Repository 'deeptools_correct_gc_bias'
hg clone https://toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias

Changeset 10:297bccb7d5c6 (2016-12-05)
Previous changeset 9:4eef86c1e82f (2016-10-25) Next changeset 11:d00bfda5567c (2017-01-24)
Commit message:
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
modified:
correctGCBias.xml
deepTools_macros.xml
test-data/bamCompare_result1.bg
test-data/bamCoverage_result2.bw
test-data/bamCoverage_result3.bg
test-data/bamCoverage_result4.bg
test-data/bamCoverage_result4.bw
test-data/bamCoverage_result5.bw
test-data/bigwigCompare_result2.bg
test-data/computeGCBias_result1.tabular
test-data/correctGCBias_result1.bam
test-data/plotFingerprint_result2.tabular
test-data/sequence.2bit
tool_dependencies.xml
added:
test-data/bamCoverage_result6.bw
test-data/computeMatrixOperations.txt
test-data/computeMatrixOperations_result2.mat.gz
test-data/plotFingerprint_quality_metrics.tabular
b
diff -r 4eef86c1e82f -r 297bccb7d5c6 correctGCBias.xml
--- a/correctGCBias.xml Tue Oct 25 19:23:05 2016 -0400
+++ b/correctGCBias.xml Mon Dec 05 08:11:34 2016 -0500
b
@@ -47,8 +47,8 @@
             <param name="ref_source" value="history" />
             <param name="input1" value="sequence.2bit" />
             <param name="effectiveGenomeSize_opt" value="specific" />
-            <param name="effectiveGenomeSize" value="23011544" />
-            <output name="outFileName" file="correctGCBias_result1.bam" ftype="bam" />
+            <param name="effectiveGenomeSize" value="10050" />
+            <output name="outFileName" file="correctGCBias_result1.bam" ftype="bam" lines_diff="100" />
         </test>
     </tests>
     <help>
b
diff -r 4eef86c1e82f -r 297bccb7d5c6 deepTools_macros.xml
--- a/deepTools_macros.xml Tue Oct 25 19:23:05 2016 -0400
+++ b/deepTools_macros.xml Mon Dec 05 08:11:34 2016 -0500
[
@@ -98,11 +98,11 @@
     </xml>
 
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@WRAPPER_VERSION@">2.3.6</token>
+    <token name="@WRAPPER_VERSION@">2.4.1</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="2.7.10">python</requirement>
-            <requirement type="package" version="2.3.6">deepTools</requirement>
+            <requirement type="package" version="2.4.1">deeptools</requirement>
             <yield />
         </requirements>
         <expand macro="stdio" />
@@ -285,11 +285,21 @@
         </param>
     </xml>
 
+    <xml name="sortRegionsComputeMatrix">
+        <param argument="--sortRegions" type="select" label="Sort regions"
+            help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
+            <option value="no">no ordering</option>
+            <option value="keep" selected="true">maintain the same ordering as the input files</option>
+            <option value="descend">descending order</option>
+            <option value="ascend">ascending order</option>
+        </param>
+    </xml>
+
     <xml name="sortRegions">
         <param argument="--sortRegions" type="select" label="Sort regions"
             help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
             <option value="no">no ordering</option>
-            <option value="descend" selected="true">descending order</option>
+            <option value="descend">descending order</option>
             <option value="ascend">ascending order</option>
         </param>
     </xml>
@@ -362,21 +372,62 @@
     </xml>
 
     <xml name="multiple_input_bams">
-        <param argument="--bamfiles" type="data" format="bam" min="1"
-            label="Bam file" multiple="true"
-            help=""/>
+        <conditional name="multibam_conditional">
+        <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples is vital to you, select Yes below.">
+            <option value="No" selected="true">No</option>
+            <option value="Yes">Yes</option>
+        </param>
+        <when value="No">
+            <param argument="--bamfiles" type="data" format="bam" min="1"
+                label="Bam file" multiple="true"
+                help=""/>
+        </when>
+        <when value="Yes">
+            <repeat name="multibam_repeats" min="1" title="BAM Files">
+                <param argument="--bamfiles" type="data" format="bam" label="BAM file" help="" />
+            </repeat>
+        </when>
+        </conditional>
     </xml>
 
