Repository 'deeptools_plot_coverage'
hg clone https://toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage

Changeset 28:9368fbc49c8b (2023-06-01)
Previous changeset 27:7fda5607e777 (2022-02-11) Next changeset 29:231994413f89 (2023-09-27)
Commit message:
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 810c1359b884661d3f5c7372be0f0f88c859a3b9
modified:
deepTools_macros.xml
plotCoverage.xml
test-data/multiBigwigSummary_result1.npz
added:
test-data/bigwigAverage2.bw
test-data/multiBigwigSummary_result2.npz
test-data/multiBigwigSummary_result2.tabular
test-data/test_compated.bw
test-data/test_half.bw
b
diff -r 7fda5607e777 -r 9368fbc49c8b deepTools_macros.xml
--- a/deepTools_macros.xml Fri Feb 11 15:16:22 2022 +0000
+++ b/deepTools_macros.xml Thu Jun 01 14:39:07 2023 +0000
[
@@ -1,10 +1,11 @@
 <macros>
 
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@WRAPPER_VERSION@">3.5.1.0</token>
+    <token name="@TOOL_VERSION@">3.5.2</token>
+    <token name="@GALAXY_VERSION@">20.01</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="3.5.1">deeptools</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">deeptools</requirement>
             <requirement type="package" version="1.9">samtools</requirement>
         </requirements>
         <expand macro="stdio" />
@@ -368,7 +369,6 @@
     <xml name="pseudocount">
         <param argument="--pseudocount" type="text" value="1 1" label="Pseudocount" help="Small number to avoid dividing by zero. You can specify separate values for the pseudocount added to the numerator and denominator by providing two values separated by a space."/>
     </xml>
-
     <token name="@REFERENCES@">
 
