Mercurial > repos > devteam > emboss_5
diff emboss_water.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_water.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_water.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,43 +1,37 @@ -<tool id="EMBOSS: water107" name="water" version="5.0.0"> - <description>Smith-Waterman local alignment</description> - <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>water -asequence $input1 -bsequence $input2 -outfile $out_file1 -gapopen "$gapopen" -gapextend "$gapextend" -brief $brief -aformat3 $out_format1 -auto</command> - <inputs> - <param format="fasta" name="input1" type="data"> - <label>Sequence 1</label> - </param> - <param format="fasta" name="input2" type="data"> - <label>Sequence 2</label> - </param> - <param name="gapopen" type="text" value="10.0"> - <label>Gap open penalty</label> - </param> - <param name="gapextend" type="text" value="0.5"> - <label>Gap extension penalty</label> - </param> - <param name="brief" type="select"> - <label>Brief identity and similarity</label> - <option value="yes">Yes</option> - <option value="no">No</option> - </param> - <param name="out_format1" type="select"> - <label>Output Alignment File Format</label> - <option value="srs">SRS (m)</option> - <option value="simple">Simple (m)</option> - <option value="fasta">FASTA (m)</option> - <option value="msf">MSF (m)</option> - <option value="pair">Pair (p)</option> - <option value="markx0">Markx0 (p)</option> - <option value="markx1">Markx1 (p)</option> - <option value="markx2">Markx2 (p)</option> - <option value="markx3">Markx3 (p)</option> - <option value="markx10">Markx10 (p)</option> - <option value="srspair">SRS pair (p)</option> - <option value="score">Score (p)</option> - </param> - </inputs> - <outputs> - <data format="srs" name="out_file1" /> +<tool id="EMBOSS: water107" name="water" version="5.0.0.1"> + <description>Smith-Waterman local alignment</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <code file="emboss_format_corrector.py" /> + <command>water -asequence '$input1' -bsequence '$input2' -outfile '$out_file1' -gapopen $gapopen -gapextend $gapextend -brief $brief -aformat3 $out_format1 -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="gapopen" type="float" value="10.0" label="Gap open penalty" /> + <param name="gapextend" type="float" value="0.5" label="Gap extension penalty" /> + <param name="brief" type="select" label="Brief identity and similarity"> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <param name="out_format1" type="select" label="Output alignment file format"> + <option value="srs">SRS (m)</option> + <option value="simple">Simple (m)</option> + <option value="fasta">FASTA (m)</option> + <option value="msf">MSF (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> + </inputs> + <outputs> + <data name="out_file1" format="srs" /> </outputs> <tests> <test> @@ -49,26 +43,17 @@ <param name="out_format1" value="score"/> <output name="out_file1" file="emboss_water_out.score"/> </test> - </tests> - <code file="emboss_format_corrector.py" /> + </tests> <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/water.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/water.html </help> + <expand macro="citations" /> </tool>