diff tag_pileup_frequency.xml @ 3:580e8bcb6413 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 92a9933fda38241c033dad1f709a928f66756b6f"

--- a/tag_pileup_frequency.xml	Fri Jun 16 14:13:32 2017 -0400
+++ b/tag_pileup_frequency.xml	Fri Dec 06 15:32:39 2019 -0500
@@ -1,15 +1,20 @@
-<tool id="tag_pileup_frequency" name="Tag pileup frequency" version="1.0.1">
+<tool id="tag_pileup_frequency" name="Tag pileup frequency" version="1.0.2">
     <description></description>
     <requirements>
-        <requirement type="package" version="8.0.112">openjdk</requirement>
+        <requirement type="package" version="11.0.1">openjdk</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
+#import re
+#set input1_identifier = re.sub('[^\s\w\-]', '_', str($input1.element_identifier))
+#set input2_identifier = re.sub('[^\s\w\-]', '_', str($input2.element_identifier))
 mkdir -p output &&
-ln -f -s '${input1.metadata.bam_index}' '${input1}.bai' &&
+ln -s '${input1}' '${input1_identifier}' &&
+ln -s '${input2}' '${input2_identifier}' &&
+ln -s '${input1.metadata.bam_index}' '${input1_identifier}.bai' &&
 java -jar '$__tool_directory__/TagPileup.jar'
--b '$input1'
--i '${input1}.bai'
--c '$input2'
+-b '${input1_identifier}'
+-i '${input1_identifier}.bai'
+-c '$input2_identifier'
 -s $tag_shift
 -n $bin_size
 -e $tags_equal
@@ -33,13 +38,13 @@
         <param name="bin_size" type="integer" value="1" min="1" label="Bin Size (bp)" />
         <param  name="tags_equal" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set Tags to be equal?" />
         <param  name="reads" type="select" label="Reads to examine" help="Selecting combined requires paired-end BAM input">
-            <option value="0" selected="True">Read1</option>
+            <option value="0" selected="true">Read1</option>
             <option value="1">Read2</option>
             <option value="2">combined</option>
         </param>
         <param  name="proper_pe" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Require proper PE?" help="Requires paired-end BAM input"/>
         <param  name="combine_strands" type="select" label="Combine strands?">
-            <option value="0" selected="True">No</option>
+            <option value="0" selected="true">No</option>
             <option value="1">Yes</option>
         </param>
         <param name="composite_smoothing_window" type="integer" value="0" min="0" label="Composite smoothing window (bp)" />
@@ -64,10 +69,10 @@
             <param name="combine_strands" value="0" />
             <param name="composite_smoothing_window" value="0" />
             <param name="output_heatmap" value="true" />
-            <output name="output1" file="output1.tabular" ftype="tabular"/>
+            <output name="output1" file="output1.tabular" ftype="tabular" compare="contains"/>
             <output_collection name="heatmaps" type="list">
-                <element name="dataset_2_dataset_1_read1_anti.tabular" file="input2_input1_read1_anti.tabular" ftype="tabular" compare="contains"/>
-                <element name="dataset_2_dataset_1_read1_sense.tabular" file="input2_input1_read1_sense.tabular" ftype="tabular" compare="contains"/>
+                <element name="input_bed_input_bam_read1_anti.tabular" file="input2_input1_read1_anti.tabular" ftype="tabular" compare="contains"/>
+                <element name="input_bed_input_bam_read1_sense.tabular" file="input2_input1_read1_sense.tabular" ftype="tabular" compare="contains"/>
             </output_collection>
         </test>
     </tests>