Mercurial > repos > kevyin > homer
diff makeTagDirectory.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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/makeTagDirectory.xml Mon Dec 17 00:22:39 2012 -0500 @@ -0,0 +1,61 @@ +<tool id="homer_makeTagDirectory" name="homer_makeTagDirectory" version="1.0.1"> + <requirements> + <requirement type="package" >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> $out_log || echo "Error running homer_makeTagDirectory." >&2 + + </command> + <inputs> + <param name="title" label="Name for the output tag directory" type="text" default="Homer TagDirectory" /> + <param type="text" name="options" label="Extra options" value="" help="Go to link below for more options"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="/"/> + </valid> + <mapping initial="none"> + <add source="'" target="__sq__"/> + </mapping> + </sanitizer> + </param> + <repeat name="alignmentFiles" title="Alignment Files"> + <param name="file" label="Add file" type="data" format="sam,bed" /> + </repeat> + </inputs> + <outputs> + <!--<data format="homerTagDirectory" name="tagDir" label="${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> +