# HG changeset patch
# User jeremyjliu
# Date 1425009249 18000
# Node ID 4ce22698acb083cc1ce82940baad71091fef1046
# Parent  fe8a884363dfef67f774499e754c4faecf9b333b
Uploaded

diff -r fe8a884363df -r 4ce22698acb0 pwms/jaspar.jolma.pwms.from.seq.RData
Binary file pwms/jaspar.jolma.pwms.from.seq.RData has changed
diff -r fe8a884363df -r 4ce22698acb0 pwms/mm9.pwms.from.seq.RData
Binary file pwms/mm9.pwms.from.seq.RData has changed
diff -r fe8a884363df -r 4ce22698acb0 pwms/pouya.pwms.from.seq.RData
Binary file pwms/pouya.pwms.from.seq.RData has changed
diff -r fe8a884363df -r 4ce22698acb0 region_motif_compare.r
--- a/region_motif_compare.r	Tue Feb 10 02:03:15 2015 -0500
+++ b/region_motif_compare.r	Thu Feb 26 22:54:09 2015 -0500
@@ -4,13 +4,12 @@
 # corrections. All enrichment ratios relative to overall count / gc ratios.
 # Author: Jeremy liu
 # Email: jeremy.liu@yale.edu
-# Date: 15/02/04
+# Date: 15/02/11
 # Note: This script is meant to be invoked with the following command
-# R --slave --vanilla -f ./region_motif_compare.r --args <workingdir> <db> <intab1> <intab2> 
-#   <enriched_tab> <depleted_tab> <plots_png>
+# R --slave --vanilla -f ./region_motif_compare.r --args <workingdir> <pwm_file> 
+#        <intab1> <intab2> <enriched_tab> <depleted_tab> <plots_png>
 # <workingdir> is working directory of galaxy installation
-# <db> types: "t" test, "p" pouya, "j" jaspar jolma, "m" mouse, "c" combined
-# Dependencies: plotting.r
+# Dependencies: region_motif_data_manager, plotting.r
 
 # Auxiliary function to concatenate multiple strings
 concat <- function(...) {
@@ -24,20 +23,7 @@
 # Set common and data directories
 args <- commandArgs()
 workingDir = args[7]
-dbCode = args[8]
-# dbCode "c" implemented when pwmFile is loaded
-if (dbCode == "t" | dbCode == "p") {
-	pwmFile = concat(workingDir, "/pwms/pouya.pwms.from.seq.RData")
-} else if (dbCode == "j") {
-	pwmFile = concat(workingDir, "/pwms/jaspar.jolma.pwms.from.seq.RData")
-} else if (dbCode == "m") {
-	pwmFile = concat(workingDir, "/pwms/mm9.pwms.from.seq.RData")
-} else if (dbCode == "c") { # rest of dbCode "c" implemented when pwmFile loaded
-	pwmFile = concat(workingDir, "/pwms/pouya.pwms.from.seq.RData")
-	pwmFile2 = concat(workingDir, "/pwms/jaspar.jolma.pwms.from.seq.RData")
-} else {
-	pwmFile = concat(workingDir, "/pwms/pouya.pwms.from.seq.RData")
-}
+pwmFile = args[8].split(',')[0] # If duplicate entires, take first one
 
 # Set input and reference files
 inTab1 = args[9]
@@ -63,11 +49,11 @@
 # Loading motif position weight matrix (pwm) file and input tab file
 cat("Loading and reading input region motif count files...\n")
 load(pwmFile) # pwms data structure
-if (dbCode == "c") { # Remaining implementation of dbCode "c" combined 
-	temp = pwms
-	load(pwmFile2)
-	pwms = append(temp, pwms)
-}
+#if (dbCode == "c") { # Remaining implementation of dbCode "c" combined 
+#	temp = pwms
+#	load(pwmFile2)
+#	pwms = append(temp, pwms)
+#}
 region1DF = read_tsv(inTab1)
 region2DF = read_tsv(inTab2)
 region1Counts = region1DF$counts
diff -r fe8a884363df -r 4ce22698acb0 region_motif_compare.xml
--- a/region_motif_compare.xml	Tue Feb 10 02:03:15 2015 -0500
+++ b/region_motif_compare.xml	Thu Feb 26 22:54:09 2015 -0500
@@ -4,18 +4,28 @@
     <requirement type="set_environment">RMOTIF_PATH</requirement>
   </requirements>
   <command interpreter="Rscript">
-    region_motif_compare.r --args \$RMOTIF_PATH $db_type $in_tab_1 $in_tab_2 $out_enriched $out_depleted $out_plots
+    region_motif_compare.r --args \$RMOTIF_PATH $pwm_file.fields.path $in_tab_1 $in_tab_2 
+    $out_enriched 
+    $out_depleted 
+    $out_plots
   </command>
   <inputs>
     <param name="in_tab_1" type="data" format="tabular" label="Region Set 1 Motif Count File"/>
     <param name="in_tab_2" type="data" format="tabular" label="Region Set 2 Motif Count File"/>
+
+    <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 Pouya Subset (hg19)</option>
-      <option value="p">Pouya Encode Motifs (hg19)</option>
+      <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>
+    </param> -->
+
   </inputs>
   <outputs>
     <data name="out_enriched" format="tabular" label="Enriched Motifs"/>
diff -r fe8a884363df -r 4ce22698acb0 region_motif_db/MOTIF_DB_GOES_HERE
diff -r fe8a884363df -r 4ce22698acb0 region_motif_db/pouya_test_motifs.bed.bgz
Binary file region_motif_db/pouya_test_motifs.bed.bgz has changed
diff -r fe8a884363df -r 4ce22698acb0 region_motif_db/pouya_test_motifs.bed.bgz.tbi
Binary file region_motif_db/pouya_test_motifs.bed.bgz.tbi has changed
diff -r fe8a884363df -r 4ce22698acb0 region_motif_intersect.r
--- a/region_motif_intersect.r	Tue Feb 10 02:03:15 2015 -0500
+++ b/region_motif_intersect.r	Thu Feb 26 22:54:09 2015 -0500
@@ -1,9 +1,9 @@
 # Name: region_motif_intersect.r
 # Description: Takes a bed file of target regions and counts intersections
 # of each motif (in separately installed tabix database) and target regions.
-# Author: Jeremy liu
+# Author: Jeremy Liu
 # Email: jeremy.liu@yale.edu
-# Date: 15/02/04
+# Date: 15/02/11
 # Note: This script is meant to be invoked with the following command
 # R --slave --vanilla -f ./region_motif_intersect.r --args <db_bgz> <db_tbi> <inbed> <outtab>
 # Dependencies: region_motif_data_manager
@@ -16,8 +16,8 @@
 
