Mercurial > repos > lldelisle > revertr2orientationinbam

comparison revertR2orientationInBam.xml @ 1:21ddefab2e4f draft default tip

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planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit 49a42d0e75d6ae7faa3ce399524157c35546fbaa
author lldelisle
date Thu, 20 Oct 2022 10:51:18 +0000
parents 05aa21d39189
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0:05aa21d39189 1:21ddefab2e4f
1 <tool id="revertR2orientationInBam" name="revertR2orientationInBam" version="0.0.1" profile="16.04"> 1 <tool id="revertR2orientationInBam" name="revertR2orientationInBam" version="0.0.2" profile="16.04">
2 <description> Revert the mapped orientation of R2 mates in a bam.</description> 2 <description> Revert the mapped orientation of R2 mates in a bam.</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.9">samtools</requirement> 4 <requirement type="package" version="1.16.1">samtools</requirement>
5 <requirement type="package" version="5.1.0">gawk</requirement>
5 </requirements> 6 </requirements>
6 <stdio> 7 <stdio>
7 <!-- Anything other than zero is an error --> 8 <!-- Anything other than zero is an error -->
8 <exit_code range="1:" /> 9 <exit_code range="1:" />
9 <exit_code range=":-1" /> 10 <exit_code range=":-1" />
11 <regex match="Error:" /> 12 <regex match="Error:" />
12 <regex match="Exception:" /> 13 <regex match="Exception:" />
13 </stdio> 14 </stdio>
14 <command> 15 <command>
15 <![CDATA[ 16 <![CDATA[
16 bash $__tool_directory__/revertR2orientationInBam.sh $input $output 17 set -o pipefail;
18 bash $__tool_directory__/revertR2orientationInBam.sh '$input' '$output'
17 ]]> 19 ]]>
18 </command> 20 </command>
19 <inputs> 21 <inputs>
20 <!-- note unsorted bam includes all derived bam types (inlcuding bam which is sorted) --> 22 <!-- note unsorted bam includes all derived bam types (inlcuding bam which is sorted) -->
21 <param name="input" type="data" format="sam,bam" label="Select a sam or bam file."/> 23 <param name="input" type="data" format="sam,bam" label="Select a sam or bam file."/>
25 </outputs> 27 </outputs>
26 28
27 <tests> 29 <tests>
28 <test> 30 <test>
29 <param name="input" value="input.sam"/> 31 <param name="input" value="input.sam"/>
30 <output name="output" file="output.bam" ftype="bam"/> 32 <output name="output" file="output.bam" ftype="bam" lines_diff="2"/>
31 </test> 33 </test>
32 </tests> 34 </tests>
33 <help> 35 <help>
34 <![CDATA[ 36 <![CDATA[
35 This tool is very useful when you have paired-end stranded RNA-seq. 37 This tool is very useful when you have paired-end stranded RNA-seq.