Merge branch 'release/3.0.1'

Author: dpryan79

.planemo.sh

@@ -1,24 +1,29 @@
 #!/bin/bash
 planemo=$HOME/miniconda/envs/planemo/bin/planemo
 
-$planemo test --no_dependency_resolution --install_galaxy \
-galaxy/wrapper/alignmentSieve.xml \
-galaxy/wrapper/bamCompare.xml \
-galaxy/wrapper/bamCoverage.xml \
-galaxy/wrapper/bamPEFragmentSize.xml \
-galaxy/wrapper/bigwigCompare.xml \
-galaxy/wrapper/computeGCBias.xml \
-galaxy/wrapper/computeMatrix.xml \
-galaxy/wrapper/computeMatrixOperations.xml \
-galaxy/wrapper/correctGCBias.xml \
-galaxy/wrapper/estimateReadFiltering.xml \
-galaxy/wrapper/multiBamSummary.xml \
-galaxy/wrapper/multiBigwigSummary.xml \
-galaxy/wrapper/plotCorrelation.xml \
-galaxy/wrapper/plotCoverage.xml \
-galaxy/wrapper/plotEnrichment.xml \
-galaxy/wrapper/plotFingerprint.xml \
-galaxy/wrapper/plotHeatmap.xml \
-galaxy/wrapper/plotPCA.xml \
-galaxy/wrapper/plotProfiler.xml 2>&1 | grep -v -e "^galaxy" | grep -v -e "^requests"
+if [[ $1 == "1" ]] ; then
+    wrappers="galaxy/wrapper/alignmentSieve.xml \
+    galaxy/wrapper/bamCompare.xml \
+    galaxy/wrapper/bamCoverage.xml \
+    galaxy/wrapper/bamPEFragmentSize.xml \
+    galaxy/wrapper/bigwigCompare.xml \
+    galaxy/wrapper/computeGCBias.xml"
+elif [[ $1 == "2" ]] ; then
+    wrappers="galaxy/wrapper/computeMatrix.xml \
+    galaxy/wrapper/computeMatrixOperations.xml \
+    galaxy/wrapper/correctGCBias.xml \
+    galaxy/wrapper/estimateReadFiltering.xml \
+    galaxy/wrapper/multiBamSummary.xml \
+    galaxy/wrapper/multiBigwigSummary.xml"
+else
+    wrappers="galaxy/wrapper/plotCorrelation.xml \
+    galaxy/wrapper/plotCoverage.xml \
+    galaxy/wrapper/plotEnrichment.xml \
+    galaxy/wrapper/plotFingerprint.xml \
+    galaxy/wrapper/plotHeatmap.xml \
+    galaxy/wrapper/plotPCA.xml \
+    galaxy/wrapper/plotProfiler.xml"
+fi
+
+${planemo} test --no_dependency_resolution --install_galaxy ${wrappers} 2>&1 | grep -v -e "^galaxy" | grep -v -e "^requests"
 test ${PIPESTATUS[0]} -eq 0

.travis.yml

@@ -7,10 +7,18 @@ os:
   - osx
 jobs:
   include:
-    - stage: galaxy36
+    - stage: galaxy36_1
       env:
         - TESTGALAXY="1"
         - TRAVIS_PYTHON_VERSION=3.6
+    - stage: galaxy36_2
+      env:
+        - TESTGALAXY="2"
+        - TRAVIS_PYTHON_VERSION=3.6
+    - stage: galaxy36_3
+      env:
+        - TESTGALAXY="3"
+        - TRAVIS_PYTHON_VERSION=3.6
 
 # Setup anaconda
 before_install:
@@ -23,7 +31,7 @@ before_install:
   - hash -r
   - conda config --set always_yes yes --set changeps1 no
   - conda update -q conda
-  - if [[ "$TRAVIS_OS_NAME" == "linux" && "$TRAVIS_PYTHON_VERSION" == "3.6" && ${TESTGALAXY:-"0"} == "1" ]] ; then conda create -c conda-forge -c bioconda -n planemo planemo; fi
+  - if [[ "$TRAVIS_OS_NAME" == "linux" && "$TRAVIS_PYTHON_VERSION" == "3.6" && ${TESTGALAXY:-"0"} != "0" ]] ; then conda create -c conda-forge -c bioconda -n planemo planemo; fi
 
   # Useful for debugging any issues with conda
   - conda info -a
@@ -35,11 +43,12 @@ install:
 
 # command to run tests
 script:
-  - if [[ ${TESTGALAXY:-"2"} == "2" ]] ; then flake8 . --exclude=.venv,.build,foo,build,deeptoolsintervals/__init__.py --ignore=E501,F403,E402,F999,F405,E722 ; fi
-  - if [[ ${TESTGALAXY:-"2"} == "2" ]] ; then export owd=`pwd` ; fi
-  - if [[ ${TESTGALAXY:-"2"} == "2" ]] ; then cd ~/ && nosetests --with-doctest -sv deeptools ; fi
-  - if [[ ${TESTGALAXY:-"2"} == "2" ]] ; then nosetests --with-doctest -sv deeptoolsintervals ; fi
-  - if [[ ${TESTGALAXY:-"2"} == "2" ]] ; then cd ${owd} ; fi
+  - if [[ ${TESTGALAXY:-"0"} == "0" ]] ; then flake8 . --exclude=.venv,.build,foo,build,deeptoolsintervals/__init__.py --ignore=E501,F403,E402,F999,F405,E722 ; fi
+  - if [[ ${TESTGALAXY:-"0"} == "0" ]] ; then export owd=`pwd` ; fi
+  - if [[ ${TESTGALAXY:-"0"} == "0" ]] ; then cd ~/ && nosetests --with-doctest -sv deeptools ; fi
+  - if [[ ${TESTGALAXY:-"0"} == "0" ]] ; then nosetests --with-doctest -sv deeptoolsintervals ; fi
+  - if [[ ${TESTGALAXY:-"0"} == "0" ]] ; then cd ${owd} ; fi
   - if [[ "$TRAVIS_OS_NAME" == "linux" && ${TESTGALAXY:-"0"} == "1" ]] ; then /home/travis/miniconda/envs/planemo/bin/planemo lint galaxy/wrapper/ ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "linux" && ${TESTGALAXY:-"0"} == "1" ]] ; then ./.planemo.sh ; fi
+  - if [[ "$TRAVIS_OS_NAME" == "linux" && ${TESTGALAXY:-"0"} != "0" ]] ; then ./.planemo.sh ${TESTGALAXY}; fi
+
 sudo: false

