diff computeMatrix.xml @ 7:021729469baf draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ae00542731230245927953207977833a0f020b69

--- a/computeMatrix.xml	Wed Dec 23 04:00:26 2015 -0500
+++ b/computeMatrix.xml	Wed Dec 23 07:34:34 2015 -0500
@@ -1,5 +1,5 @@
 <tool id="deeptools_compute_matrix" name="computeMatrix" version="@WRAPPER_VERSION@.0">
-    <description>preparation step to plot a heatmap or a profile</description>
+    <description>prepares data for plotting a heatmap or a profile of given regions</description>
     <macros>
         <token name="@BINARY@">computeMatrix</token>
         <import>deepTools_macros.xml</import>
@@ -9,28 +9,22 @@
 <![CDATA[
         #import tempfile
 
-        #for $rf in $regionsFiles:
-            cat "$rf.regionsFile" >> ./temp_input_path;
-            #if str($rf.label.value).strip():
-                echo "\#$rf.label.value" >> ./temp_input_path;
-            #else:
-                echo "\#$rf.regionsFile.name" >> ./temp_input_path;
-            #end if
-        #end for
-
         @BINARY@
 
             $mode.mode_select
-            --regionsFileName ./temp_input_path
-            --scoreFileName '$scoreFile'
+            --regionsFileName
+            #for $rf in $regionsFiles:
+                '$rf.regionsFile' 
+            #end for
+            --scoreFileName
+            #for $bw in $scoreFileName:
+                '$bw' 
+            #end for
             --outFileName '$outFileName'
 
             @THREADS@
 
             #if $output.showOutputSettings == "yes"
-                #if $output.saveData:
-                    --outFileNameData '$outFileNameData' 
-                #end if
                 #if $output.saveMatrix:
                 --outFileNameMatrix '$outFileNameMatrix'
                 #end if
@@ -47,8 +41,6 @@
                 --afterRegionStartLength $mode.afterRegionStartLength
             #else
                 --regionBodyLength $mode.regionBodyLength
-                --startLabel "$mode.startLabel"
-                --endLabel "$mode.endLabel"
                 #if $mode.regionStartLength.regionStartLength_select == "yes":
                     --beforeRegionStartLength $mode.regionStartLength.beforeRegionStartLength
                     --afterRegionStartLength $mode.regionStartLength.afterRegionStartLength
@@ -78,19 +70,17 @@
     </command>
     <inputs>
 
-        <repeat name="regionsFiles" title="regions to plot" min="1">
+        <repeat name="regionsFiles" title="Select regions" min="1">
             <param name="regionsFile" format="bed" type="data" label="Regions to plot"
                 help="File, in BED format, containing the regions to plot."/>
-            <param name="label" type="text" size="30" optional="true" value="" label="Label"
-                help="Label to use in the output."/>
         </repeat>
 
-        <param name="scoreFile" format="bigwig" type="data"
-            label="Score file"
+        <param name="scoreFileName" format="bigwig" type="data"
+            label="Score file" multiple="True"
             help="Should be a bigWig file (containing a score, usually covering
             the whole genome). You can generate a bigWig file either from a
             bedGraph or WIG file using UCSC tools or from a BAM file using the
-            deepTool bamCoverage. (-scoreFile)"/>
+            deepTool bamCoverage. (--scoreFileName)"/>
 
         <conditional name="mode" >
             <param name="mode_select" type="select"
@@ -100,7 +90,7 @@
                 by the user. Reference-point refers to a position within the BED
                 regions (e.g start of region). In the reference-point mode only
                 those genomic positions before (downstream) and/or after (upstream)
-                the reference point will be plotted.">
+                the reference point will be considered.">
                 <option value="scale-regions" selected="true">scale-regions</option>
                 <option value="reference-point">reference-point</option>
             </param>
@@ -108,14 +98,6 @@
             <when value="scale-regions" >
                 <param argument="--regionBodyLength" type="integer" value="500"
                     label="Distance in bp to which all regions are going to be fitted" help=""/>
-                <param argument="--startLabel" type="text" value="TSS" size="10"
-                    label="Label for the region start"
-                    help ="Label shown in the plot for the start of the region.
-                    Default is TSS (transcription start site), but could be changed to anything,
-                    e.g. &quot;peak start&quot;." />
-                <param argument="--endLabel" type="text" value="TES" size="10"
-                    label="Label for the region end"
-                    help="Label shown in the plot for the region end. Default is TES (transcription end site)."/>
                 <conditional name="regionStartLength">
                     <param name="regionStartLength_select" type="select" label="Set distance up- and downstream of the given regions">
                         <option value="no" selected="true">no</option>
@@ -186,7 +168,7 @@
                     label="Convert missing values to 0?."
                     help="If set to 'yes', missing values (NAs) are converted to 0.
                           The default is to ignore such cases, which will be
-                          depicted as black areas in the heatmap by default." />
+                          depicted as black areas once a heatmap is created." />
 
                 <expand macro="skipZeros" />
                 <expand macro="skipNAs" />
@@ -214,12 +196,12 @@
         <expand macro="output_save_matrix_values" />
     </outputs>
     <!--
-    computeMatrix -S test.bw -R test2.bed -a 100 -b 100 -bs 1 
+    computeMatrix -S test.bw -R test2.bed -a 100 -b 100 -bs 1
     -->
     <tests>
         <test>
             <param name="regionsFile" value="computeMatrix1.bed" ftype="bed" />
-            <param name="scoreFile" value="bamCoverage_result4.bw" ftype="bigwig" />
+            <param name="scoreFileName" value="bamCoverage_result4.bw" ftype="bigwig" />
             <param name="showAdvancedOpt" value="yes" />
             <param name="mode_select" value="reference-point" />
             <param name="binSize" value="10" />
@@ -232,7 +214,7 @@
         </test>
         <test>
             <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" />
-            <param name="scoreFile" value="computeMatrix2.bw" ftype="bigwig" />
+            <param name="scoreFileName" value="computeMatrix2.bw" ftype="bigwig" />
             <param name="showAdvancedOpt" value="yes" />
             <param name="mode_select" value="reference-point" />
             <param name="binSize" value="10" />
@@ -242,7 +224,7 @@
         </test>
         <test>
             <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" />
-            <param name="scoreFile" value="computeMatrix2.bw" ftype="bigwig" />
+            <param name="scoreFileName" value="computeMatrix2.bw" ftype="bigwig" />
             <param name="showAdvancedOpt" value="yes" />
             <param name="mode_select" value="scale-regions" />
             <param name="endLabel" value="END" />
@@ -271,7 +253,7 @@
    :alt: Relationship between computeMatrix, heatmapper and profiler
 
 
-You can find more details on the computeMatrix wiki page: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-computeMatrix
+You can find more details on the computeMatrix doc page: https://deeptools.readthedocs.org/en/release-1.6/content/tools/computeMatrix.html
 
 
 -----