/emboss_coderet.xml
+++ b/tools/emboss_5/emboss_coderet.xml
@@ -72,8 +72,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_compseq.xml
--- a/tools/emboss_5/emboss_compseq.xml
+++ b/tools/emboss_5/emboss_compseq.xml
@@ -41,8 +41,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_cpgplot.xml
--- a/tools/emboss_5/emboss_cpgplot.xml
+++ b/tools/emboss_5/emboss_cpgplot.xml
@@ -32,8 +32,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_cpgreport.xml
--- a/tools/emboss_5/emboss_cpgreport.xml
+++ b/tools/emboss_5/emboss_cpgreport.xml
@@ -48,8 +48,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_cusp.xml
--- a/tools/emboss_5/emboss_cusp.xml
+++ b/tools/emboss_5/emboss_cusp.xml
@@ -29,8 +29,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_cutseq.xml
--- a/tools/emboss_5/emboss_cutseq.xml
+++ b/tools/emboss_5/emboss_cutseq.xml
@@ -71,8 +71,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_dan.xml
--- a/tools/emboss_5/emboss_dan.xml
+++ b/tools/emboss_5/emboss_dan.xml
@@ -83,8 +83,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_degapseq.xml
--- a/tools/emboss_5/emboss_degapseq.xml
+++ b/tools/emboss_5/emboss_degapseq.xml
@@ -57,8 +57,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_descseq.xml
--- a/tools/emboss_5/emboss_descseq.xml
+++ b/tools/emboss_5/emboss_descseq.xml
@@ -71,8 +71,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_diffseq.xml
--- a/tools/emboss_5/emboss_diffseq.xml
+++ b/tools/emboss_5/emboss_diffseq.xml
@@ -63,8 +63,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_digest.xml
--- a/tools/emboss_5/emboss_digest.xml
+++ b/tools/emboss_5/emboss_digest.xml
@@ -64,8 +64,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_dotmatcher.xml
--- a/tools/emboss_5/emboss_dotmatcher.xml
+++ b/tools/emboss_5/emboss_dotmatcher.xml
@@ -28,8 +28,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_dotpath.xml
--- a/tools/emboss_5/emboss_dotpath.xml
+++ b/tools/emboss_5/emboss_dotpath.xml
@@ -35,8 +35,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_dottup.xml
--- a/tools/emboss_5/emboss_dottup.xml
+++ b/tools/emboss_5/emboss_dottup.xml
@@ -29,8 +29,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_dreg.xml
--- a/tools/emboss_5/emboss_dreg.xml
+++ b/tools/emboss_5/emboss_dreg.xml
@@ -21,8 +21,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_einverted.xml
--- a/tools/emboss_5/emboss_einverted.xml
+++ b/tools/emboss_5/emboss_einverted.xml
@@ -49,8 +49,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_epestfind.xml
--- a/tools/emboss_5/emboss_epestfind.xml
+++ b/tools/emboss_5/emboss_epestfind.xml
@@ -64,8 +64,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_equicktandem.xml
--- a/tools/emboss_5/emboss_equicktandem.xml
+++ b/tools/emboss_5/emboss_equicktandem.xml
@@ -59,8 +59,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_est2genome.xml
--- a/tools/emboss_5/emboss_est2genome.xml
+++ b/tools/emboss_5/emboss_est2genome.xml
@@ -102,8 +102,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_etandem.xml
--- a/tools/emboss_5/emboss_etandem.xml
+++ b/tools/emboss_5/emboss_etandem.xml
@@ -75,8 +75,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_extractfeat.xml
--- a/tools/emboss_5/emboss_extractfeat.xml
+++ b/tools/emboss_5/emboss_extractfeat.xml
@@ -97,6 +97,8 @@
**Citation**
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_extractseq.xml
--- a/tools/emboss_5/emboss_extractseq.xml
+++ b/tools/emboss_5/emboss_extractseq.xml
@@ -67,8 +67,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_freak.xml
--- a/tools/emboss_5/emboss_freak.xml
+++ b/tools/emboss_5/emboss_freak.xml
@@ -35,8 +35,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_fuzznuc.xml
--- a/tools/emboss_5/emboss_fuzznuc.xml
+++ b/tools/emboss_5/emboss_fuzznuc.xml
@@ -74,8 +74,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_fuzzpro.xml
