# HG changeset patch
# User iuc
# Date 1575664359 18000
# Node ID 580e8bcb6413e0fd4b8b84442ee6fbf7ab118bf0
# Parent  6432735cdb22a5ff594854c299fd8104de35b3a6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 92a9933fda38241c033dad1f709a928f66756b6f"

diff -r 6432735cdb22 -r 580e8bcb6413 tag_pileup_frequency.xml
--- 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>
diff -r 6432735cdb22 -r 580e8bcb6413 test-data/output1.tabular
--- a/test-data/output1.tabular	Fri Jun 16 14:13:32 2017 -0400
+++ b/test-data/output1.tabular	Fri Dec 06 15:32:39 2019 -0500
@@ -1,3 +1,3 @@
 	-28.0	-27.0	-26.0	-25.0	-24.0	-23.0	-22.0	-21.0	-20.0	-19.0	-18.0	-17.0	-16.0	-15.0	-14.0	-13.0	-12.0	-11.0	-10.0	-9.0	-8.0	-7.0	-6.0	-5.0	-4.0	-3.0	-2.0	-1.0	0.0	1.0	2.0	3.0	4.0	5.0	6.0	7.0	8.0	9.0	10.0	11.0	12.0	13.0	14.0	15.0	16.0	17.0	18.0	19.0	20.0	21.0	22.0	23.0	24.0	25.0	26.0	27.0	28.0	29.0	30.0
-dataset_2_dataset_1_read1_sense.tabular	0.3170731707317073	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.024390243902439025	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
-dataset_2_dataset_1_read1_anti.tabular	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.024390243902439025	0.0	0.0
+tabular	0.3170731707317073	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.024390243902439025	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
+.tabular	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.024390243902439025	0.0	0.0