Merge pull request #1354 from deeptools/tests

Tests

Author: WardDeb

.planemo.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 # Some versions of planemo don't handle symlinks
 unlink galaxy/wrapper/test-data/test.bw
-cp deeptools/test/test_heatmapper/test.bw galaxy/wrapper/test-data/test.bw
+cp pydeeptools/deeptools/test/test_heatmapper/test.bw galaxy/wrapper/test-data/test.bw
 
 if [[ $1 == "1" ]] ; then
     wrappers="galaxy/wrapper/alignmentSieve.xml \

galaxy/wrapper/alignmentSieve.xml

@@ -131,7 +131,7 @@
             <param name="bamfile" value="paired_chr2L.bam" ftype="bam"/>
             <param name="minMappingQuality" value="10"/>
             <param name="filterMetrics" value="True"/>
-            <output name="outFile" file="alignmentSieve.bam" ftype="bam" lines_diff="1"/>
+            <output name="outFile" file="alignmentSieve.bam" ftype="bam" lines_diff="2"/>
             <output name="filterMetricsFile" file="alignmentSieve.txt" ftype="tabular"/>
         </test>
         <test expect_num_outputs="1">
@@ -145,13 +145,13 @@
             <param name="bamfile" value="paired_chr2L.bam" ftype="bam"/>
             <param name="minMappingQuality" value="10"/>
             <param name="shift" value="1 -2 3 -4"/>
-            <output name="outFile" file="alignmentSieve2.bam" ftype="bam" lines_diff="2"/>
+            <output name="outFile" file="alignmentSieve2.bam" ftype="bam" lines_diff="4"/>
         </test>
         <test expect_num_outputs="1">
             <param name="bamfile" value="paired_chr2L.cram" ftype="cram"/>
             <param name="minMappingQuality" value="10"/>
             <param name="shift" value="1 -2 3 -4"/>
-            <output name="outFile" file="alignmentSieve3.bam" ftype="bam" lines_diff="2"/>
+            <output name="outFile" file="alignmentSieve3.bam" ftype="bam" lines_diff="4"/>
         </test>
     </tests>
     <help>

galaxy/wrapper/plotCorrelation.xml

@@ -109,7 +109,7 @@
         </data>
     </outputs>
     <tests>
-        <test expect_num_outputs="1">
+        <test expect_num_outputs="2">
             <param name="corData" value="multiBamSummary_result1.npz" ftype="deeptools_coverage_matrix" />
             <param name="outFileFormat" value="png" />
             <param name="outFileCorMatrix" value="True" />

galaxy/wrapper/plotCoverage.xml

@@ -114,7 +114,7 @@
         </data>
     </outputs>
     <tests>
-        <test expect_num_outputs="2">
+        <test expect_num_outputs="3">
             <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
             <!--param name="outFileFormat" value="png" /-->
             <param name="showAdvancedOpt" value="yes" />