diff computeMatrixOperations.xml @ 10:848ce8f81e6e draft

planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 38cfe39e3b3c82bbc0c2013e3068bd71adc3a9cb

--- a/computeMatrixOperations.xml	Thu Apr 05 10:56:44 2018 -0400
+++ b/computeMatrixOperations.xml	Mon Jul 09 18:55:26 2018 -0400
@@ -12,6 +12,15 @@
                 info
                 -m $submodule.matrixFile
                 > $outFileTxt
+            #else if $submodule.command == "relabel":
+                relabel
+                -m $submodule.matrixFile
+                #if $submodule.groupLabels is not None and str($submodule.groupLabels) != '':
+                    --groupLabels $submodule.groupLabels
+                #end if
+                #if $submodule.sampleLabels is not None and str($submodule.sampleLabels) != '':
+                    --sampleLabels $submodule.sampleLabels
+                #end if
             #else if $submodule.command == "subset":
                 subset
                 -m $submodule.matrixFile
@@ -27,6 +36,16 @@
                 -m $submodule.matrixFile
                 --strand $submodule.strand
                 -o $outFileName
+            #else if $submodule.command == "filterValues":
+                filterValues
+                -m $submodule.matrixFile
+                #if $submodule.minValue is not None and str($submodule.minValue) != '':
+                    --min $submodule.minValue
+                #end if
+                #if $submodule.maxValue is not None and str($submodule.maxValue) != '':
+                    --max $submodule.maxValue
+                #end if
+                -o $outFileName
             #else if $submodule.command == "rbind":
                 #set $files=[]
                 #for $f in $submodule.matrixFiles:
@@ -59,8 +78,10 @@
         <conditional name="submodule">
             <param name="command" type="select" label="Operation type">
                 <option value="info" selected="true">Print information (info)</option>
+                <option value="relabel">Relabel the samples and/or groups (relabel)</option>
                 <option value="subset">Subset by samples and/or groups of regions (subset)</option>
                 <option value="filterStrand">Filter by strand (filterStrand)</option>
+                <option value="filterValues">Filter by min/max value (filterValues)</option>
                 <option value="rbind">Bind matrices, top to bottom (rbind)</option>
                 <option value="cbind">Bind matrices, left to right (cbind)</option>
                 <option value="sort">Sort by region order in specified files (sort)</option>
@@ -70,6 +91,15 @@
                        label="Matrix file from the computeMatrix tool" help=""/>
             </when>
 
+            <when value="relabel">
+                <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"
+                       label="Matrix file from the computeMatrix tool" help=""/>
+                <param argument="groupLabels" type="text" optional="true" label="New Region/Group Labels."
+                    help="If blank, the labels are left unchanged, otherwise they're changed to be those provided here. Multiple labels should be separated by spaces. If you provide labels, you must provide exactly one label for each group of regions."/>
+                <param argument="sampleLabels" type="text" optional="true" label="New Sample Labels."
+                    help="If blank, the labels are left unchanged, otherwise they're changed to be those provided here. Multiple labels should be separated by spaces. If you provide labels, you must provide exactly one label for each sample."/>
+            </when>
+
             <when value="subset">
                 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"
                        label="Matrix file from the computeMatrix tool" help=""/>
@@ -82,7 +112,7 @@
             <when value="filterStrand">
                 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"
                        label="Matrix file from the computeMatrix tool" help=""/>
-                <param argument="strand" type="select" label="Only include regions on this strand."
+                <param argument="--strand" type="select" label="Only include regions on this strand."
                     help="Only regions on the desired strand will be included in the output. If you desire to instead remove regions on only one strand (or the . strand), separately run this on the other strand and then use the rbind operation.">
                     <option value="+">+</option>
                     <option value="-">-</option>
@@ -90,6 +120,15 @@
                 </param>
             </when>
 
+            <when value="filterValues">
+                <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"
+                       label="Matrix file from the computeMatrix tool" help=""/>
+                <param argument="--min" type="float" optional="true" label="Minimum value"
+                       help="Exclude any row in the matrix with a value below this. By default there is no minimum value." />
+                <param argument="--max" type="float" optional="true" label="Maximum value"
+                       help="Exclude any row in the matrix with a value above this. By default there is no maximum value." />
+            </when>
+
             <when value="rbind">
                 <repeat name="matrixFiles" title="Matrix files from computeMatrix" min="2">
                 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"