CHANGES.txt

@@ -1,3 +1,8 @@
+3.0.1
+
+ * Fixed the `--perGroup` option in plotProfile and plotHeatmap when multiple groups were being used. In version 3.0.0, this would typically cause an error and deepTools to crash. (issue #673)
+ * Fixed a few issues with the Galaxy wrappers. Thanks to Ralf Gilsbach, Claudia Keller, and @bgruening (e.g., issue #678)
+
 3.0.0
 
  * plotCorrelation` now has `--log1p` and `--maxRange` options if a scatter plot is produced. `--log1p` plots the natural log of the values (plus 1). `--maxRange` sets the maximum X and Y axis ranges. If they would normally be below this value then they are left unchanged. (issue #536)

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__ = '3.0.0'
+__version__ = '3.0.1'

deeptools/plotHeatmap.py

@@ -128,8 +128,10 @@ def addProfilePlot(hm, plt, fig, grids, iterNum, iterNum2, perGroup, averageType
     for sample_id in range(iterNum):
         if perGroup:
             title = hm.matrix.group_labels[sample_id]
+            tickIdx = sample_id % hm.matrix.get_num_samples()
         else:
             title = hm.matrix.sample_labels[sample_id]
+            tickIdx = sample_id
         if sample_id > 0 and len(yMin) == 1 and len(yMax) == 1:
             ax_profile = fig.add_subplot(grids[0, sample_id], sharey=ax_list[0])
         else:
@@ -157,7 +159,7 @@ def addProfilePlot(hm, plt, fig, grids, iterNum, iterNum2, perGroup, averageType
 
         if sample_id == 0 and yAxisLabel != '':
             ax_profile.set_ylabel(yAxisLabel)
-        xticks, xtickslabel = hm.getTicks(sample_id)
+        xticks, xtickslabel = hm.getTicks(tickIdx)
         if np.ceil(max(xticks)) != float(sub_matrix['matrix'].shape[1]):
             tickscale = float(sub_matrix['matrix'].shape[1]) / max(xticks)
             xticks_use = [x * tickscale for x in xticks]

deeptools/plotProfile.py

@@ -698,10 +698,12 @@ def plot_profile(self):
                 title = self.hm.matrix.group_labels[plot]
                 if row != 0 and len(self.y_min) == 1 and len(self.y_max) == 1:
                     plt.setp(ax.get_yticklabels(), visible=False)
+                tickIdx = plot % self.hm.matrix.get_num_samples()
             else:
                 title = self.hm.matrix.sample_labels[plot]
                 if col != 0 and len(self.y_min) == 1 and len(self.y_max) == 1:
                     plt.setp(ax.get_yticklabels(), visible=False)
+                tickIdx = plot
 
             ax.set_title(title)
             for data_idx in range(self.numlines):
@@ -747,7 +749,7 @@ def plot_profile(self):
                 """
 
             totalWidth = sub_matrix['matrix'].shape[1]
-            xticks, xtickslabel = self.getTicks(plot)
+            xticks, xtickslabel = self.getTicks(tickIdx)
             if np.ceil(max(xticks)) != float(totalWidth):
                 tickscale = float(totalWidth) / max(xticks)
                 xticks_use = [x * tickscale for x in xticks]

galaxy/wrapper/computeMatrix.xml

@@ -21,7 +21,7 @@
             $mode.mode_select
             --regionsFileName '#echo "' '".join($bed_files)#'
 
-            --scoreFileName '#echo "' '".join($files)#'
+            --scoreFileName #echo ' '.join($files)#
 
             --outFileName '$outFileName'
 

galaxy/wrapper/deepTools_macros.xml

@@ -1,10 +1,10 @@
 <macros>
 
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@WRAPPER_VERSION@">3.0.0</token>
+    <token name="@WRAPPER_VERSION@">3.0.1</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="3.0.0">deeptools</requirement>
+            <requirement type="package" version="3.0.1">deeptools</requirement>
             <requirement type="package" version="1.7">samtools</requirement>
         </requirements>
         <expand macro="stdio" />
@@ -456,7 +456,6 @@ is vital to you, select Yes below.">
             #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" &&
                 #if $f.bamfiles.ext == 'bam':
                     ln -s '${f.bamfiles.metadata.bam_index}' './${counter}.bam.bai' &&
                 #else:

galaxy/wrapper/multiBigwigSummary.xml

@@ -19,8 +19,8 @@
 
             --outFileName $outFile
 
-            --bwfiles '#echo "' '".join($files)#'
-            --labels #echo " ".join($labels)#
+            --bwfiles #echo ' '.join($files)#
+            --labels #echo ' '.join($labels)#
 
             #if $outRawCounts:
                 --outRawCounts '$outFileRawCounts'