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Fixing quotes of multiple filenames in Galaxy #331

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Merged
merged 4 commits into from
Apr 5, 2016
Merged

Fixing quotes of multiple filenames in Galaxy #331

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ecbef99
change version of the dependencies
bgruening Mar 17, 2016
4b6c100
Merge branch 'master' of https://github.com/fidelram/deepTools
bgruening Mar 17, 2016
a347eda
Merge branch 'master' of https://github.com/fidelram/deepTools
bgruening Apr 5, 2016
c5353bb
fix quotes
bgruening Apr 5, 2016
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8 changes: 4 additions & 4 deletions galaxy/wrapper/bamCompare.xml
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Expand Up @@ -173,8 +173,8 @@
</outputs>
<tests>
<test>
<param name="bamFile1" value="bowtie2-test1.bam" ftype="bam" />
<param name="bamFile2" value="bowtie2-test1.bam" ftype="bam" />
<param name="bamFile1" value="bowtie2 test1.bam" ftype="bam" />
<param name="bamFile2" value="bowtie2 test1.bam" ftype="bam" />
<param name="showAdvancedOpt" value="no" />
<param name="outFileFormat" value="bigwig" />
<param name="outFileFormat" value="bedgraph" />
Expand All @@ -183,8 +183,8 @@
<output name="outFileName" file="bamCompare_result1.bg" ftype="bedgraph" />
</test>
<test>
<param name="bamFile1" value="bowtie2-test1.bam" ftype="bam" />
<param name="bamFile2" value="bowtie2-test1.bam" ftype="bam" />
<param name="bamFile1" value="bowtie2 test1.bam" ftype="bam" />
<param name="bamFile2" value="bowtie2 test1.bam" ftype="bam" />
<param name="showAdvancedOpt" value="yes" />
<param name="outFileFormat" value="bigwig" />
<param name="outFileFormat" value="bigwig" />
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6 changes: 3 additions & 3 deletions galaxy/wrapper/bamCoverage.xml
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Expand Up @@ -130,22 +130,22 @@
</outputs>
<tests>
<test>
<param name="bamInput" value="bowtie2-test1.bam" ftype="bam" />
<param name="bamInput" value="bowtie2 test1.bam" ftype="bam" />
<param name="outFileFormat" value="bigwig" />
<param name="showAdvancedOpt" value="no" />
<param name="binSize" value="10" />
<param name="type" value="no" />
<output name="outFileName" file="bamCoverage_result1.bw" ftype="bigwig" />
</test>
<test>
<param name="bamInput" value="bowtie2-test1.bam" ftype="bam" />
<param name="bamInput" value="bowtie2 test1.bam" ftype="bam" />
<param name="outFileFormat" value="bigwig" />
<param name="showAdvancedOpt" value="no" />
<param name="binSize" value="10" />
<output name="outFileName" file="bamCoverage_result2.bw" ftype="bigwig" />
</test>
<test>
<param name="bamInput" value="bowtie2-test1.bam" ftype="bam" />
<param name="bamInput" value="bowtie2 test1.bam" ftype="bam" />
<param name="outFileFormat" value="bedgraph" />
<param name="showAdvancedOpt" value="no" />
<param name="binSize" value="10" />
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2 changes: 1 addition & 1 deletion galaxy/wrapper/bamPEFragmentSize.xml
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Expand Up @@ -55,7 +55,7 @@
</outputs>
<tests>
<test>
<param name="bamInput" value="bowtie2-test1.bam" ftype="bam" />
<param name="bamInput" value="bowtie2 test1.bam" ftype="bam" />
<param name="histogram" value="True" />
<param name="plotTitle" value="Test Plot" />
<output name="outfile" file="bamPEFragmentSize_result1.txt" ftype="txt" />
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8 changes: 4 additions & 4 deletions galaxy/wrapper/multiBamSummary.xml
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Expand Up @@ -16,8 +16,8 @@
@THREADS@
--outFileName '$outFile'
--bamfiles '#echo "' '".join($files)#'
--labels '#echo "' '".join($labels)#'
--bamfiles #echo " ".join($files)#
--labels #echo " ".join($labels)#
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@dpryan79 dpryan79 Apr 5, 2016

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I assume we no longer need the # at the end of each of these lines.

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@bgruening bgruening Apr 5, 2016

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It more or less closes the cheetah template. It could be removed yes.