--- a/tools/emboss_5/emboss_fuzzpro.xml
+++ b/tools/emboss_5/emboss_fuzzpro.xml
@@ -43,8 +43,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_fuzztran.xml
--- a/tools/emboss_5/emboss_fuzztran.xml
+++ b/tools/emboss_5/emboss_fuzztran.xml
@@ -94,8 +94,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_garnier.xml
--- a/tools/emboss_5/emboss_garnier.xml
+++ b/tools/emboss_5/emboss_garnier.xml
@@ -57,8 +57,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_geecee.xml
--- a/tools/emboss_5/emboss_geecee.xml
+++ b/tools/emboss_5/emboss_geecee.xml
@@ -23,8 +23,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_getorf.xml
--- a/tools/emboss_5/emboss_getorf.xml
+++ b/tools/emboss_5/emboss_getorf.xml
@@ -128,8 +128,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_helixturnhelix.xml
--- a/tools/emboss_5/emboss_helixturnhelix.xml
+++ b/tools/emboss_5/emboss_helixturnhelix.xml
@@ -62,8 +62,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_hmoment.xml
--- a/tools/emboss_5/emboss_hmoment.xml
+++ b/tools/emboss_5/emboss_hmoment.xml
@@ -31,8 +31,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_iep.xml
--- a/tools/emboss_5/emboss_iep.xml
+++ b/tools/emboss_5/emboss_iep.xml
@@ -37,8 +37,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_infoseq.xml
--- a/tools/emboss_5/emboss_infoseq.xml
+++ b/tools/emboss_5/emboss_infoseq.xml
@@ -75,8 +75,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_isochore.xml
--- a/tools/emboss_5/emboss_isochore.xml
+++ b/tools/emboss_5/emboss_isochore.xml
@@ -82,6 +82,8 @@
**Citation**
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_lindna.xml
--- a/tools/emboss_5/emboss_lindna.xml
+++ b/tools/emboss_5/emboss_lindna.xml
@@ -98,8 +98,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_marscan.xml
--- a/tools/emboss_5/emboss_marscan.xml
+++ b/tools/emboss_5/emboss_marscan.xml
@@ -44,8 +44,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_maskfeat.xml
--- a/tools/emboss_5/emboss_maskfeat.xml
+++ b/tools/emboss_5/emboss_maskfeat.xml
@@ -71,8 +71,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_maskseq.xml
--- a/tools/emboss_5/emboss_maskseq.xml
+++ b/tools/emboss_5/emboss_maskseq.xml
@@ -71,8 +71,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_matcher.xml
--- a/tools/emboss_5/emboss_matcher.xml
+++ b/tools/emboss_5/emboss_matcher.xml
@@ -56,8 +56,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_megamerger.xml
--- a/tools/emboss_5/emboss_megamerger.xml
+++ b/tools/emboss_5/emboss_megamerger.xml
@@ -62,8 +62,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_merger.xml
--- a/tools/emboss_5/emboss_merger.xml
+++ b/tools/emboss_5/emboss_merger.xml
@@ -75,8 +75,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_msbar.xml
--- a/tools/emboss_5/emboss_msbar.xml
+++ b/tools/emboss_5/emboss_msbar.xml
@@ -116,8 +116,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_needle.xml
--- a/tools/emboss_5/emboss_needle.xml
+++ b/tools/emboss_5/emboss_needle.xml
@@ -125,8 +125,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_newcpgreport.xml
--- a/tools/emboss_5/emboss_newcpgreport.xml
+++ b/tools/emboss_5/emboss_newcpgreport.xml
@@ -43,8 +43,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_newcpgseek.xml
--- a/tools/emboss_5/emboss_newcpgseek.xml
+++ b/tools/emboss_5/emboss_newcpgseek.xml
@@ -34,8 +34,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_newseq.xml
--- a/tools/emboss_5/emboss_newseq.xml
+++ b/tools/emboss_5/emboss_newseq.xml
@@ -71,8 +71,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_noreturn.xml
--- a/tools/emboss_5/emboss_noreturn.xml
+++ b/tools/emboss_5/emboss_noreturn.xml
@@ -30,8 +30,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_notseq.xml
--- a/tools/emboss_5/emboss_notseq.xml
+++ b/tools/emboss_5/emboss_notseq.xml
@@ -68,8 +68,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_nthseq.xml
