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1 <tool id="homer_findPeaks" name="homer_findPeaks" version="0.0.7">
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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 findPeaks $tagDir.extra_files_path $options -o $outputPeakFile
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9
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10 #if $control_tagDir:
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11 -i $control_tagDir.extra_files_path
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12 #end if
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13
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14 2> $out_log || echo "Error running findPeaks." >&2
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15 </command>
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16 <inputs>
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17 <param format="homerTagDirectory" name="tagDir" type="data" label="tag directory" />
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18 <param format="homerTagDirectory" name="control_tagDir" type="data" optional="True" label="Control tag directory" />
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19 <param type="text" name="options" label="Extra options" value="" >
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20 <sanitizer>
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21 <valid initial="string.printable">
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22 <remove value="'"/>
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23 </valid>
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24 <mapping initial="none">
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25 <add source="'" target="__sq__"/>
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26 </mapping>
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27 </sanitizer>
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28 </param>
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29 </inputs>
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30 <outputs>
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31 <!--<data format="html" name="html_outfile" label="index" />-->
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32 <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
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33 <data format="txt" name="outputPeakFile" label="${tool.name} on #echo os.path.splitext(str($tagDir.name))[0]#.txt" />
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34 <data format="txt" name="out_log" label="${tool.name} on #echo os.path.splitext(str($tagDir.name))[0]#.log" />
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35 </outputs>
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36 <tests>
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37 <test>
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38 <!--<param name="input_file" value="extract_genomic_dna.fa" />-->
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39 <!--<output name="html_file" file="sample_output.html" ftype="html" />-->
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40 </test>
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41 </tests>
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42
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43 <help>
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44
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45 .. class:: infomark
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46
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47 **Homer findPeaks**
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48 http://biowhat.ucsd.edu/homer/ngs/peaks.html
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49
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50 </help>
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51 </tool>
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52
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