Merge pull request #1344 from pavanvidem/galaxy-4.0.0-update2

initial fix of the remaining Galaxy tools

Author: WardDeb

galaxy/wrapper/alignmentSieve.xml

@@ -19,14 +19,14 @@
         @THREADS@
         -b one.bam
         --label '$label'
-        #if str($filterRNAstrand) != 'no':
+        #if $filterRNAstrand:
             --filterRNAstrand '$filterRNAstrand'
         #end if
 
         $ignoreDuplicates
 
         #if $minMappingQuality:
-            --minMappingQuality '$minMappingQuality'
+            --minMappingQuality $minMappingQuality
         #end if
 
         #if $samFlagInclude:
@@ -98,10 +98,9 @@
                   take strand into consideration for strand-specific
                   protocols. Note that only properly paired reads are considered."/>
         <param argument="--ATACshift" type="boolean" label="Shift fragment ends as appropriate for ATAC-seq"/>
-        <param argument="filterRNAstrand" type="select" label="Only include reads originating from fragments from the forward or reverse strand."
+        <param argument="filterRNAstrand" type="select" optional="true" label="Only include reads originating from fragments from the forward or reverse strand."
             help="By default (the no option), all reads are processed, regardless of the strand they originated from. For RNAseq, it can be useful to separately create bigWig files for the forward or reverse strands.
                   Note that this tools assumes that a dUTP-based method was used, so fragments will be assigned to the reverse strand if the second read in a pair is reverse complemented.">
-            <option value="no" selected="true">no</option>
             <option value="forward">forward</option>
             <option value="reverse">reverse</option>
         </param>

galaxy/wrapper/deepTools_macros.xml

@@ -49,7 +49,7 @@
         $advancedOpt.ignoreDuplicates
         $advancedOpt.centerReads
         #if $advancedOpt.minMappingQuality:
-            --minMappingQuality '$advancedOpt.minMappingQuality'
+            --minMappingQuality $advancedOpt.minMappingQuality
         #end if
         #if $advancedOpt.samFlagInclude:
             --samFlagInclude $advancedOpt.samFlagInclude
@@ -716,7 +716,7 @@ is vital to you, select Yes below.">
     </xml>
 
     <xml name="output_dpi">
-        <param argument="--dpi" name="dpi" type="integer" value="200" size="3" optional="True"
+        <param argument="--dpi" type="integer" value="200" size="3" optional="True"
             label="Image dpi" help=""/>
     </xml>
 

galaxy/wrapper/multiBamSummary.xml

@@ -97,13 +97,13 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <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>
+        <test expect_num_outputs="1">
             <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" />

galaxy/wrapper/multiBigwigSummary.xml

@@ -19,7 +19,7 @@
             --outFileName $outFile
 
             --bwfiles #echo ' '.join($files)#
-            
+
             #if $custom_sample_labels_conditional.custom_labels_select == 'Yes'
                 --labels #echo ' '.join($custom_sample_labels_conditional.labels)#
             #end if
@@ -86,13 +86,13 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="bigwigfiles" value="test.bw,test.bw" ftype="bigwig" />
             <param name="modeOpt" value="bins" />
             <param name="binSize" value="10" />
             <output name="outFile" file="multiBigwigSummary_result1.npz" ftype="deeptools_coverage_matrix" compare="sim_size" />
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="bigwigfiles" value="test.bw,test.bw" ftype="bigwig" />
             <param name="modeOpt" value="bins" />
             <param name="binSize" value="10" />

galaxy/wrapper/plotCorrelation.xml

@@ -109,14 +109,14 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="corData" value="multiBamSummary_result1.npz" ftype="deeptools_coverage_matrix" />
             <param name="outFileFormat" value="png" />
             <param name="outFileCorMatrix" value="True" />
             <output name="matrix" file="plotCorrelation_result1.tabular" ftype="tabular" />
             <output name="outFileName" file="plotCorrelation_result1.png" ftype="png" compare="sim_size" delta="400" />
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="corData" value="multiBamSummary_result1.npz" ftype="deeptools_coverage_matrix" />
             <param name="outFileFormat" value="png" />
             <param name="whatToPlot" value="scatterplot" />

galaxy/wrapper/plotCoverage.xml

@@ -114,7 +114,7 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="2">
             <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
             <!--param name="outFileFormat" value="png" /-->
             <param name="showAdvancedOpt" value="yes" />
@@ -123,7 +123,7 @@
             <output name="outFileRawCounts" file="plotCoverage_result1.tabular" ftype="tabular" />
             <output name="outFileName" file="plotCoverage_result1.png" ftype="png" compare="sim_size" delta="2400" />
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
             <param name="showAdvancedOpt" value="yes" />
             <param name="plotTitle" value="Test Title from Galaxy" />

galaxy/wrapper/plotEnrichment.xml

@@ -48,7 +48,7 @@
                 $advancedOpt.perSample
 
                 $advancedOpt.variableScales
-                
+
                 $advancedOpt.perSample
 