--- a/tools/emboss_5/emboss_nthseq.xml
+++ b/tools/emboss_5/emboss_nthseq.xml
@@ -68,8 +68,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_octanol.xml
--- a/tools/emboss_5/emboss_octanol.xml
+++ b/tools/emboss_5/emboss_octanol.xml
@@ -39,6 +39,8 @@
**Citation**
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_oddcomp.xml
--- a/tools/emboss_5/emboss_oddcomp.xml
+++ b/tools/emboss_5/emboss_oddcomp.xml
@@ -39,8 +39,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_palindrome.xml
--- a/tools/emboss_5/emboss_palindrome.xml
+++ b/tools/emboss_5/emboss_palindrome.xml
@@ -52,8 +52,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_pasteseq.xml
--- a/tools/emboss_5/emboss_pasteseq.xml
+++ b/tools/emboss_5/emboss_pasteseq.xml
@@ -72,8 +72,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_patmatdb.xml
--- a/tools/emboss_5/emboss_patmatdb.xml
+++ b/tools/emboss_5/emboss_patmatdb.xml
@@ -48,8 +48,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_pepcoil.xml
--- a/tools/emboss_5/emboss_pepcoil.xml
+++ b/tools/emboss_5/emboss_pepcoil.xml
@@ -45,8 +45,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_pepinfo.xml
--- a/tools/emboss_5/emboss_pepinfo.xml
+++ b/tools/emboss_5/emboss_pepinfo.xml
@@ -27,8 +27,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_pepnet.xml
--- a/tools/emboss_5/emboss_pepnet.xml
+++ b/tools/emboss_5/emboss_pepnet.xml
@@ -32,8 +32,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_pepstats.xml
--- a/tools/emboss_5/emboss_pepstats.xml
+++ b/tools/emboss_5/emboss_pepstats.xml
@@ -29,8 +29,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_pepwheel.xml
--- a/tools/emboss_5/emboss_pepwheel.xml
+++ b/tools/emboss_5/emboss_pepwheel.xml
@@ -44,8 +44,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_pepwindow.xml
--- a/tools/emboss_5/emboss_pepwindow.xml
+++ b/tools/emboss_5/emboss_pepwindow.xml
@@ -21,8 +21,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_pepwindowall.xml
--- a/tools/emboss_5/emboss_pepwindowall.xml
+++ b/tools/emboss_5/emboss_pepwindowall.xml
@@ -21,8 +21,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_plotcon.xml
--- a/tools/emboss_5/emboss_plotcon.xml
+++ b/tools/emboss_5/emboss_plotcon.xml
@@ -21,8 +21,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_plotorf.xml
--- a/tools/emboss_5/emboss_plotorf.xml
+++ b/tools/emboss_5/emboss_plotorf.xml
@@ -39,8 +39,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_polydot.xml
--- a/tools/emboss_5/emboss_polydot.xml
+++ b/tools/emboss_5/emboss_polydot.xml
@@ -47,8 +47,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_preg.xml
--- a/tools/emboss_5/emboss_preg.xml
+++ b/tools/emboss_5/emboss_preg.xml
@@ -20,8 +20,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_prettyplot.xml
--- a/tools/emboss_5/emboss_prettyplot.xml
+++ b/tools/emboss_5/emboss_prettyplot.xml
@@ -112,8 +112,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_prettyseq.xml
--- a/tools/emboss_5/emboss_prettyseq.xml
+++ b/tools/emboss_5/emboss_prettyseq.xml
@@ -52,8 +52,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_primersearch.xml
--- a/tools/emboss_5/emboss_primersearch.xml
+++ b/tools/emboss_5/emboss_primersearch.xml
@@ -32,8 +32,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_revseq.xml
--- a/tools/emboss_5/emboss_revseq.xml
+++ b/tools/emboss_5/emboss_revseq.xml
@@ -76,8 +76,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_seqmatchall.xml
--- a/tools/emboss_5/emboss_seqmatchall.xml
+++ b/tools/emboss_5/emboss_seqmatchall.xml
@@ -53,8 +53,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_seqret.xml
--- a/tools/emboss_5/emboss_seqret.xml
+++ b/tools/emboss_5/emboss_seqret.xml
@@ -69,8 +69,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_showfeat.xml
--- a/tools/emboss_5/emboss_showfeat.xml
+++ b/tools/emboss_5/emboss_showfeat.xml
