Mercurial > repos > iuc > tag_pileup_frequency

comparison tag_pileup_frequency.xml @ 2:6432735cdb22 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit ae67f98d61e74e241a6d51378f53a3d5c00967ce
author iuc
date Fri, 16 Jun 2017 14:13:32 -0400
parents b7d7ae3963aa
children 580e8bcb6413
comparison
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1:b7d7ae3963aa 2:6432735cdb22
1 <tool id="tag_pileup_frequency" name="Tag pileup frequency" version="1.0.1"> 1 <tool id="tag_pileup_frequency" name="Tag pileup frequency" version="1.0.1">
2 <description></description> 2 <description></description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="8.0.112">openjdk</requirement> 4 <requirement type="package" version="8.0.112">openjdk</requirement>
5 </requirements> 5 </requirements>
6 <command> 6 <command detect_errors="exit_code"><![CDATA[
7 <![CDATA[ 7 mkdir -p output &&
8 mkdir -p output && 8 ln -f -s '${input1.metadata.bam_index}' '${input1}.bai' &&
9 ln -f -s "${input1.metadata.bam_index}" "${input1}.bai" && 9 java -jar '$__tool_directory__/TagPileup.jar'
10 java -jar $__tool_directory__/TagPileup.jar 10 -b '$input1'
11 -b "$input1" 11 -i '${input1}.bai'
12 -i "${input1}.bai" 12 -c '$input2'
13 -c "$input2" 13 -s $tag_shift
14 -s $tag_shift 14 -n $bin_size
15 -n $bin_size 15 -e $tags_equal
16 -e $tags_equal 16 -r $reads
17 -r $reads 17 -p $proper_pe
18 -p $proper_pe 18 -a $combine_strands
19 -a $combine_strands 19 -t "\${GALAXY_SLOTS:-4}"
20 -t "\${GALAXY_SLOTS:-4}" 20 -w $composite_smoothing_window
21 -w $composite_smoothing_window 21 -m true
22 -m "true" 22 -x '$output1'
23 -x "$output1" 23 -h $output_heatmap
24 -h $output_heatmap 24 #if str($output_heatmap) == "true":
25 #if str($output_heatmap) == "true": 25 -o output
26 -o output 26 #end if
27 #end if 27 1>/dev/null
28 1>/dev/null 28 ]]></command>
29 ]]>
30 </command>
31 <inputs> 29 <inputs>
32 <param name="input1" type="data" format="bam" label="BAM file" /> 30 <param name="input1" type="data" format="bam" label="BAM file" />
33 <param name="input2" type="data" format="bed" label="Bed file" /> 31 <param name="input2" type="data" format="bed" label="Bed file" />
34 <param name="tag_shift" type="integer" value="0" min="0" label="5' to 3' Tag Shift (bp)" /> 32 <param name="tag_shift" type="integer" value="0" min="0" label="5' to 3' Tag Shift (bp)" />
35 <param name="bin_size" type="integer" value="1" min="1" label="Bin Size (bp)" /> 33 <param name="bin_size" type="integer" value="1" min="1" label="Bin Size (bp)" />