Mercurial > repos > ldelisle > revertr2orientationinbam

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author ldelisle
date Wed, 19 Oct 2022 08:34:43 +0000
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1 <tool id="revertR2orientationInBam" name="revertR2orientationInBam" version="0.0.1" profile="16.04">
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2 <description> Revert the mapped orientation of R2 mates in a bam.</description>
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3 <requirements>
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4 <requirement type="package" version="1.9">samtools</requirement>
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5 </requirements>
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6 <stdio>
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7 <!-- Anything other than zero is an error -->
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8 <exit_code range="1:" />
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9 <exit_code range=":-1" />
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10 <!-- In case the return code has not been set propery check stderr too -->
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11 <regex match="Error:" />
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12 <regex match="Exception:" />
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13 </stdio>
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14 <command>
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15 <![CDATA[
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16 bash $__tool_directory__/revertR2orientationInBam.sh $input $output
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17 ]]>
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18 </command>
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19 <inputs>
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20 <!-- note unsorted bam includes all derived bam types (inlcuding bam which is sorted) -->
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21 <param name="input" type="data" format="sam,bam" label="Select a sam or bam file."/>
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22 </inputs>
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23 <outputs>
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24 <data format="bam" name="output" label="$input.name with R2 orientation reversed"/>
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25 </outputs>
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26
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27 <tests>
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28 <test>
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29 <param name="input" value="input.sam"/>
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30 <output name="output" file="output.bam" ftype="bam"/>
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31 </test>
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32 </tests>
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33 <help>
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34 <![CDATA[
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35 This tool is very useful when you have paired-end stranded RNA-seq.
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36 Using this tool prior to a bedtools genome coverage allow to have strand specific coverage using both mates.
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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.
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38 ]]>
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39 </help>
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40 </tool>