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annotate micall-lite.xml @ 13:1c7832516ccd draft

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planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/micall-lite commit c8241b460c9def5b434fa4350924599b09b17a69-dirty
author dfornika
date Fri, 20 Sep 2019 20:02:17 -0400
parents 7747ba1a5557
children 79d9866da30f
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ce0afe2b18d0 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/micall-lite commit c8241b460c9def5b434fa4350924599b09b17a69-dirty
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1 <tool id="micall-lite" name="micall-lite" version="@TOOL_VERSION@+galaxy0">
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2 <description></description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
ce0afe2b18d0 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/micall-lite commit c8241b460c9def5b434fa4350924599b09b17a69-dirty
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">micall-lite</requirement>
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8 </requirements>
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9 <version_command>echo "@TOOL_VERSION@"</version_command>
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10 <command detect_errors="exit_code">
ddae1e5b4bb2 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/micall-lite commit c8241b460c9def5b434fa4350924599b09b17a69-dirty
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11 <![CDATA[
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12 ln -s '${input_pair.forward}' '${input_pair.element_identifier}_R1.fastq.gz' &&
ddae1e5b4bb2 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/micall-lite commit c8241b460c9def5b434fa4350924599b09b17a69-dirty
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13 ln -s '${input_pair.reverse}' '${input_pair.element_identifier}_R2.fastq.gz' &&
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14 mkdir 'outdir' &&
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ddae1e5b4bb2 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/micall-lite commit c8241b460c9def5b434fa4350924599b09b17a69-dirty
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15 micall
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16 '${input_pair.element_identifier}_R1.fastq.gz'
ddae1e5b4bb2 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/micall-lite commit c8241b460c9def5b434fa4350924599b09b17a69-dirty
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17 '${input_pair.element_identifier}_R2.fastq.gz'
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18 --readlen ${readlen}
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19 --outdir 'outdir' &&
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20 mv outdir/*.align.csv ${align} &&
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21 mv outdir/*.amino.csv ${amino} &&
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22 mv outdir/*.conseq.csv ${conseq} &&
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23 mv outdir/*.insert.csv ${insert} &&
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24 mv outdir/*.nuc.csv ${nuc}
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25 ]]>
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26 </command>
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27 <inputs>
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28 <param format="fastqsanger,fastqsanger.gz" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTQ datasets" />
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29 <param name="readlen" type="integer" min="1" value="251" max="600" label="Read Length" help="Read Length" />
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30 </inputs>
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31 <outputs>
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32 <data name="align" format="tabular" />
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33 <data name="amino" format="tabular" />
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34 <data name="conseq" format="tabular" />
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35 <data name="insert" format="tabular" />
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36 <data name="nuc" format="tabular" />
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37 </outputs>
ce0afe2b18d0 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/micall-lite commit c8241b460c9def5b434fa4350924599b09b17a69-dirty
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38 <tests>
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39 <test>
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40 </test>
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41 </tests>
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42 <help><![CDATA[
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43 ]]></help>
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44 <expand macro="citations" />
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45 </tool>