                 $advancedOpt.variableScales
@@ -175,7 +175,7 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="2">
             <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
             <param name="BED" value="multiBamSummary_regions.bed,multiBamSummary_regions.bed" ftype="bed" />
             <param name="outRawCounts" value="true" />

galaxy/wrapper/plotFingerprint.xml

@@ -114,13 +114,13 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <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>
+        <test expect_num_outputs="3">
             <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
             <param name="showAdvancedOpt" value="yes" />
             <param name="showOutputSettings" value="yes" />

galaxy/wrapper/plotHeatmap.xml

@@ -143,12 +143,13 @@
                 <param argument="--sortUsingSamples" type="text"
                     label="List of samples to be used for sorting"
                     help="List of sample numbers (order as in matrix), which are used by --sortUsing for sorting.
-                    If no value is set, it uses all samples. Example: 1 3 (space separated!)" />
+                    If no value is set, it uses all samples. Example: 1 3 (space separated!)">
                     <sanitizer>
                         <valid initial="string.printable">
                             <add value=" "/>
                         </valid>
                     </sanitizer>
+                </param>
                 <param argument="--linesAtTickMarks" type="boolean" truevalue="--linesAtTickMarks" falsevalue=""
                     label="Draw dashed lines in heatmap above all tick marks?" />
                 <param argument="--averageTypeSummaryPlot" type="select"
@@ -246,12 +247,13 @@
                 <param argument="--clusterUsingSamples" type="text"
                     label="List of samples to be used for clustering"
                     help="List of sample numbers (order as in matrix), which are used by --kmeans or --hclust for clustering.
-                    If no value is set, it uses all samples. Example: 1 3 (space separated!)"/>
+                    If no value is set, it uses all samples. Example: 1 3 (space separated!)">
                     <sanitizer>
                         <valid initial="string.printable">
                             <add value=" "/>
                         </valid>
                     </sanitizer>
+                </param>
             </when>
         </conditional>
     </inputs>
@@ -261,11 +263,11 @@
         <expand macro="output_save_matrix_values" />
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
             <output name="outFileName" file="heatmapper_result1.png" ftype="png" compare="sim_size" delta="4000" />
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
             <param name="showAdvancedOpt" value="yes" />
             <param name="whatToShow" value="heatmap and colorbar" />

galaxy/wrapper/plotPCA.xml

@@ -44,16 +44,16 @@
             <when value="no" />
             <when value="yes">
                 <expand macro="plotWidthHeight" PLOTWIDTH="10.0" PLOTHEIGHT="10.0" />
-                <param name="PCs" argument="--PCs" label="Principal components to plot" value="1 2" type="text"
+                <param argument="--PCs" label="Principal components to plot" value="1 2" type="text"
                     help="The principal components to plot. If specified, you must provide two different integers, greater than zero, separated by a space. An example (and the default) is '1 2'." />
-                <param name="ntop" argument="--ntop" label="Number of rows to use" value="1000" type="integer"
+                <param argument="--ntop" label="Number of rows to use" value="1000" type="integer"
                     help="Use only the top N most variable rows in the original matrix. Specifying 0 will result in all rows being used. If the matrix is to be transposed, rows with 0 variance are always excluded, even if a values of 0 is specified. The default is 1000." />
-                <param name="log2" argument="--log2" type="boolean" truevalue="--log2" falsevalue="" label="log2 transform data" help="log2 transform the datapoints prior to computing the PCA. Note that 0.01 is added to all values to prevent 0 values from becoming -infinity. Using this option with input that contains negative values will result in an error." />
+                <param argument="--log2" type="boolean" truevalue="--log2" falsevalue="" label="log2 transform data" help="log2 transform the datapoints prior to computing the PCA. Note that 0.01 is added to all values to prevent 0 values from becoming -infinity. Using this option with input that contains negative values will result in an error." />
                 <param argument="--transpose" type="boolean" label="Transpose Matrix?" help="Perform the PCA on the transpose of the matrix, (i.e., with samples as rows and features/genes as columns). This then matches what is typically done in R for RNAseq data." truevalue="--transpose" falsevalue="" />
                 <param argument="--rowCenter" type="boolean" label="Center Rows?" help="When specified, each row (bin, gene, etc.) in the matrix is centered at 0 before the PCA is computed. This is useful only if you have a strong bin/gene/etc. correlation and the resulting principal component has samples stacked vertically. This option is not applicable if the PCA is performed on the transposed matrix." truevalue="--rowCenter" falsevalue="" />
-                <param argument="--colors" type="text" name="colors" label="Symbol colors" value="" optional="True"
+                <param argument="--colors" type="text" label="Symbol colors" value="" optional="True"
                     help="A list of colors for the symbols. Color names and html hex string (e.g., #eeff22) are accepted. The color names should be space separated. For example, --colors 'red blue green'. If not specified, the symbols will be given automatic colors." />
-                <param argument="--markers" type="text" name="markers" label="Custom markers" value="" optional="True"
+                <param argument="--markers" type="text" label="Custom markers" value="" optional="True"
                     help="A list of markers for the symbols. (e.g., '&lt;','&gt;','o') are accepted. The marker values should be space separated. For example, 's' 'o' 's' 'o'. If not specified, the symbols will be given automatic shapes." />
             </when>
         </conditional>
@@ -65,14 +65,14 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="corData" value="multiBamSummary_result2b.npz" ftype="deeptools_coverage_matrix" />
             <param name="plotTitle" value="Test Plot" />
             <param name="outFileFormat" value="png" />
             <param name="showAdvancedOpt" value="yes" />
             <output name="outFileName" file="plotPCA_result1.png" ftype="png" compare="sim_size" delta="12000" />
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="corData" value="multiBamSummary_result2b.npz" ftype="deeptools_coverage_matrix" />
             <param name="plotTitle" value="Test Plot" />
             <param name="outFileFormat" value="png" />