@@ -122,8 +122,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_shuffleseq.xml
--- a/tools/emboss_5/emboss_shuffleseq.xml
+++ b/tools/emboss_5/emboss_shuffleseq.xml
@@ -61,8 +61,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_sigcleave.xml
--- a/tools/emboss_5/emboss_sigcleave.xml
+++ b/tools/emboss_5/emboss_sigcleave.xml
@@ -54,8 +54,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_sirna.xml
--- a/tools/emboss_5/emboss_sirna.xml
+++ b/tools/emboss_5/emboss_sirna.xml
@@ -117,8 +117,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_sixpack.xml
--- a/tools/emboss_5/emboss_sixpack.xml
+++ b/tools/emboss_5/emboss_sixpack.xml
@@ -161,8 +161,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_skipseq.xml
--- a/tools/emboss_5/emboss_skipseq.xml
+++ b/tools/emboss_5/emboss_skipseq.xml
@@ -58,8 +58,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_splitter.xml
--- a/tools/emboss_5/emboss_splitter.xml
+++ b/tools/emboss_5/emboss_splitter.xml
@@ -78,8 +78,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_supermatcher.xml
--- a/tools/emboss_5/emboss_supermatcher.xml
+++ b/tools/emboss_5/emboss_supermatcher.xml
@@ -63,8 +63,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_syco.xml
--- a/tools/emboss_5/emboss_syco.xml
+++ b/tools/emboss_5/emboss_syco.xml
@@ -196,8 +196,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_tcode.xml
--- a/tools/emboss_5/emboss_tcode.xml
+++ b/tools/emboss_5/emboss_tcode.xml
@@ -43,8 +43,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_textsearch.xml
--- a/tools/emboss_5/emboss_textsearch.xml
+++ b/tools/emboss_5/emboss_textsearch.xml
@@ -57,8 +57,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_tmap.xml
--- a/tools/emboss_5/emboss_tmap.xml
+++ b/tools/emboss_5/emboss_tmap.xml
@@ -38,8 +38,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_tranalign.xml
--- a/tools/emboss_5/emboss_tranalign.xml
+++ b/tools/emboss_5/emboss_tranalign.xml
@@ -83,8 +83,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_transeq.xml
--- a/tools/emboss_5/emboss_transeq.xml
+++ b/tools/emboss_5/emboss_transeq.xml
@@ -121,8 +121,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_trimest.xml
--- a/tools/emboss_5/emboss_trimest.xml
+++ b/tools/emboss_5/emboss_trimest.xml
@@ -91,8 +91,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_trimseq.xml
--- a/tools/emboss_5/emboss_trimseq.xml
+++ b/tools/emboss_5/emboss_trimseq.xml
@@ -96,8 +96,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_twofeat.xml
--- a/tools/emboss_5/emboss_twofeat.xml
+++ b/tools/emboss_5/emboss_twofeat.xml
@@ -129,8 +129,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_union.xml
--- a/tools/emboss_5/emboss_union.xml
+++ b/tools/emboss_5/emboss_union.xml
@@ -64,8 +64,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_vectorstrip.xml
--- a/tools/emboss_5/emboss_vectorstrip.xml
+++ b/tools/emboss_5/emboss_vectorstrip.xml
@@ -81,8 +81,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_water.xml
--- a/tools/emboss_5/emboss_water.xml
+++ b/tools/emboss_5/emboss_water.xml
@@ -65,8 +65,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_wobble.xml
--- a/tools/emboss_5/emboss_wobble.xml
+++ b/tools/emboss_5/emboss_wobble.xml
@@ -39,8 +39,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_wordcount.xml
--- a/tools/emboss_5/emboss_wordcount.xml
+++ b/tools/emboss_5/emboss_wordcount.xml
@@ -34,8 +34,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_wordmatch.xml
--- a/tools/emboss_5/emboss_wordmatch.xml
+++ b/tools/emboss_5/emboss_wordmatch.xml
@@ -73,8 +73,10 @@
------
-**Citation**
-
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_
+
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>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/7897af491f07/
changeset: 7897af491f07
user: jgoecks
date: 2011-11-15 21:50:36
summary: Fix bug in Trackster's 'Add Datasets to Visualization' button.
