fix quotes

Author: bgruening

galaxy/wrapper/bamCompare.xml

@@ -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" />
@@ -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" />

galaxy/wrapper/bamCoverage.xml

@@ -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" />

galaxy/wrapper/bamPEFragmentSize.xml

@@ -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" />

galaxy/wrapper/multiBamSummary.xml

@@ -16,8 +16,8 @@
             @THREADS@
 
             --outFileName '$outFile'
-            --bamfiles '#echo "' '".join($files)#'
-            --labels '#echo "' '".join($labels)#'
+            --bamfiles #echo " ".join($files)#
+            --labels #echo " ".join($labels)#
 
             #if $outRawCounts:
                 --outRawCounts '$outFileRawCounts'
@@ -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" />

galaxy/wrapper/multiBigwigSummary.xml

@@ -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'

galaxy/wrapper/plotCoverage.xml

@@ -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:
@@ -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>

galaxy/wrapper/plotFingerprint.xml

@@ -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" />

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

@@ -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

galaxy/wrapper/test-data/plotCoverage_result1.tabular

@@ -1,4 +1,4 @@
-'bowtie2-test1.bam'	'bowtie2-test1.bam'
+'bowtie2 test1.bam'	'bowtie2 test1.bam'
 68	68
 65	65
 61	61