Mercurial > repos > bgruening > deeptools_compute_matrix

changeset 23:f305afa8ff0d draft

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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3cefc7d64faa53ef9a4e5984c7b275fc47cbdaaf
author bgruening
date Wed, 20 Feb 2019 08:03:23 -0500
parents a2e50c362097
children 167788df3b46
files computeMatrix.xml deepTools_macros.xml test-data/estimateReadFiltering.txt
diffstat 3 files changed, 6 insertions(+), 16 deletions(-) [+]
line wrap: on
line diff
--- a/computeMatrix.xml	Tue Feb 19 10:06:00 2019 -0500
+++ b/computeMatrix.xml	Wed Feb 20 08:03:23 2019 -0500
@@ -24,6 +24,7 @@
             --scoreFileName #echo ' '.join($files)#
 
             --outFileName '$outFileName'
+            --samplesLabel #echo ' '.join($labels)#
 
             @THREADS@
 
@@ -72,9 +73,6 @@
                 #if $advancedOpt.scale is not None and str($advancedOpt.scale) != '':
                     --scale $advancedOpt.scale
                 #end if
-                #if $advancedOpt.samplesLabel is not None and str($advancedOpt.samplesLabel) != '':
-                    --samplesLabel $advancedOpt.samplesLabel
-                #end if
 
                 @ADVANCED_OPTS_GTF@
 
@@ -91,6 +89,7 @@
         </repeat>
 
         <expand macro="multiple_input_bigwigs" MIN="1" LABEL="Score file" TITLE="Score files"/>
+        <expand macro="custom_sample_labels" />
 
         <conditional name="mode" >
             <param name="mode_select" type="select"
@@ -207,15 +206,6 @@
                     bias the average values. (--maxThreshold)"/>
                 <param name="scale" type="float" optional="True" label="Scaling factor"
                     help="If set, all values are multiplied by this number. (--scale)"/>
-                <param argument="--samplesLabel" type="text" size="30"
-                    label="Labels for the samples (each bigwig)"
-                    help="The default is to use the history item label. The sample labels should be separated by
-                    spaces and quoted if a label itself contains a space E.g. label-1 &quot;label 2&quot;">
-                    <sanitizer>
-                        <valid initial="string.printable">
-                        </valid>
-                    </sanitizer>
-                </param>
 
                 <expand macro="gtf_options" />
 
--- a/deepTools_macros.xml	Tue Feb 19 10:06:00 2019 -0500
+++ b/deepTools_macros.xml	Wed Feb 20 08:03:23 2019 -0500
@@ -512,7 +512,7 @@
 
     <token name="@multiple_input_bigwigs@">
 <![CDATA[
-        #if $custom_labels_conditional.custom_labels_select == "Yes":
+        #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
             #set custom_labels=labels
         #end if
         #set files=[]
@@ -533,7 +533,7 @@
                 #silent $labels.append("'%s'" % $identifier)
             #end for
         #end if
-        #if $custom_labels_conditional.custom_labels_select == "Yes":
+        #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
             #set labels=custom_labels
         #end if
 ]]>
--- a/test-data/estimateReadFiltering.txt	Tue Feb 19 10:06:00 2019 -0500
+++ b/test-data/estimateReadFiltering.txt	Wed Feb 20 08:03:23 2019 -0500
@@ -1,3 +1,3 @@
 Sample	Total Reads	Mapped Reads	Alignments in blacklisted regions	Estimated mapped reads filtered	Below MAPQ	Missing Flags	Excluded Flags	Internally-determined Duplicates	Marked Duplicates	Singletons	Wrong strand
-paired_chr2L.bam	12644	12589	0	1395.9	4149.0	0.0	0.0	0.0	0.0	55.0	0.0
-paired_chr2L.bam	12644	12589	0	1395.9	4149.0	0.0	0.0	0.0	0.0	55.0	0.0
+paired_chr2L.bam	12644	12589	0	4192.0	4149.0	0.0	0.0	0.0	0.0	55.0	0.0
+paired_chr2L.bam	12644	12589	0	4192.0	4149.0	0.0	0.0	0.0	0.0	55.0	0.0