Mercurial > repos > kevyin > homer
view findPeaks.xml @ 14:d9658163c29e draft
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author | kevyin |
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date | Mon, 17 Dec 2012 00:46:29 -0500 |
parents | 4356089c8e7f |
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<tool id="homer_findPeaks" name="homer_findPeaks" version="0.1.2"> <requirements> <requirement type="package" version="4.1">homer</requirement> </requirements> <description>Homer's peakcaller. Requires tag directories (see makeTagDirectory)</description> <!--<version_command></version_command>--> <command> findPeaks $tagDir.extra_files_path $options -o $outputPeakFile #if $control_tagDir: -i $control_tagDir.extra_files_path #end if 2> $out_log || echo "Error running findPeaks." >&2 </command> <inputs> <param format="homerTagDirectory" name="tagDir" type="data" label="tag directory" help="Must be made with homer_makeTagDirectory" /> <param format="homerTagDirectory" name="control_tagDir" type="data" optional="True" label="Control tag directory" help="Must be made with homer_makeTagDirectory" /> <param type="text" name="options" label="Extra options" value="" help="Go to link below for more options"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="/"/> </valid> <mapping initial="none"> <add source="'" target="__sq__"/> </mapping> </sanitizer> </param> </inputs> <outputs> <!--<data format="html" name="html_outfile" label="index" />--> <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />--> <data format="txt" name="outputPeakFile" label="${tool.name} on #echo os.path.splitext(str($tagDir.name))[0]#.txt" /> <data format="txt" name="out_log" label="${tool.name} on #echo os.path.splitext(str($tagDir.name))[0]#.log" /> </outputs> <tests> <test> <!--<param name="input_file" value="extract_genomic_dna.fa" />--> <!--<output name="html_file" file="sample_output.html" ftype="html" />--> </test> </tests> <help> .. class:: infomark **Homer findPeaks** For more options, look under: "Command line options for findPeaks" http://biowhat.ucsd.edu/homer/ngs/peaks.html TIP: use homer_bed2pos and homer_pos2bed to convert between the homer peak positions and the BED format. </help> </tool>