Mercurial > repos > thanhlv > biotradis
view biotradis_remove_tags.xml @ 11:47269fae5647 draft default tip
"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 4d5e56c87ec94e7853b88a4d0a6f20e411640885-dirty"
author | thanhlv |
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date | Fri, 17 Jan 2020 12:47:22 -0500 |
parents | 09c1f97a5bcc |
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<tool id="remove_tradis_tags" name="remove tradis tags" version="@VERSION@"> <description>Removes transposon sequence and quality tags from the read strings</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ remove_tradis_tags -f $input_bam -t $tag -m $mismatches -o removed -v > $log ]]> </command> <inputs> <param name="input_fastq" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="Fastq file"/> <param name="tag" type="text" label="Tags to remove" /> <param name="mismatches" type="integer" min="0" value ="0" label="Number of mismatches to allow when matching tag" /> </inputs> <outputs> <data name="log" format="txt" label="${tool.name} on ${on_string}: Log"/> <data name="filtered_tags" format="fastqsanger" label="${tool.name} on ${on_string}" from_work_dir="removed.rmtag.fatsq" /> </outputs> <tests> </tests> <help><![CDATA[ Adds transposon sequence and quality tags to the read strings and outputs a BAM. Usage: add_tags -b file.bam [options] Options: -b : bam file with tradis tags -v : verbose debugging output ]]> </help> <expand macro="citations" /> </tool>