Mercurial > repos > kevyin > homer
view makeTagDirectory.xml @ 2:7268cbc535e5 draft
findpeaks and maketagdirectory
author | kevyin |
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date | Fri, 23 Nov 2012 00:30:27 -0500 |
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<tool id="homer_makeTagDirectory" name="homer_makeTagDirectory" version="0.0.8"> <requirements> <requirement type="package" >homer</requirement> </requirements> <description>makeTagDirectory</description> <version_command>echo "Doh!"</version_command> <command> makeTagDirectory ${tagDir.extra_files_path} #for $alignF in $alignmentFiles $alignF.file -format $alignF.file.ext #end for 2> $out_log || echo "Error running homer_makeTagDirectory." >&2 </command> <inputs> <param name="title" label="Name for the output tag directory" type="text" default="Homer TagDirectory" /> <repeat name="alignmentFiles" title="Alignment Files"> <param name="file" label="Add file" type="data" format="sam,bed" /> </repeat> </inputs> <outputs> <data format="homerTagDirectory" name="tagDir" label="${title}" /> <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 After the job finishes, save the zip file, unzip and open "index.html" The actual meme-chip command is displayed under "Command line summary" Defaults: http://meme.nbcr.net/meme/doc/meme-chip.html </help> </tool>