Mercurial > repos > jeremyjliu > region_motif_enrichment
comparison region_motif_compare.xml @ 35:4ce22698acb0 draft
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| author | jeremyjliu |
|---|---|
| date | Thu, 26 Feb 2015 22:54:09 -0500 |
| parents | d73892a1e7e6 |
| children | aa921c733d10 |
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| 34:fe8a884363df | 35:4ce22698acb0 |
|---|---|
| 2 <description>for comparing the motif counts in different region sets</description> | 2 <description>for comparing the motif counts in different region sets</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="set_environment">RMOTIF_PATH</requirement> | 4 <requirement type="set_environment">RMOTIF_PATH</requirement> |
| 5 </requirements> | 5 </requirements> |
| 6 <command interpreter="Rscript"> | 6 <command interpreter="Rscript"> |
| 7 region_motif_compare.r --args \$RMOTIF_PATH $db_type $in_tab_1 $in_tab_2 $out_enriched $out_depleted $out_plots | 7 region_motif_compare.r --args \$RMOTIF_PATH $pwm_file.fields.path $in_tab_1 $in_tab_2 |
| 8 $out_enriched | |
| 9 $out_depleted | |
| 10 $out_plots | |
| 8 </command> | 11 </command> |
| 9 <inputs> | 12 <inputs> |
| 10 <param name="in_tab_1" type="data" format="tabular" label="Region Set 1 Motif Count File"/> | 13 <param name="in_tab_1" type="data" format="tabular" label="Region Set 1 Motif Count File"/> |
| 11 <param name="in_tab_2" type="data" format="tabular" label="Region Set 2 Motif Count File"/> | 14 <param name="in_tab_2" type="data" format="tabular" label="Region Set 2 Motif Count File"/> |
| 15 | |
| 16 <param name="pwm_file" type="select" label="Using motif database PWM file"> | |
| 17 <options from_data_table="motif_databases"/> | |
| 18 </param> | |
| 19 | |
| 20 <!-- COMBINED OPTION IS LOST | |
| 12 <param name="db_type" type="select" label="Select Motif Database" > | 21 <param name="db_type" type="select" label="Select Motif Database" > |
| 13 <option value="t">Test Pouya Subset (hg19)</option> | 22 <option value="t">Test Encode Motifs (hg19)</option> |
| 14 <option value="p">Pouya Encode Motifs (hg19)</option> | 23 <option value="e">Encode Motifs (hg19)</option> |
| 15 <option value="j">Jaspar and Jolma Motifs (hg19)</option> | 24 <option value="j">Jaspar and Jolma Motifs (hg19)</option> |
| 16 <option value="m">Mouse Motifs (mm9)</option> | 25 <option value="m">Mouse Motifs (mm9)</option> |
| 17 <option value="c">Pouya, Jaspar, and Jolma Combined (hg19)</option> | 26 <option value="c">Pouya, Jaspar, and Jolma Combined (hg19)</option> |
| 18 </param> | 27 </param> --> |
| 28 | |
| 19 </inputs> | 29 </inputs> |
| 20 <outputs> | 30 <outputs> |
| 21 <data name="out_enriched" format="tabular" label="Enriched Motifs"/> | 31 <data name="out_enriched" format="tabular" label="Enriched Motifs"/> |
| 22 <data name="out_depleted" format="tabular" label="Depleted Motifs"/> | 32 <data name="out_depleted" format="tabular" label="Depleted Motifs"/> |
| 23 <data name="out_plots" format="png" label="Motif Count Comparison Plots"/> | 33 <data name="out_plots" format="png" label="Motif Count Comparison Plots"/> |