affected #: 1 file
diff -r a87d7b85c5771372550bd786bd15606f8e29cf41 -r 7897af491f07535915e2cd917afd0da981a1b45c static/scripts/trackster.js
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -909,7 +909,7 @@
this.content_div = this.viewport_container;
is_container(this.viewport_container, view);
// Introduction div shown when there are no tracks.
- this.intro_div = $("<div/>").addClass("intro");
+ this.intro_div = $("<div/>").addClass("intro").appendTo(this.viewport_container).hide();
var add_tracks_button = $("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function () {
add_tracks();
});
@@ -1077,10 +1077,10 @@
/** Add or remove intro div depending on view state. */
update_intro_div: function() {
if (this.drawables.length === 0) {
- this.intro_div.appendTo(this.viewport_container);
+ this.intro_div.show();
}
else {
- this.intro_div.remove();
+ this.intro_div.hide();
}
},
update_location: function(low, high) {
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/4412842dc738/
changeset: 4412842dc738
user: greg
date: 2011-11-15 20:50:08
summary: A tool shed admin will now receive content alerts (as part of the alert message) for each file uploaded to a repository that contains either image content or html content if the admin has chosen to receive email alerts for changes to the repository.
affected #: 3 files
diff -r 3a49bca428c3f71a431a3d6f5a5c4397941aac55 -r 4412842dc7380ea74e03aba442fa9b655832bda1 lib/galaxy/webapps/community/controllers/common.py
--- a/lib/galaxy/webapps/community/controllers/common.py
+++ b/lib/galaxy/webapps/community/controllers/common.py
@@ -26,6 +26,8 @@
Change description:
${description}
+${content_alert_str}
+
-----------------------------------------------------------------------------
This change alert was sent from the Galaxy tool shed hosted on the server
"${host}"
@@ -520,7 +522,7 @@
def get_user( trans, id ):
"""Get a user from the database by id"""
return trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( id ) )
-def handle_email_alerts( trans, repository ):
+def handle_email_alerts( trans, repository, content_alert_str='' ):
repo_dir = repository.repo_path
repo = hg.repository( get_configured_ui(), repo_dir )
smtp_server = trans.app.config.smtp_server
@@ -541,14 +543,25 @@
username = ctx.user().split()[0]
except:
username = ctx.user()
- # Build the email message
+ # We'll use 2 template bodies because we only want to send content
+ # alerts to tool shed admin users.
+ admin_body = string.Template( email_alert_template ) \
+ .safe_substitute( host=trans.request.host,
+ repository_name=repository.name,
+ revision='%s:%s' %( str( ctx.rev() ), ctx ),
+ display_date=display_date,
+ description=ctx.description(),
+ username=username,
+ content_alert_str=content_alert_str )
body = string.Template( email_alert_template ) \
.safe_substitute( host=trans.request.host,
repository_name=repository.name,
revision='%s:%s' %( str( ctx.rev() ), ctx ),
display_date=display_date,
description=ctx.description(),
- username=username )
+ username=username,
+ content_alert_str='' )
+ admin_users = trans.app.config.get( "admin_users", "" ).split( "," )
frm = email_from
subject = "Galaxy tool shed repository update alert"
email_alerts = from_json_string( repository.email_alerts )
@@ -556,7 +569,10 @@
to = email.strip()
# Send it
try:
- util.send_mail( frm, to, subject, body, trans.app.config )
+ if to in admin_users:
+ util.send_mail( frm, to, subject, admin_body, trans.app.config )
+ else:
+ util.send_mail( frm, to, subject, body, trans.app.config )
except Exception, e:
log.exception( "An error occurred sending a tool shed repository update alert by email." )
def update_for_browsing( trans, repository, current_working_dir, commit_message='' ):
@@ -567,30 +583,20 @@
repo = hg.repository( get_configured_ui(), repo_dir )
