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1 <tool id="homer_annotatePeaks" name="homer_annotatePeaks" version="0.0.4">
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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 peaks 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 <param type="text" name="options" label="Extra options" value="" help="Go to link below for more options">
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17 <sanitizer>
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18 <valid initial="string.printable">
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19 <remove value="'"/>
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20 <remove value="/"/>
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21 </valid>
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22 <mapping initial="none">
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23 <add source="'" target="__sq__"/>
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24 </mapping>
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25 </sanitizer>
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26 </param>
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27 </inputs>
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28 <outputs>
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29 <!--<data format="html" name="html_outfile" label="index" />-->
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30 <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
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31 <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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32 <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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33 </outputs>
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34 <tests>
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35 <test>
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36 <!--<param name="input_file" value="extract_genomic_dna.fa" />-->
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37 <!--<output name="html_file" file="sample_output.html" ftype="html" />-->
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38 </test>
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39 </tests>
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40
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41 <help>
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42
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43 .. class:: infomark
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44
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45 **Homer annoatePeaks**
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46
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47 More information on accepted formats and options
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48
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49 http://biowhat.ucsd.edu/homer/ngs/annotation.html
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50
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51 TIP: use homer_bed2pos and homer_pos2bed to convert between the homer peak positions and the BED format.
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52
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53 </help>
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54 </tool>
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