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annotate emboss_seqmatchall.xml @ 20:21a9fb508031 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Tue, 31 Aug 2021 08:05:39 +0000
parents 27c43fb015f0
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27c43fb015f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 9844cae766e7471d9fa6b2e8356e5194e77f6753
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1 <tool id="EMBOSS: seqmatchall83" name="seqmatchall" version="@VERSION@.1">
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2 <description>All-against-all comparison of a set of sequences</description>
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21a9fb508031 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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3 <expand macro="bio_tools" />
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4 <macros>
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5 <import>macros.xml</import>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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6 </macros>
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7 <expand macro="requirements" />
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8 <code file="emboss_format_corrector.py" />
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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9 <command>seqmatchall -sequence '$input1' -outfile '$out_file1' -wordsize $wordsize -aformat2 $out_format1 -auto</command>
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10 <inputs>
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11 <param name="input1" type="data" format="fasta" label="Sequences" />
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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12 <param name="wordsize" type="integer" value="4" label="Word size" />
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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13 <param name="out_format1" type="select" label="Output alignment file format">
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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14 <option value="match">Match (m)</option>
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15 <option value="simple">Simple (m)</option>
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16 <option value="fasta">FASTA (m)</option>
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17 <option value="msf">MSF (m)</option>
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18 <option value="srs">SRS (m)</option>
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19 <option value="pair">Pair (p)</option>
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20 <option value="markx0">Markx0 (p)</option>
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21 <option value="markx1">Markx1 (p)</option>
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22 <option value="markx2">Markx2 (p)</option>
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23 <option value="markx3">Markx3 (p)</option>
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24 <option value="markx10">Markx10 (p)</option>
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25 <option value="srspair">SRS pair (p)</option>
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26 <option value="score">Score (p)</option>
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27 <option value="seqmatchall">Seqmatchall Output File</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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28 </param>
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29 </inputs>
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30 <outputs>
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31 <data name="out_file1" format="seqmatchall" />
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32 </outputs>
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33 <tests>
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34 <test>
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35 <param name="input1" value="2.fasta"/>
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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36 <param name="wordsize" value="2"/>
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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37 <param name="out_format1" value="fasta"/>
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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38 <output name="out_file1" file="emboss_seqmatchall_out.fasta"/>
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39 </test>
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40 </tests>
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41 <help>
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42 .. class:: warningmark
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44 The input dataset needs to be sequences.
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46 -----
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48 You can view the original documentation here_.
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49
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50 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/seqmatchall.html
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51 </help>
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52 <expand macro="citations" />
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53 </tool>