# The following will delete the disk copy of only the files in the repository.
#os.system( 'hg update -r null > /dev/null 2>&1' )
- repo.ui.pushbuffer()
files_to_remove_from_disk = []
files_to_commit = []
- commands.status( repo.ui, repo, all=True )
- status_and_file_names = repo.ui.popbuffer().strip().split( "\n" )
- if status_and_file_names and status_and_file_names[ 0 ] not in [ '' ]:
- # status_and_file_names looks something like:
- # ['? README', '? tmap_tool/tmap-0.0.9.tar.gz', '? dna_filtering.py', 'C filtering.py', 'C filtering.xml']
- # The codes used to show the status of files are:
- # M = modified
- # A = added
- # R = removed
- # C = clean
- # ! = deleted, but still tracked
- # ? = not tracked
- # I = ignored
- for status_and_file_name in status_and_file_names:
- if status_and_file_name.startswith( '?' ) or status_and_file_name.startswith( 'I' ):
- files_to_remove_from_disk.append( os.path.abspath( os.path.join( repo_dir, status_and_file_name.split()[1] ) ) )
- elif status_and_file_name.startswith( 'M' ) or status_and_file_name.startswith( 'A' ) or status_and_file_name.startswith( 'R' ):
- files_to_commit.append( os.path.abspath( os.path.join( repo_dir, status_and_file_name.split()[1] ) ) )
# We may have files on disk in the repo directory that aren't being tracked, so they must be removed.
- # We'll use mercurial's purge extension to do this. Using this extension requires the following entry
- # in the repository's hgrc file which was not required for some time, so we'll add it if it's missing.
+ # The codes used to show the status of files are as follows.
+ # M = modified
+ # A = added
+ # R = removed
+ # C = clean
+ # ! = deleted, but still tracked
+ # ? = not tracked
+ # I = ignored
+ # We'll use mercurial's purge extension to remove untracked file. Using this extension requires the
+ # following entry in the repository's hgrc file which was not required for some time, so we'll add it
+ # if it's missing.
# [extensions]
# hgext.purge=
lines = repo.opener( 'hgrc', 'rb' ).readlines()
@@ -624,9 +630,14 @@
commit_message = 'Committed changes to: %s' % ', '.join( files_to_commit )
repo.dirstate.write()
repo.commit( user=trans.user.username, text=commit_message )
+ cmd = 'hg update > /dev/null 2>&1'
os.chdir( repo_dir )
- os.system( 'hg update > /dev/null 2>&1' )
+ proc = subprocess.Popen( args=cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT )
+ return_code = proc.wait()
os.chdir( current_working_dir )
+ if return_code != 0:
+ output = proc.stdout.read( 32768 )
+ log.debug( 'hg update > /dev/null 2>&1 failed in repository directory %s, reason: %s' % ( repo_dir, output ) )
def load_tool( trans, config_file ):
"""
Load a single tool from the file named by `config_file` and return
diff -r 3a49bca428c3f71a431a3d6f5a5c4397941aac55 -r 4412842dc7380ea74e03aba442fa9b655832bda1 lib/galaxy/webapps/community/controllers/upload.py
--- a/lib/galaxy/webapps/community/controllers/upload.py
+++ b/lib/galaxy/webapps/community/controllers/upload.py
@@ -101,12 +101,12 @@
full_path = os.path.abspath( os.path.join( repo_dir, upload_point, uploaded_file_filename ) )
else:
full_path = os.path.abspath( os.path.join( repo_dir, uploaded_file_filename ) )
- # TODO: enhance this method to set a flag and alert an admin to review content since
- # the hard checks are too restrictive.
