Mercurial > repos > iuc > mothur_reverse_seqs

annotate reverse.seqs.xml @ 1:c7cde36b331a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 721531d2e9fd1e208a3fba8cfbe5dcd572599ca2
author iuc
date Tue, 05 Sep 2017 17:17:59 -0400
parents a8a1a7c5ab14
children 503898f17f42
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1 <tool profile="16.07" id="mothur_reverse_seqs" name="Reverse.seqs" version="@WRAPPER_VERSION@.0">
a8a1a7c5ab14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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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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11
a8a1a7c5ab14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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12 ## create symlinks to input datasets
a8a1a7c5ab14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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13 ln -s "$fasta" fasta.dat &&
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(
a8a1a7c5ab14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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16 fasta=fasta.dat
a8a1a7c5ab14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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17 )'
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18 | sed 's/ //g' ## mothur trips over whitespace
a8a1a7c5ab14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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19 | mothur
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20 | tee mothur.out.log
a8a1a7c5ab14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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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>
a8a1a7c5ab14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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23 <param name="fasta" type="data" format="fasta,mothur.align" label="fasta - Sequences to reverse complement"/>
a8a1a7c5ab14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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24 </inputs>
a8a1a7c5ab14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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25 <outputs>
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26 <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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27 <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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28 </outputs>
a8a1a7c5ab14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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29 <tests>
a8a1a7c5ab14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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30 <test>
a8a1a7c5ab14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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31 <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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32 <output name="out_fasta" file="Mock_S280_L001_R1_001_small.trim.contigs.good.rc.align_head"/>
a8a1a7c5ab14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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33 <expand macro="logfile-test"/>
a8a1a7c5ab14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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34 </test>
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35 </tests>
a8a1a7c5ab14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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36 <help>
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37 <![CDATA[
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38
a8a1a7c5ab14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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39 @MOTHUR_OVERVIEW@
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40
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41 **Command Documentation**
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42
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43 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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44
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45 .. _reverse.seqs: https://www.mothur.org/wiki/Reverse.seqs
a8a1a7c5ab14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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46 ]]>
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47 </help>
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48 <expand macro="citations"/>
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49 </tool>