|
20
|
1 <tool id="region_motif_compare" name="Region Motif Count Compare">
|
|
|
2 <description>for comparing the motif counts in different region sets</description>
|
|
|
3 <requirements>
|
|
|
4 <requirement type="set_environment">RMOTIF_PATH</requirement>
|
|
|
5 </requirements>
|
|
|
6 <command interpreter="Rscript">
|
|
35
|
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
|
|
20
|
11 </command>
|
|
|
12 <inputs>
|
|
|
13 <param name="in_tab_1" type="data" format="tabular" label="Region Set 1 Motif Count File"/>
|
|
|
14 <param name="in_tab_2" type="data" format="tabular" label="Region Set 2 Motif Count File"/>
|
|
35
|
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
|
|
20
|
21 <param name="db_type" type="select" label="Select Motif Database" >
|
|
35
|
22 <option value="t">Test Encode Motifs (hg19)</option>
|
|
|
23 <option value="e">Encode Motifs (hg19)</option>
|
|
20
|
24 <option value="j">Jaspar and Jolma Motifs (hg19)</option>
|
|
|
25 <option value="m">Mouse Motifs (mm9)</option>
|
|
|
26 <option value="c">Pouya, Jaspar, and Jolma Combined (hg19)</option>
|
|
35
|
27 </param> -->
|
|
|
28
|
|
20
|
29 </inputs>
|
|
|
30 <outputs>
|
|
|
31 <data name="out_enriched" format="tabular" label="Enriched Motifs"/>
|
|
|
32 <data name="out_depleted" format="tabular" label="Depleted Motifs"/>
|
|
|
33 <data name="out_plots" format="png" label="Motif Count Comparison Plots"/>
|
|
|
34 </outputs>
|
|
|
35
|
|
|
36 <help>
|
|
|
37 This tools reads in two counts file and determines enriched and depleted
|
|
|
38 motifs in two different region sets based on poisson calculation with
|
|
|
39 gc correction.
|
|
|
40 </help>
|
|
|
41
|
|
|
42 </tool> |
