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

Changeset 6:8e41fe2f3661 (2016-04-24)
Previous changeset 5:eb48e332a41f (2016-03-18) Next changeset 7:d5d57b40b29a (2016-05-13)
Commit message:
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 43d23f495200449aec91a41fd537603014aa93ba-dirty
modified:
bamCompare.xml
deepTools_macros.xml
test-data/plotCoverage_result1.tabular
test-data/plotFingerprint_result2.tabular
added:
test-data/bowtie2 test1.bam
removed:
test-data/bowtie2-test1.bam
b
diff -r eb48e332a41f -r 8e41fe2f3661 bamCompare.xml
--- a/bamCompare.xml Fri Mar 18 08:50:37 2016 -0400
+++ b/bamCompare.xml Sun Apr 24 17:18:27 2016 -0400
b
@@ -173,8 +173,8 @@
     </outputs>
     <tests>
         <test>
-            <param name="bamFile1" value="bowtie2-test1.bam" ftype="bam" />
-            <param name="bamFile2" value="bowtie2-test1.bam" ftype="bam" />
+            <param name="bamFile1" value="bowtie2 test1.bam" ftype="bam" />
+            <param name="bamFile2" value="bowtie2 test1.bam" ftype="bam" />
             <param name="showAdvancedOpt" value="no" />
             <param name="outFileFormat" value="bigwig" />
             <param name="outFileFormat" value="bedgraph" />
@@ -183,8 +183,8 @@
             <output name="outFileName" file="bamCompare_result1.bg" ftype="bedgraph" />
         </test>
         <test>
-            <param name="bamFile1" value="bowtie2-test1.bam" ftype="bam" />
-            <param name="bamFile2" value="bowtie2-test1.bam" ftype="bam" />
+            <param name="bamFile1" value="bowtie2 test1.bam" ftype="bam" />
+            <param name="bamFile2" value="bowtie2 test1.bam" ftype="bam" />
             <param name="showAdvancedOpt" value="yes" />
             <param name="outFileFormat" value="bigwig" />
             <param name="outFileFormat" value="bigwig" />
b
diff -r eb48e332a41f -r 8e41fe2f3661 deepTools_macros.xml
--- a/deepTools_macros.xml Fri Mar 18 08:50:37 2016 -0400
+++ b/deepTools_macros.xml Sun Apr 24 17:18:27 2016 -0400
b
@@ -68,16 +68,22 @@
     <xml name="region_limit_operation">
         <param argument="--region" type="text" value=""
             label="Region of the genome to limit the operation to"
-            help="This is useful when testing parameters to reduce the time required. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;." />
+            help="This is useful when testing parameters to reduce the time required. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;.">
+            <sanitizer>
+                <valid initial="string.letters,string.digits">
+                    <add value="|"/>
+                 </valid>
+            </sanitizer>
+        </param>
     </xml>
 
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@WRAPPER_VERSION@">2.2.2</token>
+    <token name="@WRAPPER_VERSION@">2.2.3</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="2.7.10">python</requirement>
             <requirement type="binary">@BINARY@</requirement>
-            <requirement type="package" version="2.2.2">deepTools</requirement>
+            <requirement type="package" version="2.2.3">deepTools</requirement>
             <yield />
         </requirements>
         <expand macro="stdio" />
@@ -302,7 +308,7 @@
     </token>
     <xml name="citations">
         <citations>
-            <citation type="doi">10.1093/nar/gku365</citation>
+            <citation type="doi">10.1093/nar/gkw257</citation>
             <yield />
         </citations>
     </xml>
b
diff -r eb48e332a41f -r 8e41fe2f3661 test-data/bowtie2 test1.bam
b
Binary file test-data/bowtie2 test1.bam has changed
b
diff -r eb48e332a41f -r 8e41fe2f3661 test-data/bowtie2-test1.bam
b
Binary file test-data/bowtie2-test1.bam has changed
b
diff -r eb48e332a41f -r 8e41fe2f3661 test-data/plotCoverage_result1.tabular
--- a/test-data/plotCoverage_result1.tabular Fri Mar 18 08:50:37 2016 -0400
+++ b/test-data/plotCoverage_result1.tabular Sun Apr 24 17:18:27 2016 -0400
b
@@ -1,4 +1,4 @@
-#'chr' 'start' 'end' 'bowtie2-test1.bam' 'bowtie2-test1.bam'
+#'chr' 'start' 'end' 'bowtie2 test1.bam' 'bowtie2 test1.bam'
 chrM 0 1 23.0 23.0
 chrM 1 2 35.0 35.0
 chrM 2 3 35.0 35.0
b
diff -r eb48e332a41f -r 8e41fe2f3661 test-data/plotFingerprint_result2.tabular
--- a/test-data/plotFingerprint_result2.tabular Fri Mar 18 08:50:37 2016 -0400
+++ b/test-data/plotFingerprint_result2.tabular Sun Apr 24 17:18:27 2016 -0400
b
@@ -1,4 +1,4 @@
-'bowtie2-test1.bam' 'bowtie2-test1.bam'
+'bowtie2 test1.bam' 'bowtie2 test1.bam'
 68 68
 65 65
 61 61