Mercurial > repos > lldelisle > revertr2orientationinbam
comparison revertR2orientationInBam.xml @ 0:05aa21d39189 draft
planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit fe9813fe41ba241b47f7b2b4e4c9672ef35c0b35-dirty
| author | lldelisle |
|---|---|
| date | Wed, 19 Oct 2022 08:50:18 +0000 |
| parents | |
| children | 21ddefab2e4f |
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| -1:000000000000 | 0:05aa21d39189 |
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| 1 <tool id="revertR2orientationInBam" name="revertR2orientationInBam" version="0.0.1" profile="16.04"> | |
| 2 <description> Revert the mapped orientation of R2 mates in a bam.</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.9">samtools</requirement> | |
| 5 </requirements> | |
| 6 <stdio> | |
| 7 <!-- Anything other than zero is an error --> | |
| 8 <exit_code range="1:" /> | |
| 9 <exit_code range=":-1" /> | |
| 10 <!-- In case the return code has not been set propery check stderr too --> | |
| 11 <regex match="Error:" /> | |
| 12 <regex match="Exception:" /> | |
| 13 </stdio> | |
| 14 <command> | |
| 15 <![CDATA[ | |
| 16 bash $__tool_directory__/revertR2orientationInBam.sh $input $output | |
| 17 ]]> | |
| 18 </command> | |
| 19 <inputs> | |
| 20 <!-- note unsorted bam includes all derived bam types (inlcuding bam which is sorted) --> | |
| 21 <param name="input" type="data" format="sam,bam" label="Select a sam or bam file."/> | |
| 22 </inputs> | |
| 23 <outputs> | |
| 24 <data format="bam" name="output" label="$input.name with R2 orientation reversed"/> | |
| 25 </outputs> | |
| 26 | |
| 27 <tests> | |
| 28 <test> | |
| 29 <param name="input" value="input.sam"/> | |
| 30 <output name="output" file="output.bam" ftype="bam"/> | |
| 31 </test> | |
| 32 </tests> | |
| 33 <help> | |
| 34 <![CDATA[ | |
| 35 This tool is very useful when you have paired-end stranded RNA-seq. | |
| 36 Using this tool prior to a bedtools genome coverage allow to have strand specific coverage using both mates. | |
| 37 It uses samtools to convert input to sam format and then awk to modify the flag "reverse strand" for the second mate of pairs. | |
| 38 ]]> | |
| 39 </help> | |
| 40 </tool> |