Mercurial > repos > iuc > mothur_reverse_seqs

annotate reverse.seqs.xml @ 2:503898f17f42 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 21:55:28 -0400
parents a8a1a7c5ab14
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1 <tool profile="16.07" id="mothur_reverse_seqs" name="Reverse.seqs" version="@WRAPPER_VERSION@.0">
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2 <description>Reverse complement the sequences</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
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10 @SHELL_OPTIONS@
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a8a1a7c5ab14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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11
2
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12 ## create symlinks to input datasets
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13 ln -s '$fasta' fasta.dat &&
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a8a1a7c5ab14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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14
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15 echo 'reverse.seqs(
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16 fasta=fasta.dat
503898f17f42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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17 )'
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18 | sed 's/ //g' ## mothur trips over whitespace
503898f17f42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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19 | mothur
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20 | tee mothur.out.log
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21 ]]></command>
a8a1a7c5ab14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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22 <inputs>
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23 <param name="fasta" type="data" format="fasta,mothur.align" label="fasta - Sequences to reverse complement"/>
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24 <expand macro="param-savelog"/>
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a8a1a7c5ab14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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25 </inputs>
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26 <outputs>
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27 <expand macro="logfile-output"/>
a8a1a7c5ab14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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28 <data name="out_fasta" format_source="fasta" from_work_dir="fasta*.rc.*" label="${tool.name} on ${on_string}: rc.fasta"/>
a8a1a7c5ab14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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29 </outputs>
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30 <tests>
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31 <test>
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32 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
a8a1a7c5ab14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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33 <output name="out_fasta" file="Mock_S280_L001_R1_001_small.trim.contigs.good.rc.align_head"/>
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34 <param name="savelog" value="true"/>
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35 <expand macro="logfile-test"/>
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36 </test>
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37 </tests>
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38 <help><![CDATA[
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40 @MOTHUR_OVERVIEW@
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42 **Command Documentation**
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44 The reverse.seqs_ command will generate a fasta containing the reverse complement of each sequence in the input fasta.
a8a1a7c5ab14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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46 .. _reverse.seqs: https://www.mothur.org/wiki/Reverse.seqs
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47
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48 ]]></help>
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49 <expand macro="citations"/>
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50 </tool>