Mvdbeek element identifier (#500)

* Use `element_identifier` to label samples according to their name in the history

* Use `element_identifier` instead of `display_name`

`element_identifier` corresponds to the sample id in in a collection,
while it is equivalent to `name` or `display_name` in normal galaxy
history items.

* Update test-data for element_identifier changes

* Use $sampleLabels also if inferring names from element_identifier

* Use the old numpy matrix, since it's reasonable for a PCA.

* Copy over the old output files, though the tabular output has been modified slightly.

* Correct Galaxy tests

Author: dpryan79

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'

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

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
 ]]>

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" />

galaxy/wrapper/test-data/bamPEFragmentSize_histogram_result1.png

@@ -1,4 +1,4 @@
 Groups:
 	genes
 Samples:
-	file_0
+	bamCoverage_result4_bw_0