Mercurial > repos > jeremyjliu > region_motif_enrichment
changeset 38:aa921c733d10 draft default tip
Uploaded
| author | jeremyjliu |
|---|---|
| date | Sat, 16 May 2015 22:34:54 -0400 |
| parents | 76e108a19e64 |
| children | |
| files | region_motif_compare.xml region_motif_intersect.xml repository_dependencies.xml test-data/ENCFF002CJA.narrowPeak test-data/ENCFF002DAS.narrowPeak |
| diffstat | 5 files changed, 18416 insertions(+), 11 deletions(-) [+] |
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--- a/region_motif_compare.xml Tue Apr 07 23:22:43 2015 -0400 +++ b/region_motif_compare.xml Sat May 16 22:34:54 2015 -0400 @@ -16,23 +16,25 @@ <param name="pwm_file" type="select" label="Using motif database PWM file"> <options from_data_table="motif_databases"/> </param> - - <!-- COMBINED OPTION IS LOST - <param name="db_type" type="select" label="Select Motif Database" > - <option value="t">Test Encode Motifs (hg19)</option> - <option value="e">Encode Motifs (hg19)</option> - <option value="j">Jaspar and Jolma Motifs (hg19)</option> - <option value="m">Mouse Motifs (mm9)</option> - <option value="c">Pouya, Jaspar, and Jolma Combined (hg19)</option> - </param> --> + </inputs> - </inputs> <outputs> <data name="out_enriched" format="tabular" label="Enriched Motifs"/> <data name="out_depleted" format="tabular" label="Depleted Motifs"/> <data name="out_plots" format="png" label="Motif Count Comparison Plots"/> </outputs> + <tests> + <test> + <param name="in_tab_1" value="XXX.tab" /> + <param name="in_tab_2" value="XXX.tab" /> + <param name="pwm_file" value="XXX.meme.txt" /> + <output name="out_enriched" file="XXX.tab" /> + <output name="out_depleted" file="XXX.tab" /> + <output name="out_plots" file="XXX.png" /> + </test> + </tests> + <help> This tools reads in two counts file and determines enriched and depleted motifs in two different region sets based on poisson calculation with
--- a/region_motif_intersect.xml Tue Apr 07 23:22:43 2015 -0400 +++ b/region_motif_intersect.xml Sat May 16 22:34:54 2015 -0400 @@ -24,6 +24,21 @@ <data name="out_tab" format="tabular" /> </outputs> + <tests> + <test> + <param name="in_bed" value="XXX.bed" /> + <param name="bgz_file" value="XXX" /> + <param name="tbi_file" value="XXX" /> + <output name="output" file="XXX.tab" /> + </test> + <test> + <param name="in_bed" value="XXX.bed" /> + <param name="bgz_file" value="XXX" /> + <param name="tbi_file" value="XXX" /> + <output name="out_tab" file="XXX.tab" /> + </test> + </tests> + <help> This tool computes the motifs and the number of motifs that intersect any region in a input set of regions.
--- a/repository_dependencies.xml Tue Apr 07 23:22:43 2015 -0400 +++ b/repository_dependencies.xml Sat May 16 22:34:54 2015 -0400 @@ -1,4 +1,4 @@ <?xml version="1.0"?> <repositories description="Region_Motif_Enrichment requires Region_Motif_Data_Manager motif databases"> - <repository changeset_revision="24a2c2783fb8" name="region_motif_data_manager" owner="jeremyjliu" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="377723319b45" name="region_motif_data_manager" owner="jeremyjliu" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </repositories>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ENCFF002CJA.narrowPeak Sat May 16 22:34:54 2015 -0400 @@ -0,0 +1,5473 @@ +chr9 129439041 129439399 . 1000 . 387.949249368388 -1 4.37311438120346 196 +chr11 92283662 92283923 . 1000 . 379.31868153692 -1 4.37311438120346 134 +chr6 92009376 92009658 . 1000 . 344.416413366755 -1 4.37311438120346 146 +chr16 9077536 9077828 . 1000 . 337.485094726747 -1 4.37311438120346 141 +chr7 157103058 157103313 . 1000 . 332.408892269792 -1 4.37311438120346 122 +chr2 149335745 149335997 . 1000 . 298.507146331354 -1 4.37311438120346 124 +chr2 45030052 45030295 . 1000 . 297.599439795846 -1 4.37311438120346 133 +chr20 55807184 55807446 . 1000 . 292.709229393885 -1 4.37311438120346 128 +chr6 31139711 31139982 . 1000 . 291.615265640317 -1 4.37311438120346 125 +chr15 71496031 71496283 . 1000 . 285.898693852219 -1 4.37311438120346 132 +chr12 130255896 130256146 . 1000 . 271.685447126894 -1 4.37311438120346 122 +chr14 42805182 42805428 . 1000 . 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ENCFF002DAS.narrowPeak Sat May 16 22:34:54 2015 -0400 @@ -0,0 +1,12915 @@ +chr17 41438326 41438863 . 1000 . 240.64731300772 -1 4.18261434773635 278 +chr17 73775685 73775987 . 1000 . 230.61588565354 -1 4.18261434773635 149 +chr17 8076602 8077024 . 1000 . 227.53665417044 -1 4.18261434773635 234 +chr22 43011156 43011657 . 1000 . 203.379397557946 -1 4.18261434773635 253 +chr2 121832564 121833076 . 1000 . 200.372488790708 -1 4.18261434773635 233 +chr2 38978312 38978613 . 1000 . 197.937175045724 -1 4.18261434773635 157 +chr11 62608824 62609194 . 1000 . 197.109447078249 -1 4.18261434773635 264 +chr1 11968105 11968465 . 1000 . 194.899160981989 -1 4.18261434773635 199 +chr1 28975012 28975380 . 1000 . 188.094591342913 -1 4.18261434773635 165 +chr1 144533902 144534365 . 1000 . 184.659308362229 -1 4.18261434773635 235 +chr6 133135594 133135878 . 1000 . 184.157163601262 -1 4.18261434773635 134 +chr1 153963112 153963416 . 1000 . 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