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

Changeset 14:d4fdd10516f6 (2017-05-14)
Previous changeset 13:b8431744eab3 (2017-03-31) Next changeset 15:7e361d147872 (2017-05-15)
Commit message:
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28
modified:
deepTools_macros.xml
plotCoverage.xml
repository_dependencies.xml
test-data/bamPEFragmentSize_result1.txt
test-data/plotFingerprint_quality_metrics.tabular
removed:
tool_dependencies.xml
b
diff -r b8431744eab3 -r d4fdd10516f6 deepTools_macros.xml
--- a/deepTools_macros.xml Fri Mar 31 18:13:32 2017 -0400
+++ b/deepTools_macros.xml Sun May 14 18:54:36 2017 -0400
[
@@ -1,10 +1,9 @@
 <macros>
 
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@WRAPPER_VERSION@">2.5.0</token>
+    <token name="@WRAPPER_VERSION@">2.5.1.0</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="2.7.10">python</requirement>
             <requirement type="package" version="@WRAPPER_VERSION@">deeptools</requirement>
             <yield />
         </requirements>
@@ -25,6 +24,21 @@
         </conditional>
     </xml>
 
+    <token name="@PLOTWIDTHHEIGHT@">
+        --plotWidth '$advancedOpt.plotWidth'
+        --plotHeight '$advancedOpt.plotHeight'
+    </token>
+
+    <xml name="plotWidthHeight" tokens="PLOTWIDTH,PLOTHEIGHT">
+        <param argument="--plotHeight" type="float" value="@PLOTHEIGHT@" min="1.0"
+            label="Plot height"
+            help="Height in cm. The default for the plot height is @PLOTHEIGHT@ centimeters. The minimum value is 1 cm." />
+
+        <param argument="--plotWidth" type="float" value="@PLOTWIDTH@" min="1.0"
+            label="Plot width"
+            help="Width in cm. The default value is @PLOTWIDTH@ centimeters. The minimum value is 1 cm." />
+    </xml>
+
     <token name="@ADVANCED_OPTS_READ_PROCESSING@">
         #if $advancedOpt.doExtendCustom.doExtend == 'custom':
             --extendReads $advancedOpt.doExtendCustom.extendReadsValue
@@ -369,46 +383,26 @@
         </citations>
     </xml>
 
-    <xml name="multiple_input_bams">
+    <xml name="multiple_input_bams" tokens="MIN">
         <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"
+            <param argument="--bamfiles" type="data" format="bam" min="@MIN@"
                 label="Bam file" multiple="true"
                 help=""/>
         </when>
         <when value="Yes">
-            <repeat name="multibam_repeats" min="1" title="BAM Files">
+            <repeat name="multibam_repeats" min="@MIN@" title="BAM Files">
                 <param argument="--bamfiles" type="data" format="bam" label="BAM file" help="" />
             </repeat>
         </when>
         </conditional>
     </xml>
 
-    <xml name="multiple_input_bams_min2">
-        <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">
+    <xml name="multiple_input_bigwigs" tokens="MIN,LABEL,TITLE">
         <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.">
@@ -416,13 +410,13 @@
             <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."/>
+            <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="@MIN@"
+                label="@LABEL@"
+                help="You can generate a bigWig file from a BAM file using the bamCoverage tool."/>
         </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 name="multibigwig_repeats" min="@MIN@" title="@TITLE@">
+                <param argument="--bigwigfiles" type="data" format="bigwig" label="@LABEL@" help="You can generate a bigWig file from a BAM file using the bamCoverage tool."/>
             </repeat>
         </when>
         </conditional>
@@ -467,16 +461,16 @@
         #import re
         #if $multibigwig_conditional.orderMatters == "No":
             #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles):
-            #set identifier = re.sub('[^\.\s\w\-]', '_', str($bigwig.element_identifier))
-                ln -s "${bigwig}" "${counter}.bw" &&
-                #silent $files.append('%s.bw' % $counter)
+                #set identifier = re.sub('[^\.\s\w\-]', '_', str($bigwig.element_identifier))
+                ln -f -s "${bigwig}" "${identifier}_${counter}.bw" &&
+                #silent $files.append('%s_%s.bw' % ($identifier, $counter))
                 #silent $labels.append("'%s'" % $identifier)
             #end for
         #else:
             #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats):
                 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bigwigfiles.element_identifier))
-                ln -s "${f.bigwigfiles}" "${counter}.bw" &&
-                #silent $files.append('%s.bw' % $counter)
+                ln -f -s "${f.bigwigfiles}" "${identifier}_${counter}.bw" &&
+                #silent $files.append('%s_%s.bw' % ($identifier, $counter))
                 #silent $labels.append("'%s'" % $identifier)
             #end for
         #end if
b
diff -r b8431744eab3 -r d4fdd10516f6 plotCoverage.xml
--- a/plotCoverage.xml Fri Mar 31 18:13:32 2017 -0400
+++ b/plotCoverage.xml Sun May 14 18:54:36 2017 -0400
b
@@ -38,6 +38,7 @@
                     --plotTitle '$advancedOpt.plotTitle'
                 #end if
                 @ADVANCED_OPTS_READ_PROCESSING@
+                @PLOTWIDTHHEIGHT@
                 @blacklist@
             #end if
 
