Mercurial > repos > iuc > pe_histogram

comparison pe_histogram.xml @ 2:9be99db0304a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram commit 3954cb556516f7154287656f492e2e20e5776fb3
author iuc
date Tue, 11 Jul 2017 14:36:59 -0400
parents b1a427b17e9c
children bd1416eea1f0
comparison
equal deleted inserted replaced
1:b1a427b17e9c 2:9be99db0304a
1 <tool id="pe_histogram" name="Paired-end histogram" version="1.0.1"> 1 <tool id="pe_histogram" name="Paired-end histogram" version="1.0.1">
2 <description>of insert size frequency</description> 2 <description>of insert size frequency</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 <stdio> 6 <command detect_errors="aggressive"><![CDATA[
7 <!-- Anything other than zero is an error --> 7 ln -s '${input_bam}' localbam.bam &&
8 <exit_code range=":-1" /> 8 ln -f -s '${input_bam.metadata.bam_index}' localbam.bam.bai &&
9 <exit_code range="1:" /> 9 java -jar '$__tool_directory__/PEHistogram.jar'
10 <!-- Check stderr in case the return code has not been set --> 10 -B localbam.bam
11 <regex match="Error:" /> 11 -I localbam.bam.bai
12 <regex match="Exception:" /> 12 #if str($lower_limit):
13 </stdio> 13 -l $lower_limit
14 <command> 14 #end if
15 <![CDATA[ 15 #if str($upper_limit):
16 ln -s "${input_bam}" "localbam.bam" && 16 -u $upper_limit
17 ln -f -s "${input_bam.metadata.bam_index}" "localbam.bam.bai" && 17 #end if
18 java -jar $__tool_directory__/PEHistogram.jar 18 -p '$output1'
19 -B "localbam.bam" 19 -t '$output2'
20 -I "localbam.bam.bai" 20 1>/dev/null
21 #if str($lower_limit) != '': 21 ]]></command>
22 -l $lower_limit
23 #end if
24 #if str($upper_limit) != '':
25 -u $upper_limit
26 #end if
27 -p "$output1"
28 -t "$output2" 1>/dev/null
29 ]]>
30 </command>
31 <inputs> 22 <inputs>
32 <param name="input_bam" type="data" format="bam" label="BAM file" /> 23 <param name="input_bam" type="data" format="bam" label="BAM file" />
33 <param name="lower_limit" type="integer" value="" optional="True" min="0" label="Lower bp limit (optional)" help="The lower bp limit on insert size for calculating the histogram."/> 24 <param name="lower_limit" type="integer" value="" optional="True" min="0" label="Lower bp limit (optional)" help="The lower bp limit on insert size for calculating the histogram."/>
34 <param name="upper_limit" type="integer" value="" optional="True" min="0" label="Upper bp limit (optional)" help="The upper bp limit on insert size for calculating the histogram." /> 25 <param name="upper_limit" type="integer" value="" optional="True" min="0" label="Upper bp limit (optional)" help="The upper bp limit on insert size for calculating the histogram." />
35 </inputs> 26 </inputs>