#if $outRawCounts:
--outRawCounts '$outFileRawCounts'
Expand Down Expand Up @@ -85,13 +85,13 @@
</outputs>
<tests>
<test>
<param name="bamfiles" value="bowtie2-test1.bam,bowtie2-test1.bam" ftype="bam" />
<param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
<param name="modeOpt" value="bins" />
<param name="binSize" value="10" />
<output name="outFile" file="multiBamSummary_result1.npz" ftype="deeptools_coverage_matrix" compare="sim_size" />
</test>
<test>
<param name="bamfiles" value="bowtie2-test1.bam,bowtie2-test1.bam" ftype="bam" />
<param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
<param name="modeOpt" value="BED-file" />
<param name="region_file" value="multiBamSummary_regions.bed" />
<output name="outFile" file="multiBamSummary_result2.npz" ftype="deeptools_coverage_matrix" compare="sim_size" />
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4 changes: 2 additions & 2 deletions galaxy/wrapper/multiBigwigSummary.xml
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Expand Up @@ -18,8 +18,8 @@
@THREADS@

--outFileName $outFile
--bwfiles '#echo "' '".join($files)#'
--labels '#echo "' '".join($labels)#'
--bwfiles #echo " ".join($files)#
--labels #echo " ".join($labels)#

#if $outRawCounts:
--outRawCounts '$outFileRawCounts'
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8 changes: 4 additions & 4 deletions galaxy/wrapper/plotCoverage.xml
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Expand Up @@ -17,8 +17,8 @@
@THREADS@

--plotFile '$outFileName'
--bamfiles '#echo "' '".join($files)#'
--labels '#echo "' '".join($labels)#'
--bamfiles #echo " ".join($files)#
--labels #echo " ".join($labels)#
--plotFileFormat "$outFileFormat"

#if $outRawCounts:
Expand Down Expand Up @@ -76,13 +76,13 @@
</outputs>
<tests>
<test>
<param name="bamfiles" value="bowtie2-test1.bam,bowtie2-test1.bam" ftype="bam" />
<param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
<!--param name="outFileFormat" value="png" /-->
<param name="showAdvancedOpt" value="yes" />
<param name="plotTitle" value="Test Title from Galaxy" />
<param name="outRawCounts" value="True" />
<output name="outFileRawCounts" file="plotCoverage_result1.tabular" ftype="tabular" />
<output name="outFileName" file="plotCoverage_result1.png" ftype="png" compare="sim_size" delta="2200" />
<output name="outFileName" file="plotCoverage_result1.png" ftype="png" compare="sim_size" delta="2400" />
</test>
</tests>
<help>
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4 changes: 2 additions & 2 deletions galaxy/wrapper/plotFingerprint.xml
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Expand Up @@ -94,13 +94,13 @@
</outputs>
<tests>
<test>
<param name="bamfiles" value="bowtie2-test1.bam,bowtie2-test1.bam" ftype="bam" />
<param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
<param name="showAdvancedOpt" value="no" />
<param name="showOutputSettings" value="no" />
<output name="outFileName" file="plotFingerprint_result1.png" ftype="png" compare="sim_size" />
</test>
<test>
<param name="bamfiles" value="bowtie2-test1.bam,bowtie2-test1.bam" ftype="bam" />
<param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
<param name="showAdvancedOpt" value="yes" />
<param name="showOutputSettings" value="yes" />
<param name="saveRawCounts" value="True" />
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0 galaxy/wrapper/test-data/bowtie2-test1.bam → galaxy/wrapper/test-data/bowtie2 test1.bam
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File renamed without changes.
2 changes: 1 addition & 1 deletion galaxy/wrapper/test-data/plotCoverage_result1.tabular
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@@ -1,4 +1,4 @@
#'chr' 'start' 'end' 'bowtie2-test1.bam' 'bowtie2-test1.bam'
#'chr' 'start' 'end' 'bowtie2 test1.bam' 'bowtie2 test1.bam'
chrM 0 1 23.0 23.0
chrM 1 2 35.0 35.0
chrM 2 3 35.0 35.0
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2 changes: 1 addition & 1 deletion galaxy/wrapper/test-data/plotFingerprint_result2.tabular
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@@ -1,4 +1,4 @@
'bowtie2-test1.bam' 'bowtie2-test1.bam'
'bowtie2 test1.bam' 'bowtie2 test1.bam'
68 68
65 65
61 61
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4 changes: 2 additions & 2 deletions galaxy/wrapper/tool_dependencies.xml
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Expand Up @@ -3,7 +3,7 @@
<package name="python" version="2.7.10">
<repository name="package_python_2_7_10" owner="iuc" prior_installation_required="True" />
</package>
<package name="deepTools" version="2.1.0">
<repository name="package_python_2_7_deeptools_2_1_0" owner="iuc"/>
<package name="deepTools" version="2.2.2">
<repository name="package_python_2_7_deeptools_2_2_2" owner="iuc"/>
</package>
</tool_dependency>