Mercurial > repos > jeremyjliu > region_motif_enrichment
view region_motif_intersect.xml @ 36:b868314320e2 draft
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author | jeremyjliu |
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date | Fri, 06 Mar 2015 13:24:03 -0500 |
parents | 4ce22698acb0 |
children | aa921c733d10 |
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<tool id="region_motif_intersect" name="Region Motif Intersect"> <description>for computing the motifs that lie inside a region set</description> <command interpreter="Rscript"> region_motif_intersect.r --args $bgz_file.fields.path $tbi_file.fields.path $in_bed $out_tab </command> <inputs> <param name="in_bed" type="data" format="bed" label="Input BED File" /> <param name="bgz_file" type="select" label="Using motif database BGZ file"> <options from_data_table="motif_databases"/> </param> <param name="tbi_file" type="select" label="Using motif database TBI file"> <options from_data_table="motif_databases"/> </param> <!--<param name="db_type" type="select" label="Select Motif Database" > <option value="t">Test Encode Motifs (hg19)</option> <option value="e">Encode Motifs (hg19)</option> <option value="j">Jaspar and Jolma Motifs (hg19)</option> <option value="m">Mouse Motifs (mm9)</option> </param>--> </inputs> <outputs> <data name="out_tab" format="tabular" /> </outputs> <help> This tool computes the motifs and the number of motifs that intersect any region in a input set of regions. </help> </tool>