Mercurial > repos > lldelisle > revertr2orientationinbam

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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
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21ddefab2e4f planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit 49a42d0e75d6ae7faa3ce399524157c35546fbaa
lldelisle
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1 <tool id="revertR2orientationInBam" name="revertR2orientationInBam" version="0.0.2" profile="16.04">
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05aa21d39189 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit fe9813fe41ba241b47f7b2b4e4c9672ef35c0b35-dirty
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2 <description> Revert the mapped orientation of R2 mates in a bam.</description>
05aa21d39189 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit fe9813fe41ba241b47f7b2b4e4c9672ef35c0b35-dirty
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3 <requirements>
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21ddefab2e4f planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit 49a42d0e75d6ae7faa3ce399524157c35546fbaa
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4 <requirement type="package" version="1.16.1">samtools</requirement>
21ddefab2e4f planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit 49a42d0e75d6ae7faa3ce399524157c35546fbaa
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5 <requirement type="package" version="5.1.0">gawk</requirement>
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05aa21d39189 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit fe9813fe41ba241b47f7b2b4e4c9672ef35c0b35-dirty
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6 </requirements>
05aa21d39189 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit fe9813fe41ba241b47f7b2b4e4c9672ef35c0b35-dirty
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7 <stdio>
05aa21d39189 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit fe9813fe41ba241b47f7b2b4e4c9672ef35c0b35-dirty
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8 <!-- Anything other than zero is an error -->
05aa21d39189 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit fe9813fe41ba241b47f7b2b4e4c9672ef35c0b35-dirty
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9 <exit_code range="1:" />
05aa21d39189 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit fe9813fe41ba241b47f7b2b4e4c9672ef35c0b35-dirty
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10 <exit_code range=":-1" />
05aa21d39189 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit fe9813fe41ba241b47f7b2b4e4c9672ef35c0b35-dirty
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11 <!-- In case the return code has not been set propery check stderr too -->
05aa21d39189 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit fe9813fe41ba241b47f7b2b4e4c9672ef35c0b35-dirty
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12 <regex match="Error:" />
05aa21d39189 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit fe9813fe41ba241b47f7b2b4e4c9672ef35c0b35-dirty
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13 <regex match="Exception:" />
05aa21d39189 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit fe9813fe41ba241b47f7b2b4e4c9672ef35c0b35-dirty
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14 </stdio>
05aa21d39189 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit fe9813fe41ba241b47f7b2b4e4c9672ef35c0b35-dirty
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15 <command>
05aa21d39189 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit fe9813fe41ba241b47f7b2b4e4c9672ef35c0b35-dirty
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16 <![CDATA[
1
21ddefab2e4f planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit 49a42d0e75d6ae7faa3ce399524157c35546fbaa
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17 set -o pipefail;
21ddefab2e4f planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit 49a42d0e75d6ae7faa3ce399524157c35546fbaa
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18 bash $__tool_directory__/revertR2orientationInBam.sh '$input' '$output'
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05aa21d39189 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit fe9813fe41ba241b47f7b2b4e4c9672ef35c0b35-dirty
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19 ]]>
05aa21d39189 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit fe9813fe41ba241b47f7b2b4e4c9672ef35c0b35-dirty
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20 </command>
05aa21d39189 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit fe9813fe41ba241b47f7b2b4e4c9672ef35c0b35-dirty
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21 <inputs>
05aa21d39189 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit fe9813fe41ba241b47f7b2b4e4c9672ef35c0b35-dirty
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22 <!-- note unsorted bam includes all derived bam types (inlcuding bam which is sorted) -->
05aa21d39189 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit fe9813fe41ba241b47f7b2b4e4c9672ef35c0b35-dirty
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23 <param name="input" type="data" format="sam,bam" label="Select a sam or bam file."/>
05aa21d39189 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit fe9813fe41ba241b47f7b2b4e4c9672ef35c0b35-dirty
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24 </inputs>
05aa21d39189 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit fe9813fe41ba241b47f7b2b4e4c9672ef35c0b35-dirty
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25 <outputs>
05aa21d39189 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit fe9813fe41ba241b47f7b2b4e4c9672ef35c0b35-dirty
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26 <data format="bam" name="output" label="$input.name with R2 orientation reversed"/>
05aa21d39189 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit fe9813fe41ba241b47f7b2b4e4c9672ef35c0b35-dirty
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27 </outputs>
05aa21d39189 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit fe9813fe41ba241b47f7b2b4e4c9672ef35c0b35-dirty
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28
05aa21d39189 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit fe9813fe41ba241b47f7b2b4e4c9672ef35c0b35-dirty
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29 <tests>
05aa21d39189 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit fe9813fe41ba241b47f7b2b4e4c9672ef35c0b35-dirty
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30 <test>
05aa21d39189 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit fe9813fe41ba241b47f7b2b4e4c9672ef35c0b35-dirty
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31 <param name="input" value="input.sam"/>
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21ddefab2e4f planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit 49a42d0e75d6ae7faa3ce399524157c35546fbaa
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32 <output name="output" file="output.bam" ftype="bam" lines_diff="2"/>
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05aa21d39189 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit fe9813fe41ba241b47f7b2b4e4c9672ef35c0b35-dirty
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33 </test>
05aa21d39189 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit fe9813fe41ba241b47f7b2b4e4c9672ef35c0b35-dirty
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34 </tests>
05aa21d39189 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit fe9813fe41ba241b47f7b2b4e4c9672ef35c0b35-dirty
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35 <help>
05aa21d39189 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit fe9813fe41ba241b47f7b2b4e4c9672ef35c0b35-dirty
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36 <![CDATA[
05aa21d39189 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit fe9813fe41ba241b47f7b2b4e4c9672ef35c0b35-dirty
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37 This tool is very useful when you have paired-end stranded RNA-seq.
05aa21d39189 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit fe9813fe41ba241b47f7b2b4e4c9672ef35c0b35-dirty
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38 Using this tool prior to a bedtools genome coverage allow to have strand specific coverage using both mates.
05aa21d39189 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit fe9813fe41ba241b47f7b2b4e4c9672ef35c0b35-dirty
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39 It uses samtools to convert input to sam format and then awk to modify the flag "reverse strand" for the second mate of pairs.
05aa21d39189 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit fe9813fe41ba241b47f7b2b4e4c9672ef35c0b35-dirty
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40 ]]>
05aa21d39189 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit fe9813fe41ba241b47f7b2b4e4c9672ef35c0b35-dirty
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41 </help>
05aa21d39189 planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit fe9813fe41ba241b47f7b2b4e4c9672ef35c0b35-dirty
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42 </tool>