# HG changeset patch
# User bgruening
# Date 1450443606 18000
# Node ID 66947f20a9a830fd1b2ee65c0e8885d2b499f3ca
# Parent af2607db5c8994cc317d67ebc3580beac8277873
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427
diff -r af2607db5c89 -r 66947f20a9a8 bamCoverage.xml
--- a/bamCoverage.xml Wed Dec 16 16:37:45 2015 -0500
+++ b/bamCoverage.xml Fri Dec 18 08:00:06 2015 -0500
@@ -41,7 +41,7 @@
#end if
@ADVANCED_OPTS_READ_PROCESSING@
- $advancedOpt.keepNAs
+ $advancedOpt.skipNAs
if str($advancedOpt.ignoreForNormalization).strip() != '':
--ignoreForNormalization $advancedOpt.ignoreForNormalization
@@ -98,7 +98,7 @@
considering samples with unequal coverage across
chromosomes like male samples. Example: chrX chrM" />
- <expand macro="keepNAs" />
+ <expand macro="skipNAs" />
<expand macro="read_processing_options" />
<param argument="--MNase" type="boolean" truevalue="--MNase" falsevalue=""
diff -r af2607db5c89 -r 66947f20a9a8 deepTools_macros.xml
--- a/deepTools_macros.xml Wed Dec 16 16:37:45 2015 -0500
+++ b/deepTools_macros.xml Fri Dec 18 08:00:06 2015 -0500
@@ -61,36 +61,6 @@
</when>
</conditional>
-<!--
- $mode.advancedOpt.includeZeros
-
-
- #if $plotTitle and str($plotTitle).strip() != "":
- - -plotTitle '$plotTitle'
- #end if
-
-
--->
-
- <xml name="bigwigCorrelate_mode_actions">
- <expand macro="region_limit_operation" />
-
- <conditional name="advancedOpt">
- <param name="showAdvancedOpt" type="select" label="Show advanced options" >
- <option value="no" selected="true">no</option>
- <option value="yes">yes</option>
- </param>
- <when value="no" />
- <when value="yes">
- <expand macro="includeZeros" />
- <expand macro="zMin_zMax" />
- <expand macro="colorMap" />
- <expand macro="plotTitle" />
- <expand macro="plotNumbers" />
- </when>
- </conditional>
- </xml>
-
<xml name="includeZeros">
<param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
label="Include zeros"
@@ -111,7 +81,7 @@
</xml>
<token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
- <token name="@WRAPPER_VERSION@">1.5.11</token>
+ <token name="@WRAPPER_VERSION@">2.0.0</token>
<xml name="requirements">
<requirements>
<requirement type="package" version="2.7.10">python</requirement>
@@ -418,13 +388,17 @@
</param>
</xml>
- <xml name="keepNAs">
- <param argument="--keepNAs" type="boolean" truevalue="--keepNAs" falsevalue="" checked="False"
- label="Treat missing data as zero"
- help="If set, missing data (NAs) will be treated as zeros.
- The default is to ignore missing data and not included
- in the output file. Missing data is defined as those
- bins for which no overlapping reads are found." />
+ <xml name="skipNAs">
+ <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False"
+ label="Ignore missing data?"
+ help="This parameter determines if non-covered regions
+ (regions without overlapping reads) in a bam/bigWig file
+ should be skipped. The default is to treat those
+ regions as having a value of zero. The decision to
+ skip non-covered regions depends on the interpretation
+ of the data. Non-covered regions may represent for
+ example repetitive regions that want to be skipped.
+ (default: False)" />
</xml>
<xml name="input_save_matrix_values">