| Previous changeset 22:a2e50c362097 (2019-02-19) Next changeset 24:167788df3b46 (2019-04-02) |
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Commit message:
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3cefc7d64faa53ef9a4e5984c7b275fc47cbdaaf |
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modified:
computeMatrix.xml deepTools_macros.xml test-data/estimateReadFiltering.txt |
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| diff -r a2e50c362097 -r f305afa8ff0d computeMatrix.xml --- a/computeMatrix.xml Tue Feb 19 10:06:00 2019 -0500 +++ b/computeMatrix.xml Wed Feb 20 08:03:23 2019 -0500 |
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| @@ -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 "label 2""> - <sanitizer> - <valid initial="string.printable"> - </valid> - </sanitizer> - </param> <expand macro="gtf_options" /> |
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| diff -r a2e50c362097 -r f305afa8ff0d deepTools_macros.xml --- a/deepTools_macros.xml Tue Feb 19 10:06:00 2019 -0500 +++ b/deepTools_macros.xml Wed Feb 20 08:03:23 2019 -0500 |
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| @@ -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 ]]> |
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| diff -r a2e50c362097 -r f305afa8ff0d test-data/estimateReadFiltering.txt --- 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 |
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| @@ -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 |