Mercurial > repos > kevyin > homer
view makeTagDirectory.xml @ 14:d9658163c29e draft
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author | kevyin |
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date | Mon, 17 Dec 2012 00:46:29 -0500 |
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<tool id="homer_makeTagDirectory" name="homer_makeTagDirectory" version="1.0.1"> <requirements> <requirement type="package" version="4.1">homer</requirement> </requirements> <description>Simple wrapper for makeTagDirectory. Used by findPeaks</description> <!--<version_command></version_command>--> <command interpreter="python">makeTagDirectory.py ${tagDir.files_path} #for $alignF in $alignmentFiles $alignF.file -f $alignF.file.ext #end for -o $tagDir 2> $out_log || echo "Error running homer_makeTagDirectory." >&2 </command> <inputs> <param name="title" label="Name for the output tag directory" type="text" default="Homer TagDirectory" /> <param type="text" name="options" label="Extra options" value="" help="Go to link below for more options"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="/"/> </valid> <mapping initial="none"> <add source="'" target="__sq__"/> </mapping> </sanitizer> </param> <repeat name="alignmentFiles" title="Alignment Files"> <param name="file" label="Add file" type="data" format="sam,bed" help="Alignments in SAM or BED format" /> </repeat> </inputs> <outputs> <!--<data format="homerTagDirectory" name="tagDir" label="${title} tag directory" />--> <data format="html" name="tagDir" label="${title} tag directory" /> <data format="txt" name="out_log" label="${title}.log" /> <!--<data format="html" name="html_outfile" label="index" />--> <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />--> </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 makeTagDirectory** For more options, look under: "Command line options" http://biowhat.ucsd.edu/homer/ngs/tagDir.html </help> </tool>