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Merge pull request #331 from fidelram/quotes
Fixing quotes of multiple filenames in Galaxy
2 parents cb6111b + c5353bb commit 1943c8e

11 files changed

+24
-24
lines changed

‎galaxy/wrapper/bamCompare.xml‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -173,8 +173,8 @@
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</outputs>
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<tests>
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<test>
176-
<param name="bamFile1" value="bowtie2-test1.bam" ftype="bam" />
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<param name="bamFile2" value="bowtie2-test1.bam" ftype="bam" />
176+
<param name="bamFile1" value="bowtie2 test1.bam" ftype="bam" />
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<param name="bamFile2" value="bowtie2 test1.bam" ftype="bam" />
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<param name="showAdvancedOpt" value="no" />
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<param name="outFileFormat" value="bigwig" />
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<param name="outFileFormat" value="bedgraph" />
@@ -183,8 +183,8 @@
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<output name="outFileName" file="bamCompare_result1.bg" ftype="bedgraph" />
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</test>
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<test>
186-
<param name="bamFile1" value="bowtie2-test1.bam" ftype="bam" />
187-
<param name="bamFile2" value="bowtie2-test1.bam" ftype="bam" />
186+
<param name="bamFile1" value="bowtie2 test1.bam" ftype="bam" />
187+
<param name="bamFile2" value="bowtie2 test1.bam" ftype="bam" />
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<param name="showAdvancedOpt" value="yes" />
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<param name="outFileFormat" value="bigwig" />
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<param name="outFileFormat" value="bigwig" />

‎galaxy/wrapper/bamCoverage.xml‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -130,22 +130,22 @@
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</outputs>
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<tests>
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<test>
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<param name="bamInput" value="bowtie2-test1.bam" ftype="bam" />
133+
<param name="bamInput" value="bowtie2 test1.bam" ftype="bam" />
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<param name="outFileFormat" value="bigwig" />
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<param name="showAdvancedOpt" value="no" />
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<param name="binSize" value="10" />
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<param name="type" value="no" />
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<output name="outFileName" file="bamCoverage_result1.bw" ftype="bigwig" />
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</test>
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<test>
141-
<param name="bamInput" value="bowtie2-test1.bam" ftype="bam" />
141+
<param name="bamInput" value="bowtie2 test1.bam" ftype="bam" />
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<param name="outFileFormat" value="bigwig" />
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<param name="showAdvancedOpt" value="no" />
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<param name="binSize" value="10" />
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<output name="outFileName" file="bamCoverage_result2.bw" ftype="bigwig" />
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</test>
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<test>
148-
<param name="bamInput" value="bowtie2-test1.bam" ftype="bam" />
148+
<param name="bamInput" value="bowtie2 test1.bam" ftype="bam" />
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<param name="outFileFormat" value="bedgraph" />
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<param name="showAdvancedOpt" value="no" />
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<param name="binSize" value="10" />

‎galaxy/wrapper/bamPEFragmentSize.xml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -55,7 +55,7 @@
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</outputs>
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<tests>
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<test>
58-
<param name="bamInput" value="bowtie2-test1.bam" ftype="bam" />
58+
<param name="bamInput" value="bowtie2 test1.bam" ftype="bam" />
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<param name="histogram" value="True" />
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<param name="plotTitle" value="Test Plot" />
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<output name="outfile" file="bamPEFragmentSize_result1.txt" ftype="txt" />

‎galaxy/wrapper/multiBamSummary.xml‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -16,8 +16,8 @@
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@THREADS@
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--outFileName '$outFile'
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--bamfiles '#echo "' '".join($files)#'
20-
--labels '#echo "' '".join($labels)#'
19+
--bamfiles #echo " ".join($files)#
20+
--labels #echo " ".join($labels)#
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#if $outRawCounts:
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--outRawCounts '$outFileRawCounts'
@@ -85,13 +85,13 @@
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</outputs>
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<tests>
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<test>
88-
<param name="bamfiles" value="bowtie2-test1.bam,bowtie2-test1.bam" ftype="bam" />
88+
<param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
8989
<param name="modeOpt" value="bins" />
9090
<param name="binSize" value="10" />
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<output name="outFile" file="multiBamSummary_result1.npz" ftype="deeptools_coverage_matrix" compare="sim_size" />
9292
</test>
9393
<test>
94-
<param name="bamfiles" value="bowtie2-test1.bam,bowtie2-test1.bam" ftype="bam" />
94+
<param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
9595
<param name="modeOpt" value="BED-file" />
9696
<param name="region_file" value="multiBamSummary_regions.bed" />
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<output name="outFile" file="multiBamSummary_result2.npz" ftype="deeptools_coverage_matrix" compare="sim_size" />

