Mercurial > repos > jeremyjliu > region_motif_enrichment

comparison region_motif_compare.xml @ 38:aa921c733d10 draft default tip

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author jeremyjliu
date Sat, 16 May 2015 22:34:54 -0400
parents 4ce22698acb0
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37:76e108a19e64 38:aa921c733d10
14 <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 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 19 </inputs>
20 <!-- COMBINED OPTION IS LOST
21 <param name="db_type" type="select" label="Select Motif Database" >
22 <option value="t">Test Encode Motifs (hg19)</option>
23 <option value="e">Encode Motifs (hg19)</option>
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>
27 </param> -->
28 20
29 </inputs>
30 <outputs> 21 <outputs>
31 <data name="out_enriched" format="tabular" label="Enriched Motifs"/> 22 <data name="out_enriched" format="tabular" label="Enriched Motifs"/>
32 <data name="out_depleted" format="tabular" label="Depleted Motifs"/> 23 <data name="out_depleted" format="tabular" label="Depleted Motifs"/>
33 <data name="out_plots" format="png" label="Motif Count Comparison Plots"/> 24 <data name="out_plots" format="png" label="Motif Count Comparison Plots"/>
34 </outputs> 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>
35 37
36 <help> 38 <help>
37 This tools reads in two counts file and determines enriched and depleted 39 This tools reads in two counts file and determines enriched and depleted
38 motifs in two different region sets based on poisson calculation with 40 motifs in two different region sets based on poisson calculation with
39 gc correction. 41 gc correction.