|
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>
|
|
38
|
19 </inputs>
|
|
35
|
20
|
|
20
|
21 <outputs>
|
|
|
22 <data name="out_enriched" format="tabular" label="Enriched Motifs"/>
|
|
|
23 <data name="out_depleted" format="tabular" label="Depleted Motifs"/>
|
|
|
24 <data name="out_plots" format="png" label="Motif Count Comparison Plots"/>
|
|
|
25 </outputs>
|
|
|
26
|
|
38
|
27 <tests>
|
|
|
28 <test>
|
|
|
29 <param name="in_tab_1" value="XXX.tab" />
|
|
|
30 <param name="in_tab_2" value="XXX.tab" />
|
|
|
31 <param name="pwm_file" value="XXX.meme.txt" />
|
|
|
32 <output name="out_enriched" file="XXX.tab" />
|
|
|
33 <output name="out_depleted" file="XXX.tab" />
|
|
|
34 <output name="out_plots" file="XXX.png" />
|
|
|
35 </test>
|
|
|
36 </tests>
|
|
|
37
|
|
20
|
38 <help>
|
|
|
39 This tools reads in two counts file and determines enriched and depleted
|
|
|
40 motifs in two different region sets based on poisson calculation with
|
|
|
41 gc correction.
|
|
|
42 </help>
|
|
|
43
|
|
|
44 </tool> |
