Mercurial > repos > kevyin > homer
view annotatePeaks.xml @ 10:7efeace8bd32 draft
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author | kevyin |
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date | Mon, 17 Dec 2012 00:22:39 -0500 |
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<tool id="homer_annotatePeaks" name="homer_annotatePeaks" version="0.0.4"> <requirements> <requirement type="package">homer</requirement> </requirements> <description></description> <!--<version_command></version_command>--> <command> annotatePeaks.pl $input_bed $genome_selector 1> $out_annotated 2> $out_log || echo "Error running annotatePeaks." >&2 </command> <inputs> <param format="tabular,bed" name="input_bed" type="data" label="Homer peaks OR BED format"/> <param name="genome_selector" type="select" label="Genome version"> <option value="hg19" selected="true">hg19</option> </param> <param type="text" name="options" label="Extra options" value="" help="Go to link below for more options"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="/"/> </valid> <mapping initial="none"> <add source="'" target="__sq__"/> </mapping> </sanitizer> </param> </inputs> <outputs> <!--<data format="html" name="html_outfile" label="index" />--> <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />--> <data format="csv" name="out_annotated" label="${tool.name} on #echo os.path.splitext(str($input_bed.name))[0]#_genome_${genome_selector}" /> <data format="txt" name="out_log" label="${tool.name} on #echo os.path.splitext(str($input_bed.name))[0]#_genome_${genome_selector}.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 annoatePeaks** More information on accepted formats and options http://biowhat.ucsd.edu/homer/ngs/annotation.html TIP: use homer_bed2pos and homer_pos2bed to convert between the homer peak positions and the BED format. </help> </tool>