Mercurial > repos > jeremyjliu > region_motif_enrichment
comparison region_motif_intersect.xml @ 31:0e031bf8c5b1 draft
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| author | jeremyjliu |
|---|---|
| date | Wed, 04 Feb 2015 13:52:22 -0500 |
| parents | da0bc6dead0d |
| children | 4ce22698acb0 |
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| 30:da0bc6dead0d | 31:0e031bf8c5b1 |
|---|---|
| 1 <tool id="region_motif_intersect" name="Region Motif Intersect"> | 1 <tool id="region_motif_intersect" name="Region Motif Intersect"> |
| 2 <description>for computing the motifs that lie inside a region set</description> | 2 <description>for computing the motifs that lie inside a region set</description> |
| 3 <requirements> | 3 <!--<requirements> |
| 4 <requirement type="set_environment">RMOTIF_PATH</requirement> | 4 <requirement type="package" version="1.0.0">MOTIF_DATA_MANAGER</requirement> |
| 5 <requirement type="package" version="1.0.0">MOTIFS</requirement> | 5 </requirements>--> |
| 6 </requirements> | |
| 7 <command interpreter="Rscript"> | 6 <command interpreter="Rscript"> |
| 8 region_motif_intersect.r --args \$RMOTIF_PATH $db_type $in_bed $out_tab | 7 region_motif_intersect.r --args $bgz_file.fields.path $tbi_file.fields.path $in_bed $out_tab |
| 9 </command> | 8 </command> |
| 10 <inputs> | 9 <inputs> |
| 11 <param name="in_bed" type="data" format="bed" label="Input BED File" /> | 10 <param name="in_bed" type="data" format="bed" label="Input BED File" /> |
| 12 <param name="db_type" type="select" label="Select Motif Database" > | 11 |
| 12 <param name="bgz_file" type="select" label="Using motif database BGZ file"> | |
| 13 <options from_data_table="motif_databases"/> | |
| 14 </param> | |
| 15 <param name="tbi_file" type="select" label="Using motif database TBI file"> | |
| 16 <options from_data_table="motif_databases"/> | |
| 17 </param> | |
| 18 | |
| 19 <!--<param name="db_type" type="select" label="Select Motif Database" > | |
| 13 <option value="t">Test Pouya Subset (hg19)</option> | 20 <option value="t">Test Pouya Subset (hg19)</option> |
| 14 <option value="p">Pouya Encode Motifs (hg19)</option> | 21 <option value="p">Pouya Encode Motifs (hg19)</option> |
| 15 <option value="j">Jaspar and Jolma Motifs (hg19)</option> | 22 <option value="j">Jaspar and Jolma Motifs (hg19)</option> |
| 16 <option value="m">Mouse Motifs (mm9)</option> | 23 <option value="m">Mouse Motifs (mm9)</option> |
| 17 </param> | 24 </param>--> |
| 18 </inputs> | 25 </inputs> |
| 19 <outputs> | 26 <outputs> |
| 20 <data name="out_tab" format="tabular" /> | 27 <data name="out_tab" format="tabular" /> |
| 21 </outputs> | 28 </outputs> |
| 22 | 29 |