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comparison region_motif_compare.xml @ 3:cab2db9d058b draft

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author jeremyjliu
date Sat, 16 May 2015 22:35:26 -0400
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2:2538677b6004 3:cab2db9d058b
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">
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
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"/>
15
16 <param name="pwm_file" type="select" label="Using motif database PWM file">
17 <options from_data_table="motif_databases"/>
18 </param>
19 </inputs>
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
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
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>