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1 <tool id="homer_annotatePeaks" name="homer_annotatePeaks" version="0.0.2">
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2 <requirements>
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3 <requirement type="package">homer</requirement>
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4 </requirements>
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5 <description></description>
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6 <!--<version_command></version_command>-->
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7 <command>
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8 annotatePeaks.pl $input_bed $genome_selector 1> $out_annotated
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9 2> $out_log || echo "Error running annotatePeaks." >&2
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10 </command>
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11 <inputs>
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12 <param format="tabular,bed" name="input_bed" type="data" label="Homer peak positions or BED format" />
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13 <param name="genome_selector" type="select" label="Genome version">
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14 <option value="hg19" selected="true">hg19</option>
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15 </param>
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16 </inputs>
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17 <outputs>
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18 <!--<data format="html" name="html_outfile" label="index" />-->
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19 <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
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20 <data format="csv" name="out_annotated" label="${tool.name} on #echo os.path.splitext(str($input_bed.name))[0]#_genome_${genome_selector}" />
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21 <data format="txt" name="out_log" label="${tool.name} on #echo os.path.splitext(str($input_bed.name))[0]#_genome_${genome_selector}.log" />
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22 </outputs>
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23 <tests>
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24 <test>
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25 <!--<param name="input_file" value="extract_genomic_dna.fa" />-->
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26 <!--<output name="html_file" file="sample_output.html" ftype="html" />-->
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27 </test>
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28 </tests>
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29
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30 <help>
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31
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32 .. class:: infomark
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33
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34 **Homer annoatePeaks**
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35 More information on accepted formats
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36 http://biowhat.ucsd.edu/homer/ngs/annotation.html
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37
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38
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39 </help>
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40 </tool>
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