 # Retrive motif database path
 args <- commandArgs()
-motifDB_bgz = args[7]
-motifDB_tbi = args[8]
+motifDB_bgz = args[7].split(',')[0] # Handles duplicate entries in data table
+motifDB_tbi = args[8].split(',')[0] # Just takes the first one
 
 # Set input and reference files, comment to toggle commmand line arguments
 inBed = args[9]
diff -r fe8a884363df -r 4ce22698acb0 region_motif_intersect.xml
--- a/region_motif_intersect.xml	Tue Feb 10 02:03:15 2015 -0500
+++ b/region_motif_intersect.xml	Thu Feb 26 22:54:09 2015 -0500
@@ -1,8 +1,5 @@
 <tool id="region_motif_intersect" name="Region Motif Intersect">
   <description>for computing the motifs that lie inside a region set</description>
-  <!--<requirements>
-    <requirement type="package" version="1.0.0">MOTIF_DATA_MANAGER</requirement>
-  </requirements>-->
   <command interpreter="Rscript">
     region_motif_intersect.r --args $bgz_file.fields.path $tbi_file.fields.path $in_bed $out_tab
   </command>
@@ -17,8 +14,8 @@
     </param>
 
     <!--<param name="db_type" type="select" label="Select Motif Database" >
-      <option value="t">Test Pouya Subset (hg19)</option>
-      <option value="p">Pouya Encode Motifs (hg19)</option>
+      <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>
     </param>-->
diff -r fe8a884363df -r 4ce22698acb0 repository_dependencies.xml
--- a/repository_dependencies.xml	Tue Feb 10 02:03:15 2015 -0500
+++ b/repository_dependencies.xml	Thu Feb 26 22:54:09 2015 -0500
@@ -1,4 +1,4 @@
 <?xml version="1.0"?>
 <repositories description="Region_Motif_Enrichment requires Region_Motif_Data_Manager motif databases">
-     <repository changeset_revision="e4229c66d78d" name="region_motif_data_manager" owner="jeremyjliu" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+     <repository changeset_revision="a5421f83f972" name="region_motif_data_manager" owner="jeremyjliu" toolshed="http://testtoolshed.g2.bx.psu.edu" />
 </repositories>
diff -r fe8a884363df -r 4ce22698acb0 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Feb 10 02:03:15 2015 -0500
+++ b/tool_dependencies.xml	Thu Feb 26 22:54:09 2015 -0500
@@ -3,14 +3,4 @@
     <set_environment version="1.0">
         <environment_variable name="RMOTIF_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>  
     </set_environment>
-    <!--<package name="MOTIFS" version="1.0.0">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://gehlenborg.com/wp-content/uploads/motif/pouya_test_motifs.bed.bgz</action>
-                <action type="shell_command">mv pouya_test_motifs.bed.bgz $REPOSITORY_INSTALL_DIR/region_motif_db</action>
-                <action type="download_by_url">http://gehlenborg.com/wp-content/uploads/motif/pouya_test_motifs.bed.bgz.tbi</action>
-                <action type="shell_command">mv pouya_test_motifs.bed.bgz.tbi $REPOSITORY_INSTALL_DIR/region_motif_db</action>
-            </actions>
-        </install>
-    </package>-->
 </tool_dependency>
\ No newline at end of file