Mercurial > repos > devteam > emboss_5
diff emboss_wordmatch.xml @ 11:0e2484b6829b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
| author | iuc |
|---|---|
| date | Mon, 30 Jan 2017 13:27:40 -0500 |
| parents | 9b98d3d903c6 |
| children | 27c43fb015f0 |
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--- a/emboss_wordmatch.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_wordmatch.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,51 +1,46 @@ -<tool id="EMBOSS: wordmatch110" name="wordmatch" version="5.0.0"> - <description>Finds all exact matches of a given size between 2 sequences</description> - <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>wordmatch -asequence $input1 -bsequence $input2 -outfile $out_file1 -aoutfeat $out_file2 -boutfeat $out_file3 -wordsize "$wordsize" -aformat3 $out_format1 -offormat4 $out_format2 - -offormat5 $out_format3 -auto</command> - <inputs> - <param format="fasta" name="input1" type="data"> - <label>Sequence 1</label> - </param> - <param format="fasta" name="input2" type="data"> - <label>Sequence 2</label> - </param> - <param name="wordsize" type="text" value="4"> - <label>Word size</label> - </param> - <param name="out_format1" type="select"> - <label>Output Alignment File Format</label> - <option value="match">Match (m)</option> - <option value="simple">Simple (m)</option> - <option value="fasta">FASTA (m)</option> - <option value="msf">MSF (m)</option> - <option value="srs">SRS (m)</option> - <option value="pair">Pair (p)</option> - <option value="markx0">Markx0 (p)</option> - <option value="markx1">Markx1 (p)</option> - <option value="markx2">Markx2 (p)</option> - <option value="markx3">Markx3 (p)</option> - <option value="markx10">Markx10 (p)</option> - <option value="srspair">SRS pair (p)</option> - <option value="score">Score (p)</option> - </param> - <param name="out_format2" type="select"> - <label>Output Feature 1 File Format</label> - <option value="gff">GFF</option> - <option value="embl">EMBL</option> - <option value="swiss">SwissProt</option> - </param> - <param name="out_format3" type="select"> - <label>Output Feature 2 File Format</label> - <option value="gff">GFF</option> - <option value="embl">EMBL</option> - <option value="swiss">SwissProt</option> - </param> - </inputs> - <outputs> - <data format="match" name="out_file1" /> - <data format="gff" name="out_file2" /> - <data format="gff" name="out_file3" /> +<tool id="EMBOSS: wordmatch110" name="wordmatch" version="5.0.0.1"> + <description>Finds all exact matches of a given size between 2 sequences</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <code file="emboss_format_corrector.py" /> + <command>wordmatch -asequence '$input1' -bsequence '$input2' -outfile '$out_file1' -aoutfeat '$out_file2' -boutfeat '$out_file3' -wordsize $wordsize -aformat3 $out_format1 -offormat4 $out_format2 + -offormat5 $out_format3 -auto</command> + <inputs> + <param name="input1" type="data" format="fasta" label="Sequence 1" /> + <param name="input2" type="data" format="fasta" label="Sequence 2" /> + <param name="wordsize" type="integer" value="4" label="Word size" /> + <param name="out_format1" type="select" label="Output alignment file format"> + <option value="match">Match (m)</option> + <option value="simple">Simple (m)</option> + <option value="fasta">FASTA (m)</option> + <option value="msf">MSF (m)</option> + <option value="srs">SRS (m)</option> + <option value="pair">Pair (p)</option> + <option value="markx0">Markx0 (p)</option> + <option value="markx1">Markx1 (p)</option> + <option value="markx2">Markx2 (p)</option> + <option value="markx3">Markx3 (p)</option> + <option value="markx10">Markx10 (p)</option> + <option value="srspair">SRS pair (p)</option> + <option value="score">Score (p)</option> + </param> + <param name="out_format2" type="select" label="Output feature 1 file format"> + <option value="gff">GFF</option> + <option value="embl">EMBL</option> + <option value="swiss">SwissProt</option> + </param> + <param name="out_format3" type="select" label="Output feature 2 file format"> + <option value="gff">GFF</option> + <option value="embl">EMBL</option> + <option value="swiss">SwissProt</option> + </param> + </inputs> + <outputs> + <data name="out_file1" format="match" /> + <data name="out_file2" format="gff" /> + <data name="out_file3" format="gff" /> </outputs> <!-- <tests> <test> @@ -56,27 +51,18 @@ <param name="out_format2" value="gff"/> <param name="out_format3" value="gff"/> <output name="ofile2" file="emboss_wordmatch_out.embl"/> - </test> - </tests> test takes a long time to run--> - <code file="emboss_format_corrector.py" /> + </test> + </tests> test takes a long time to run--> <help> +.. class:: warningmark -.. class:: warningmark +The input datasets need to be sequences. -The input datasets need to be sequences. - ------ +----- You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/wordmatch.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/wordmatch.html </help> -</tool> + <expand macro="citations" /> +</tool>