Mercurial > repos > jeremyjliu > region_motif_enrichment

comparison region_motif_compare.xml @ 5:4803f5186f1a draft default tip

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author jeremyjliu
date Tue, 26 May 2015 12:44:08 -0400
parents cab2db9d058b
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4:53e45130e6f9 5:4803f5186f1a
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 $pwm_file.fields.path $in_tab_1 $in_tab_2 7 region_motif_compare.r --args \$RMOTIF_PATH $pwm_file.fields.path $in_tab_a $in_tab_b
8 $out_enriched 8 $out_enriched_a
9 $out_depleted 9 $out_enriched_b
10 $out_plots 10 $out_plots
11 </command> 11 </command>
12 <inputs> 12 <inputs>
13 <param name="in_tab_1" type="data" format="tabular" label="Region Set 1 Motif Count File"/> 13 <param name="in_tab_a" type="data" format="tabular" label="Region Set A Motif Count File"/>
14 <param name="in_tab_2" type="data" format="tabular" label="Region Set 2 Motif Count File"/> 14 <param name="in_tab_b" type="data" format="tabular" label="Region Set B Motif Count File"/>
15 15
16 <param name="pwm_file" type="select" label="Using motif database PWM file"> 16 <param name="pwm_file" type="select" label="Using motif database PWM file">
17 <options from_data_table="motif_databases"/> 17 <options from_data_table="motif_databases"/>
18 </param> 18 </param>
19 </inputs> 19 </inputs>
20 20
21 <outputs> 21 <outputs>
22 <data name="out_enriched" format="tabular" label="Enriched Motifs"/> 22 <data name="out_enriched_a" format="tabular" label="Enriched Motifs in Region Set A"/>
23 <data name="out_depleted" format="tabular" label="Depleted Motifs"/> 23 <data name="out_enriched_b" format="tabular" label="Enriched Motifs in Region Set B"/>
24 <data name="out_plots" format="png" label="Motif Count Comparison Plots"/> 24 <data name="out_plots" format="png" label="Motif Count Comparison Plots"/>
25 </outputs> 25 </outputs>
26 26
27 <!--
27 <tests> 28 <tests>
28 <test> 29 <test>
29 <param name="in_tab_1" value="XXX.tab" /> 30 <param name="in_tab_1" value="XXX.tab" />
30 <param name="in_tab_2" value="XXX.tab" /> 31 <param name="in_tab_2" value="XXX.tab" />
31 <param name="pwm_file" value="XXX.meme.txt" /> 32 <param name="pwm_file" value="XXX.meme.txt" />
32 <output name="out_enriched" file="XXX.tab" /> 33 <output name="out_enriched" file="XXX.tab" />
33 <output name="out_depleted" file="XXX.tab" /> 34 <output name="out_depleted" file="XXX.tab" />
34 <output name="out_plots" file="XXX.png" /> 35 <output name="out_plots" file="XXX.png" />
35 </test> 36 </test>
36 </tests> 37 </tests>
38 -->
37 39
38 <help> 40 <help>
39 This tools reads in two counts file and determines enriched and depleted 41 This tools reads in two counts file and determines enriched and depleted
40 motifs in two different region sets based on poisson calculation with 42 motifs in two different region sets based on poisson calculation with
41 gc correction. 43 gc correction.