Mercurial > repos > mvdbeek > bam_readtagger
view add_matesequence.xml @ 61:210427d5c65a draft
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9f56650c365197dbf3bc1f32a0f4edffd92d488d"
author | mvdbeek |
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date | Sat, 31 Aug 2019 07:19:00 -0400 |
parents | 01acf62d5012 |
children | 16eba798cbc6 |
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<tool id="add_matesequence" name="Add matesequence" version="0.5.8"> <description>into tag field</description> <requirements> <requirement type="package" version="0.5.8">readtagger</requirement> </requirements> <version_command>add_matesequence --version</version_command> <command detect_errors="aggressive"><![CDATA[ add_matesequence --target '$file_to_annotate' --source '$annotate_source' --output_path '$output' ]]></command> <inputs> <param name="file_to_annotate" argument="--file_to_annotate" label="Annotate reads in this file with their mate sequence" type="data" format="bam"/> <param name="annotate_source" argument="--annotate_source" label="Use this file to find the mate sequence (can be same file as file_to_annotate)" type="data" format="bam"/> <param name="mate_sequence_tag" type="text" value="MS"/> </inputs> <outputs> <data name="output" format="bam" label="Add matesequence on $on_string"/> </outputs> <tests> <test> <param name="file_to_annotate" value="dm6.bam" ftype="bam"/> <param name="annotate_source" value="dm6.bam" ftype="bam"/> <output name="output" file="dm6_mate_annotated.bam" ftype="bam" lines_diff="2"/> </test> </tests> <help><![CDATA[ .. code-block:: usage: add_matesequence [-h] -a FILE_TO_ANNOTATE -s ANNOTATE_SOURE -o OUTPUT_PATH [--version] Annotate reads with Mate Sequence in tag field optional arguments: -h, --help show this help message and exit -a FILE_TO_ANNOTATE, --file_to_annotate FILE_TO_ANNOTATE Annotate reads in this file with their mate sequence -s ANNOTATE_SOURE, --annotate_soure ANNOTATE_SOURE Use this file to find the mate sequence (can be same file as file_to_annotate) -o OUTPUT_PATH, --output_path OUTPUT_PATH Write resulting BAM file to this path --version show program's version number and exit ]]></help> </tool>