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1 <tool id="homer_pos2bed" name="homer_pos2bed" version="1.0.0">
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2 <requirements>
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3 <requirement type="package" version="4.1" >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 pos2bed.pl $input_peak 1> $out_bed
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9 2> $out_log || echo "Error running pos2bed." >&2
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10 </command>
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11 <inputs>
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12 <param format="tabular" name="input_peak" type="data" label="Homer peak positions" />
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13 </inputs>
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14 <outputs>
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15 <!--<data format="html" name="html_outfile" label="index" />-->
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16 <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
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17 <data format="bed" name="out_bed" label="${tool.name} on #echo os.path.splitext(str($input_peak.name))[0]#.bed" />
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18 <data format="txt" name="out_log" label="${tool.name} on #echo os.path.splitext(str($input_peak.name))[0]#.log" />
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19 </outputs>
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20 <tests>
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21 <test>
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22 <!--<param name="input_file" value="extract_genomic_dna.fa" />-->
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23 <!--<output name="html_file" file="sample_output.html" ftype="html" />-->
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24 </test>
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25 </tests>
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26
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27 <help>
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28 .. class:: infomark
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29
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30 Converts: homer peak positions -(to)-> BED format
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31
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32 **Homer pos2bed.pl**
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33
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34 http://biowhat.ucsd.edu/homer/ngs/miscellaneous.html
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35 </help>
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36 </tool>
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37
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