- #ok, message = self.__check_file_content( uploaded_file_name )
- #if ok:
# Move the uploaded file to the load_point within the repository hierarchy.
shutil.move( uploaded_file_name, full_path )
+ if os.path.isfile( full_path ):
+ content_alert_str = self.__check_file_content( full_path )
+ else:
+ content_alert_str = ''
commands.add( repo.ui, repo, full_path )
try:
commands.commit( repo.ui, repo, full_path, user=trans.user.username, message=commit_message )
@@ -128,7 +128,7 @@
# Handle the special case where a xxx.loc.sample file is
# being uploaded by copying it to ~/tool-data/xxx.loc.
copy_sample_loc_file( trans, full_path )
- handle_email_alerts( trans, repository )
+ handle_email_alerts( trans, repository, content_alert_str=content_alert_str )
if ok:
# Update the repository files for browsing.
update_for_browsing( trans, repository, current_working_dir, commit_message=commit_message )
@@ -194,18 +194,7 @@
tar.extractall( path=full_path )
tar.close()
uploaded_file.close()
- """
- # TODO: enhance this method to set a flag and alert an admin to review content since
- # the hard checks are too restrictive.
- for filename_in_archive in filenames_in_archive:
- if os.path.isfile( filename_in_archive ):
- ok, message = self.__check_file_content( filename_in_archive )
- if not ok:
- # Refresh the repository files for browsing.
- current_working_dir = os.getcwd()
- update_for_browsing( trans, repository, current_working_dir )
- return False, message, []
- """
+ content_alert_str = ''
if remove_repo_files_not_in_tar and not repository.is_new:
# We have a repository that is not new (it contains files), so discover
# those files that are in the repository, but not in the uploaded archive.
@@ -250,6 +239,9 @@
# The directory is not empty
pass
for filename_in_archive in filenames_in_archive:
+ # Check file content to ensure it is appropriate.
+ if os.path.isfile( filename_in_archive ):
+ content_alert_str += self.__check_file_content( filename_in_archive )
commands.add( repo.ui, repo, filename_in_archive )
if filename_in_archive.endswith( 'tool_data_table_conf.xml.sample' ):
# Handle the special case where a tool_data_table_conf.xml.sample
@@ -271,7 +263,7 @@
# exception. If this happens, we'll try the following.
repo.dirstate.write()
repo.commit( user=trans.user.username, text=commit_message )
- handle_email_alerts( trans, repository )
+ handle_email_alerts( trans, repository, content_alert_str )
return True, '', files_to_remove
def uncompress( self, repository, uploaded_file_name, uploaded_file_filename, isgzip, isbz2 ):
if isgzip:
@@ -349,15 +341,9 @@
return False, message
return True, ''
def __check_file_content( self, file_path ):
- return True, ''
message = ''
- ok = True
- head, tail = os.path.split( file_path )
if check_html( file_path ):
- message = 'The file <b>%s</b> contains HTML content which cannot be uploaded to a Galaxy tool shed.' % str( tail )
- ok = False
+ message = 'The file "%s" contains HTML content.\n' % str( file_path )
elif check_image( file_path ):
- # For now we won't allow images to be uploaded.
- message = 'The file <b>%s</b> contains image content that cannot be uploaded to a Galaxy tool shed.' % str( tail )
- ok = False
- return ok, message
+ message = 'The file "%s" contains image content.\n' % str( file_path )
+ return message
diff -r 3a49bca428c3f71a431a3d6f5a5c4397941aac55 -r 4412842dc7380ea74e03aba442fa9b655832bda1 templates/webapps/community/repository/upload.mako
--- a/templates/webapps/community/repository/upload.mako
+++ b/templates/webapps/community/repository/upload.mako
@@ -64,7 +64,13 @@
<div class="toolForm"><div class="toolFormTitle">Upload a single file or a tarball</div><div class="toolFormBody">
- ## TODO: nginx
+ <div class="form-row">
+ <div class="warningmessage">
+ Uploading may take a while, depending upon the size of the file. Wait until a message is displayed in your
+ browser after clicking the <b>Upload</b> button below.
+ </div>
+ <div style="clear: both"></div>
+ </div><form id="upload_form" name="upload_form" action="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}" enctype="multipart/form-data" method="post"><div class="form-row"><label>File:</label>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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