Mercurial > repos > devteam > emboss_5
diff emboss_wordcount.xml @ 11:0e2484b6829b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
author | iuc |
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date | Mon, 30 Jan 2017 13:27:40 -0500 |
parents | 9b98d3d903c6 |
children | 27c43fb015f0 |
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--- a/emboss_wordcount.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_wordcount.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,17 +1,16 @@ -<tool id="EMBOSS: wordcount109" name="wordcount" version="5.0.0"> - <description>Counts words of a specified size in a DNA sequence</description> - <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>wordcount -sequence $input1 -outfile $out_file1 -wordsize "$wordsize" -auto</command> - <inputs> - <param format="fasta" name="input1" type="data"> - <label>Sequence</label> - </param> - <param name="wordsize" type="text" value="4"> - <label>Word size</label> - </param> - </inputs> - <outputs> - <data format="wordcount" name="out_file1" /> +<tool id="EMBOSS: wordcount109" name="wordcount" version="5.0.0.1"> + <description>Counts words of a specified size in a DNA sequence</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command>wordcount -sequence '$input1' -outfile '$out_file1' -wordsize $wordsize -auto</command> + <inputs> + <param name="input1" type="data" format="fasta" label="Sequence" /> + <param name="wordsize" type="integer" value="4" label="Word size" /> + </inputs> + <outputs> + <data name="out_file1" format="wordcount" /> </outputs> <tests> <test> @@ -19,25 +18,17 @@ <param name="wordsize" value="4"/> <output name="out_file1" file="emboss_wordcount_out.wordcount"/> </test> - </tests> + </tests> <help> +.. class:: warningmark -.. class:: warningmark +The input dataset needs to be sequences. -The input dataset needs to be sequences. - ------ +----- You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/wordcount.html - ------- - -**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>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/wordcount.html </help> + <expand macro="citations" /> </tool>