Mercurial > repos > kevyin > homer
diff findPeaks.xml @ 12:4356089c8e7f draft
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author | kevyin |
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date | Mon, 17 Dec 2012 00:25:28 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/findPeaks.xml Mon Dec 17 00:25:28 2012 -0500 @@ -0,0 +1,58 @@ +<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> +