deeptools · dpryan79 · Mar 30, 2017 · Mar 14, 2017 · Mar 24, 2017 · Mar 29, 2017
diff --git a/deeptools/_version.py b/deeptools/_version.py
@@ -2,4 +2,4 @@
 # This file is originally generated from Git information by running 'setup.py
 # version'. Distribution tarballs contain a pre-generated copy of this file.
 
-__version__ = '2.4.3'
+__version__ = '2.4.3-63-ec898ec'
diff --git a/galaxy/wrapper/bamPEFragmentSize.xml b/galaxy/wrapper/bamPEFragmentSize.xml
@@ -13,6 +13,8 @@
             --bamfiles #echo " ".join($files)
             #if $samplesLabel:
                 --samplesLabel #echo " ".join($samplesLabel)
+            #else:
+                --samplesLabel #echo " ".join($labels)
             #end if
             #if $histogram:
                 --histogram ./hist.png

diff --git a/galaxy/wrapper/deepTools_macros.xml b/galaxy/wrapper/deepTools_macros.xml
@@ -439,19 +439,22 @@ is vital to you, select Yes below.">
 <![CDATA[
         #set files=[]
         #set labels=[]
+        #import re
         #if $multibam_conditional.orderMatters == "No":
             #for $counter, $bamfile in enumerate($multibam_conditional.bamfiles):
+                #set identifier = re.sub('[^\.\s\w\-]', '_', str($bamfile.element_identifier))
                 ln -s "${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))
+                #silent $labels.append("'%s'" % identifier)
             #end for
         #else:
             #for $counter, $f in enumerate($multibam_conditional.multibam_repeats):
+                #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bamfiles.element_identifier))
                 ln -s "${f.bamfiles}" "./${counter}.bam" &&
                 ln -s "${f.bamfiles.metadata.bam_index}" "./${counter}.bam.bai" &&
                 #silent $files.append('%s.bam' % $counter)
-                #silent $labels.append("'%s'" % ($f.bamfiles.display_name))
+                #silent $labels.append("'%s'" % $identifier)
             #end for
         #end if
 ]]>
@@ -461,17 +464,20 @@ is vital to you, select Yes below.">
 <![CDATA[
         #set files=[]
         #set labels=[]
+        #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)
-                #silent $labels.append("'%s'" % ($bigwig.display_name))
+                #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)
-                #silent $labels.append("'%s'" % ($f.bigwigfiles.display_name))
+                #silent $labels.append("'%s'" % $identifier)
             #end for
         #end if
 ]]>

diff --git a/galaxy/wrapper/plotPCA.xml b/galaxy/wrapper/plotPCA.xml
@@ -33,13 +33,13 @@
     </outputs>
     <tests>
         <test>
-            <param name="corData" value="multiBamSummary_result2.npz" ftype="deeptools_coverage_matrix" />
+            <param name="corData" value="multiBamSummary_result2b.npz" ftype="deeptools_coverage_matrix" />
             <param name="plotTitle" value="Test Plot" />
             <param name="outFileFormat" value="png" />
             <output name="outFileName" file="plotPCA_result1.png" ftype="png" compare="sim_size" delta="4000" />
         </test>
         <test>
-            <param name="corData" value="multiBamSummary_result2.npz" ftype="deeptools_coverage_matrix" />
+            <param name="corData" value="multiBamSummary_result2b.npz" ftype="deeptools_coverage_matrix" />
             <param name="plotTitle" value="Test Plot" />
             <param name="outFileFormat" value="png" />
             <param name="outFileNameData" value="True" />