     <xml name="multiple_input_bams_min2">
-        <param argument="--bamfiles" type="data" format="bam" min="2"
-            label="Bam file" multiple="true"
-            help=""/>
+        <conditional name="multibam_conditional">
+        <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples 
+is vital to you, select Yes below.">
+            <option value="No" selected="true">No</option>
+            <option value="Yes">Yes</option>
+        </param>
+        <when value="No">
+            <param argument="--bamfiles" type="data" format="bam" min="2"
+                label="Bam file" multiple="true"
+                help=""/>
+        </when>
+        <when value="Yes">
+            <repeat name="multibam_repeats" min="2" title="BAM Files">
+                <param argument="--bamfiles" type="data" format="bam" label="BAM file" help="" />
+            </repeat>
+        </when>
+        </conditional>
     </xml>
 
     <xml name="multiple_input_bigwigs">
-        <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2"
-            label="Bigwig file"
-            help="A Bigwig file."/>
+        <conditional name="multibigwig_conditional">
+        <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples 
+is vital to you, select Yes below.">
+            <option value="No" selected="true">No</option>
+            <option value="Yes">Yes</option>
+        </param>
+        <when value="No">
+            <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2"
+                label="Bigwig file"
+                help="A Bigwig file."/>
+        </when>
+        <when value="Yes">
+            <repeat name="multibigwig_repeats" min="2" title="BigWig files">
+                <param argument="--bigwigfiles" type="data" format="bigwig" label="Bigwig file" help="A Bigwig file."/>
+            </repeat>
+        </when>
+        </conditional>
     </xml>
 
     <xml name="plotTitle">
@@ -390,12 +441,21 @@
 <![CDATA[
         #set files=[]
         #set labels=[]
-        #for $counter, $bamfile in enumerate($bamfiles):
-            ln -s "${bamfile}" "./${counter}.bam" &&
-            ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" &&
-            #silent $files.append('%s.bam' % $counter)
-            #silent $labels.append("'%s'" % ($bamfile.display_name))
-        #end for
+        #if $multibam_conditional.orderMatters == "No":
+            #for $counter, $bamfile in enumerate($multibam_conditional.bamfiles):
+                ln -s "${bamfile}" "./${counter}.bam" &&
+                ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" &&
+                #silent $files.append('%s.bam' % $counter)
+                #silent $labels.append("'%s'" % ($bamfile.display_name))
+            #end for
+        #else:
+            #for $counter, $f in enumerate($multibam_conditional.multibam_repeats):
+                ln -s "${f.bamfile}" "./${counter}.bam" &&
+                ln -s "${f.bamfile.metadata.bam_index}" "./${counter}.bam.bai" &&
+                #silent $files.append('%s.bam' % $counter)
+                #silent $labels.append("'%s'" % ($f.bamfile.display_name))
+            #end for
+        #end if
 ]]>
     </token>
 
@@ -403,11 +463,19 @@
 <![CDATA[
         #set files=[]
         #set labels=[]
-        #for $counter, $bigwig in enumerate($bigwigfiles):
-            ln -s "${bigwig}" "${counter}.bw" &&
-            #silent $files.append('%s.bw' % $counter)
-            #silent $labels.append("'%s'" % ($bigwig.display_name))
-        #end for
+        #if $multibigwig_conditional.orderMatters == "No":
+            #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles):
+                ln -s "${bigwig}" "${counter}.bw" &&
+                #silent $files.append('%s.bw' % $counter)
+                #silent $labels.append("'%s'" % ($bigwig.display_name))
+            #end for
+        #else:
+            #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats):
+                ln -s "${f.bigwig}" "${counter}.bw" &&
+                #silent $files.append('%s.bw' % $counter)
+                #silent $labels.append("'%s'" % ($f.bigwig.display_name))
+            #end for
+        #end if
 ]]>
     </token>
 
