Mercurial > repos > bgruening > deeptools_correct_gc_bias

changeset 29:aa56eba356f2 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28
author bgruening
date Sun, 14 May 2017 18:48:26 -0400
parents d30a20da1bef
children 4a9814880769
files deepTools_macros.xml repository_dependencies.xml test-data/bamPEFragmentSize_result1.txt test-data/plotFingerprint_quality_metrics.tabular tool_dependencies.xml
diffstat 5 files changed, 33 insertions(+), 48 deletions(-) [+]
line wrap: on
line diff
--- a/deepTools_macros.xml	Fri Mar 31 16:05:40 2017 -0400
+++ b/deepTools_macros.xml	Sun May 14 18:48:26 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
--- a/repository_dependencies.xml	Fri Mar 31 16:05:40 2017 -0400
+++ b/repository_dependencies.xml	Sun May 14 18:48:26 2017 -0400
@@ -1,4 +1,4 @@
 <?xml version="1.0"?>
 <repositories>
-    <repository changeset_revision="298d15849a14" name="data_manager_twobit_builder" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="c9896bb1f03c" name="data_manager_twobit_builder" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
 </repositories>
--- a/test-data/bamPEFragmentSize_result1.txt	Fri Mar 31 16:05:40 2017 -0400
+++ b/test-data/bamPEFragmentSize_result1.txt	Sun May 14 18:48:26 2017 -0400
@@ -1,6 +1,6 @@
 
 
-BAM file : 0.bam
+Sample label: bowtie2 test1.bam
 Sample size: 3
 
 Fragment lengths:
--- a/test-data/plotFingerprint_quality_metrics.tabular	Fri Mar 31 16:05:40 2017 -0400
+++ b/test-data/plotFingerprint_quality_metrics.tabular	Sun May 14 18:48:26 2017 -0400
@@ -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
--- a/tool_dependencies.xml	Fri Mar 31 16:05:40 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="python" version="2.7.10">
-        <repository changeset_revision="a28e3c30828d" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="deeptools" version="2.5.0">
-        <repository changeset_revision="bd5783d34dde" name="package_python_2_7_deeptools_2_5_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>