diff --git a/galaxy/wrapper/test-data/bamPEFragmentSize_histogram_result1.png b/galaxy/wrapper/test-data/bamPEFragmentSize_histogram_result1.png
diff --git a/galaxy/wrapper/test-data/computeMatrixOperations.txt b/galaxy/wrapper/test-data/computeMatrixOperations.txt
@@ -1,4 +1,4 @@
 Groups:
 	genes
 Samples:
-	file_0
+	bamCoverage_result4_bw_0
diff --git a/galaxy/wrapper/test-data/computeMatrixOperations_result2.mat.gz b/galaxy/wrapper/test-data/computeMatrixOperations_result2.mat.gz
diff --git a/galaxy/wrapper/test-data/computeMatrix_result1.gz b/galaxy/wrapper/test-data/computeMatrix_result1.gz
diff --git a/galaxy/wrapper/test-data/computeMatrix_result2.gz b/galaxy/wrapper/test-data/computeMatrix_result2.gz
diff --git a/galaxy/wrapper/test-data/computeMatrix_result3.gz b/galaxy/wrapper/test-data/computeMatrix_result3.gz
diff --git a/galaxy/wrapper/test-data/correctGCBias_result1.bam b/galaxy/wrapper/test-data/correctGCBias_result1.bam
diff --git a/galaxy/wrapper/test-data/heatmapper_result1.png b/galaxy/wrapper/test-data/heatmapper_result1.png
diff --git a/galaxy/wrapper/test-data/heatmapper_result2.png b/galaxy/wrapper/test-data/heatmapper_result2.png
diff --git a/galaxy/wrapper/test-data/multiBamSummary_result1.npz b/galaxy/wrapper/test-data/multiBamSummary_result1.npz
diff --git a/galaxy/wrapper/test-data/multiBamSummary_result2.npz b/galaxy/wrapper/test-data/multiBamSummary_result2.npz
diff --git a/galaxy/wrapper/test-data/multiBamSummary_result2b.npz b/galaxy/wrapper/test-data/multiBamSummary_result2b.npz
diff --git a/galaxy/wrapper/test-data/multiBigwigSummary_result1.npz b/galaxy/wrapper/test-data/multiBigwigSummary_result1.npz
diff --git a/galaxy/wrapper/test-data/plotCorrelation_result1.png b/galaxy/wrapper/test-data/plotCorrelation_result1.png
diff --git a/galaxy/wrapper/test-data/plotCorrelation_result1.tabular b/galaxy/wrapper/test-data/plotCorrelation_result1.tabular
@@ -1,3 +1,3 @@
-	'bowtie2-test1.bam'	'bowtie2-test1.bam'
-'bowtie2-test1.bam'	1.0000	1.0000
-'bowtie2-test1.bam'	1.0000	1.0000
+	'bowtie2 test1.bam'	'bowtie2 test1.bam'
+'bowtie2 test1.bam'	1.0000	1.0000
+'bowtie2 test1.bam'	1.0000	1.0000
diff --git a/galaxy/wrapper/test-data/plotCorrelation_result2.png b/galaxy/wrapper/test-data/plotCorrelation_result2.png
diff --git a/galaxy/wrapper/test-data/plotCoverage_result1.png b/galaxy/wrapper/test-data/plotCoverage_result1.png
diff --git a/galaxy/wrapper/test-data/plotEnrichment_output.png b/galaxy/wrapper/test-data/plotEnrichment_output.png
diff --git a/galaxy/wrapper/test-data/plotFingerprint_result1.png b/galaxy/wrapper/test-data/plotFingerprint_result1.png
diff --git a/galaxy/wrapper/test-data/plotFingerprint_result2.png b/galaxy/wrapper/test-data/plotFingerprint_result2.png
diff --git a/galaxy/wrapper/test-data/profiler_result1.png b/galaxy/wrapper/test-data/profiler_result1.png
diff --git a/galaxy/wrapper/test-data/profiler_result2.png b/galaxy/wrapper/test-data/profiler_result2.png
diff --git a/galaxy/wrapper/test-data/profiler_result2.tabular b/galaxy/wrapper/test-data/profiler_result2.tabular
@@ -1,3 +1,3 @@
 bin labels		-0.0Kb	0.0Kb
 bins		1	2
-file_0	genes	2477942.34473	2610259.65234
+bamCoverage_result4_bw_0	genes	2477942.875	2610260.125