fix #678

deeptools · Mar 1, 2018 · f65cbc4 · f65cbc4
1 parent af3fda8
commit f65cbc4
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Showing 4 changed files with 45 additions and 31 deletions.
diff --git a/.planemo.sh b/.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
diff --git a/.travis.yml b/.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
diff --git a/galaxy/wrapper/computeMatrix.xml b/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'
 

diff --git a/galaxy/wrapper/multiBigwigSummary.xml b/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'