 .. class:: infomark
@@ -483,7 +483,7 @@
     <token name="@multiple_input_bams@">
 <![CDATA[
         #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
-            #set custom_labels=labels
+            #set custom_labels=$custom_sample_labels_conditional.labels
         #end if
         #set files=[]
         #set labels=[]
@@ -498,7 +498,7 @@
                     ln -s '${bamfile.metadata.cram_index}' './${counter}.bam.crai' &&
                 #end if
                 #silent $files.append("'%s.bam'" % $counter)
-                #silent $labels.append("'%s'" % identifier)
+                #silent $labels.append("'%s'" % $identifier)
             #end for
         #else:
             #for $counter, $f in enumerate($multibam_conditional.multibam_repeats):
@@ -522,7 +522,7 @@
     <token name="@multiple_input_bigwigs@">
 <![CDATA[
         #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
-            #set custom_labels=labels
+            #set custom_labels=$custom_sample_labels_conditional.labels
         #end if
         #set files=[]
         #set labels=[]
b
diff -r 7fda5607e777 -r 9368fbc49c8b plotCoverage.xml
--- a/plotCoverage.xml Fri Feb 11 15:16:22 2022 +0000
+++ b/plotCoverage.xml Thu Jun 01 14:39:07 2023 +0000
b
@@ -1,4 +1,4 @@
-<tool id="deeptools_plot_coverage" name="plotCoverage" version="@WRAPPER_VERSION@.0" profile="18.01">
+<tool id="deeptools_plot_coverage" name="plotCoverage" version="@TOOL_VERSION@+galaxy0" profile="@GALAXY_VERSION@">
     <description>assesses the sequencing depth of BAM/CRAM files </description>
     <macros>
         <token name="@BINARY@">plotCoverage</token>
b
diff -r 7fda5607e777 -r 9368fbc49c8b test-data/bigwigAverage2.bw
b
Binary file test-data/bigwigAverage2.bw has changed
b
diff -r 7fda5607e777 -r 9368fbc49c8b test-data/multiBigwigSummary_result1.npz
b
Binary file test-data/multiBigwigSummary_result1.npz has changed
b
diff -r 7fda5607e777 -r 9368fbc49c8b test-data/multiBigwigSummary_result2.npz
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiBigwigSummary_result2.npz Thu Jun 01 14:39:07 2023 +0000
b
@@ -0,0 +1,121 @@
+#'chr' 'start' 'end' 'sample1' 'sample2'
+ch1 0 10 0.0 0.0
+ch1 10 20 0.0 0.0
+ch1 20 30 0.0 0.0
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+ch3 150 160 1.0 1.0
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+ch3 170 180 0.5 0.5
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+ch3 290 300 0.0 0.0
+ch3 300 310 0.0 0.0
+ch3 310 320 0.0 0.0
+ch3 320 330 0.0 0.0
+ch3 330 340 0.0 0.0
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+ch3 360 370 0.0 0.0
+ch3 370 380 0.0 0.0
+ch3 380 390 0.0 0.0
+ch3 390 400 0.0 0.0
b
diff -r 7fda5607e777 -r 9368fbc49c8b test-data/multiBigwigSummary_result2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiBigwigSummary_result2.tabular Thu Jun 01 14:39:07 2023 +0000
b
@@ -0,0 +1,121 @@
+#'chr' 'start' 'end' 'sample1' 'sample2'
+ch1 0 10 0.0 0.0
+ch1 10 20 0.0 0.0
+ch1 20 30 0.0 0.0
+ch1 30 40 0.0 0.0
+ch1 40 50 0.0 0.0
+ch1 50 60 0.0 0.0
+ch1 60 70 0.0 0.0
+ch1 70 80 0.0 0.0
+ch1 80 90 0.0 0.0
+ch1 90 100 0.0 0.0
+ch1 100 110 2.0 2.0
+ch1 110 120 2.0 2.0
+ch1 120 130 1.0 1.0
+ch1 130 140 0.0 0.0
+ch1 140 150 0.0 0.0
+ch1 150 160 0.0 0.0
+ch1 160 170 0.0 0.0
+ch1 170 180 0.0 0.0
+ch1 180 190 0.0 0.0
+ch1 190 200 0.0 0.0
+ch1 200 210 0.0 0.0
+ch1 210 220 0.0 0.0
+ch1 220 230 0.0 0.0
+ch1 230 240 0.0 0.0
+ch1 240 250 0.0 0.0
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+ch2 0 10 0.0 0.0
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+ch2 20 30 0.0 0.0
+ch2 30 40 0.0 0.0
+ch2 40 50 0.0 0.0
+ch2 50 60 3.0 3.0
+ch2 60 70 3.0 3.0
+ch2 70 80 1.5 1.5
+ch2 80 90 0.0 0.0
+ch2 90 100 0.0 0.0
+ch2 100 110 0.0 0.0
+ch2 110 120 0.0 0.0
+ch2 120 130 0.0 0.0
+ch2 130 140 0.0 0.0
+ch2 140 150 0.0 0.0
+ch2 150 160 1.0 1.0
+ch2 160 170 1.0 1.0
+ch2 170 180 0.5 0.5
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+ch2 190 200 0.0 0.0
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+ch2 320 330 0.0 0.0
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+ch2 360 370 0.0 0.0
+ch2 370 380 0.0 0.0
+ch2 380 390 0.0 0.0
+ch2 390 400 0.0 0.0
+ch3 0 10 0.0 0.0
+ch3 10 20 0.0 0.0
+ch3 20 30 0.0 0.0
+ch3 30 40 0.0 0.0
+ch3 40 50 0.0 0.0
+ch3 50 60 3.0 3.0
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+ch3 70 80 1.5 1.5
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b
diff -r 7fda5607e777 -r 9368fbc49c8b test-data/test_compated.bw
b
Binary file test-data/test_compated.bw has changed
b
diff -r 7fda5607e777 -r 9368fbc49c8b test-data/test_half.bw
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Binary file test-data/test_half.bw has changed