# HG changeset patch
# User iuc
# Date 1575664336 0
# Node ID 527363a5d90e00b28f9ce54c40e8990bb7f843c8
# Parent  c0d955e9afd5414aa4592a4e88dbac96d8905f8f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 92a9933fda38241c033dad1f709a928f66756b6f"

diff -r c0d955e9afd5 -r 527363a5d90e tag_pileup_frequency.xml
--- a/tag_pileup_frequency.xml	Fri Jun 16 14:13:17 2017 -0400
+++ b/tag_pileup_frequency.xml	Fri Dec 06 20:32:16 2019 +0000
@@ -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 c0d955e9afd5 -r 527363a5d90e test-data/output1.tabular
--- a/test-data/output1.tabular	Fri Jun 16 14:13:17 2017 -0400
+++ b/test-data/output1.tabular	Fri Dec 06 20:32:16 2019 +0000
@@ -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