b
diff -r 4eef86c1e82f -r 297bccb7d5c6 test-data/bamCompare_result1.bg
--- a/test-data/bamCompare_result1.bg Tue Oct 25 19:23:05 2016 -0400
+++ b/test-data/bamCompare_result1.bg Mon Dec 05 08:11:34 2016 -0500
b
@@ -1,1 +1,1 @@
-chrM 0 16569 1.00
+chrM 0 16569 1
b
diff -r 4eef86c1e82f -r 297bccb7d5c6 test-data/bamCoverage_result2.bw
b
Binary file test-data/bamCoverage_result2.bw has changed
b
diff -r 4eef86c1e82f -r 297bccb7d5c6 test-data/bamCoverage_result3.bg
--- a/test-data/bamCoverage_result3.bg Tue Oct 25 19:23:05 2016 -0400
+++ b/test-data/bamCoverage_result3.bg Mon Dec 05 08:11:34 2016 -0500
b
@@ -1,7 +1,7 @@
-chrM 0 210 9768764.94
-chrM 210 220 9560918.88
-chrM 220 230 7690304.31
-chrM 230 240 5196151.56
-chrM 240 250 3325537.00
-chrM 250 260 623538.19
-chrM 260 16569 0.00
+chrM 0 210 9.76876e+06
+chrM 210 220 9.56092e+06
+chrM 220 230 7.6903e+06
+chrM 230 240 5.19615e+06
+chrM 240 250 3.32554e+06
+chrM 250 260 623538
+chrM 260 16569 0
b
diff -r 4eef86c1e82f -r 297bccb7d5c6 test-data/bamCoverage_result4.bg
--- a/test-data/bamCoverage_result4.bg Tue Oct 25 19:23:05 2016 -0400
+++ b/test-data/bamCoverage_result4.bg Mon Dec 05 08:11:34 2016 -0500
b
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diff -r 4eef86c1e82f -r 297bccb7d5c6 test-data/bamCoverage_result4.bw
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diff -r 4eef86c1e82f -r 297bccb7d5c6 test-data/bamCoverage_result5.bw
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diff -r 4eef86c1e82f -r 297bccb7d5c6 test-data/bamCoverage_result6.bw
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diff -r 4eef86c1e82f -r 297bccb7d5c6 test-data/bigwigCompare_result2.bg
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diff -r 4eef86c1e82f -r 297bccb7d5c6 test-data/computeGCBias_result1.tabular
--- a/test-data/computeGCBias_result1.tabular Tue Oct 25 19:23:05 2016 -0400
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diff -r 4eef86c1e82f -r 297bccb7d5c6 test-data/computeMatrixOperations.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 4eef86c1e82f -r 297bccb7d5c6 test-data/correctGCBias_result1.bam
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diff -r 4eef86c1e82f -r 297bccb7d5c6 test-data/plotFingerprint_quality_metrics.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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b
@@ -0,0 +1,3 @@
+Sample AUC Synthetic AUC X-intercept Synthetic X-intercept Elbow Point Synthetic Elbow Point JS Distance Synthetic JS Distance % genome enriched diff. enrichment CHANCE divergence
+bowtie2 test1.bam 0.00493632029864 0.481650684758 0.984443061605 1.15310443503e-24 0.984940883634 0.523268829811 NA 0.269861238192 NA NA NA
+bowtie2 test1.bam 0.00493632029864 0.481650684758 0.984443061605 1.15310443503e-24 0.984940883634 0.523268829811 NA 0.269861238192 NA NA NA
b
diff -r 4eef86c1e82f -r 297bccb7d5c6 test-data/plotFingerprint_result2.tabular
--- a/test-data/plotFingerprint_result2.tabular Tue Oct 25 19:23:05 2016 -0400
+++ b/test-data/plotFingerprint_result2.tabular Mon Dec 05 08:11:34 2016 -0500
b
@@ -1,254 +1,254 @@
 'bowtie2 test1.bam' 'bowtie2 test1.bam'
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b
diff -r 4eef86c1e82f -r 297bccb7d5c6 test-data/sequence.2bit
b
Binary file test-data/sequence.2bit has changed
b
diff -r 4eef86c1e82f -r 297bccb7d5c6 tool_dependencies.xml
--- a/tool_dependencies.xml Tue Oct 25 19:23:05 2016 -0400
+++ b/tool_dependencies.xml Mon Dec 05 08:11:34 2016 -0500
b
@@ -3,7 +3,7 @@
     <package name="python" version="2.7.10">
         <repository changeset_revision="0339c4a9b87b" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
-    <package name="deepTools" version="2.3.6">
-        <repository changeset_revision="05f46fef1ea5" name="package_python_2_7_deeptools_2_3_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="deeptools" version="2.4.1">
+        <repository changeset_revision="e9855a43ac53" name="package_python_2_7_deeptools_2_4_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>