@@ -45,7 +46,7 @@
     </command>
     <inputs>
 
-        <expand macro="multiple_input_bams" />
+        <expand macro="multiple_input_bams" MIN="1"/>
 
         <conditional name="advancedOpt">
             <param name="showAdvancedOpt" type="select" label="Show advanced options" >
@@ -57,6 +58,7 @@
                 <param argument="--numberOfSamples" type="integer" value="100000" min="1"
                    label="Number of samples"
                    help="Number of samples taken from the genome to compute the scaling factors."/>
+                <expand macro="plotWidthHeight" PLOTWIDTH="15.0" PLOTHEIGHT="5.0" />
                 <expand macro="region_limit_operation" />
                 <expand macro="read_processing_options" />
                 <expand macro="skipZeros" />
b
diff -r b8431744eab3 -r d4fdd10516f6 repository_dependencies.xml
--- a/repository_dependencies.xml Fri Mar 31 18:13:32 2017 -0400
+++ b/repository_dependencies.xml Sun May 14 18:54:36 2017 -0400
b
@@ -1,4 +1,4 @@
 <?xml version="1.0"?>
 <repositories>
-    <repository changeset_revision="df883cc67fbd" name="data_manager_twobit_builder" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="9946bc39c834" name="data_manager_twobit_builder" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
 </repositories>
b
diff -r b8431744eab3 -r d4fdd10516f6 test-data/bamPEFragmentSize_result1.txt
--- a/test-data/bamPEFragmentSize_result1.txt Fri Mar 31 18:13:32 2017 -0400
+++ b/test-data/bamPEFragmentSize_result1.txt Sun May 14 18:54:36 2017 -0400
b
@@ -1,6 +1,6 @@
 
 
-BAM file : 0.bam
+Sample label: bowtie2 test1.bam
 Sample size: 3
 
 Fragment lengths:
b
diff -r b8431744eab3 -r d4fdd10516f6 test-data/plotFingerprint_quality_metrics.tabular
--- a/test-data/plotFingerprint_quality_metrics.tabular Fri Mar 31 18:13:32 2017 -0400
+++ b/test-data/plotFingerprint_quality_metrics.tabular Sun May 14 18:54:36 2017 -0400
b
@@ -1,3 +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 0.269004498068 NA NA NA
-bowtie2 test1.bam 0.00493632029864 0.481650684758 0.984443061605 1.15310443503e-24 0.984940883634 0.523268829811 NA 0.269004498068 NA NA NA
+bowtie2 test1.bam 0.00493632029864 0.481650684758 0.984443061605 1.15310443503e-24 0.984940883634 0.523268829811 0.0 0.269004498068 0 0 0
b
diff -r b8431744eab3 -r d4fdd10516f6 tool_dependencies.xml
--- a/tool_dependencies.xml Fri Mar 31 18:13:32 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
@@ -1,9 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="python" version="2.7.10">
-        <repository changeset_revision="bd7165ea6526" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="deeptools" version="2.5.0">
-        <repository changeset_revision="72856dd1f9a5" name="package_python_2_7_deeptools_2_5_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>