‎galaxy/wrapper/multiBigwigSummary.xml‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -18,8 +18,8 @@
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@THREADS@
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--outFileName $outFile
21-
--bwfiles '#echo "' '".join($files)#'
22-
--labels '#echo "' '".join($labels)#'
21+
--bwfiles #echo " ".join($files)#
22+
--labels #echo " ".join($labels)#
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#if $outRawCounts:
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--outRawCounts '$outFileRawCounts'

‎galaxy/wrapper/plotCoverage.xml‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -17,8 +17,8 @@
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@THREADS@
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--plotFile '$outFileName'
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--bamfiles '#echo "' '".join($files)#'
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--labels '#echo "' '".join($labels)#'
20+
--bamfiles #echo " ".join($files)#
21+
--labels #echo " ".join($labels)#
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--plotFileFormat "$outFileFormat"
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#if $outRawCounts:
@@ -76,13 +76,13 @@
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</outputs>
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<tests>
7878
<test>
79-
<param name="bamfiles" value="bowtie2-test1.bam,bowtie2-test1.bam" ftype="bam" />
79+
<param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
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<!--param name="outFileFormat" value="png" /-->
8181
<param name="showAdvancedOpt" value="yes" />
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<param name="plotTitle" value="Test Title from Galaxy" />
8383
<param name="outRawCounts" value="True" />
8484
<output name="outFileRawCounts" file="plotCoverage_result1.tabular" ftype="tabular" />
85-
<output name="outFileName" file="plotCoverage_result1.png" ftype="png" compare="sim_size" delta="2200" />
85+
<output name="outFileName" file="plotCoverage_result1.png" ftype="png" compare="sim_size" delta="2400" />
8686
</test>
8787
</tests>
8888
<help>

‎galaxy/wrapper/plotFingerprint.xml‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -94,13 +94,13 @@
9494
</outputs>
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<tests>
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<test>
97-
<param name="bamfiles" value="bowtie2-test1.bam,bowtie2-test1.bam" ftype="bam" />
97+
<param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
9898
<param name="showAdvancedOpt" value="no" />
9999
<param name="showOutputSettings" value="no" />
100100
<output name="outFileName" file="plotFingerprint_result1.png" ftype="png" compare="sim_size" />
101101
</test>
102102
<test>
103-
<param name="bamfiles" value="bowtie2-test1.bam,bowtie2-test1.bam" ftype="bam" />
103+
<param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
104104
<param name="showAdvancedOpt" value="yes" />
105105
<param name="showOutputSettings" value="yes" />
106106
<param name="saveRawCounts" value="True" />

‎galaxy/wrapper/test-data/bowtie2-test1.bam‎ renamed to ‎galaxy/wrapper/test-data/bowtie2 test1.bam‎

File renamed without changes.

‎galaxy/wrapper/test-data/plotCoverage_result1.tabular‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
#'chr' 'start' 'end' 'bowtie2-test1.bam' 'bowtie2-test1.bam'
1+
#'chr' 'start' 'end' 'bowtie2 test1.bam' 'bowtie2 test1.bam'
22
chrM 0 1 23.0 23.0
33
chrM 1 2 35.0 35.0
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chrM 2 3 35.0 35.0

‎galaxy/wrapper/test-data/plotFingerprint_result2.tabular‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
'bowtie2-test1.bam' 'bowtie2-test1.bam'
1+
'bowtie2 test1.bam' 'bowtie2 test1.bam'
22
68 68
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65 65
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61 61

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