Mercurial > repos > thanhlv > biotradis
diff biotradis_remove_tags.xml @ 0:afe9a515d145 draft
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
author | thanhlv |
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date | Thu, 25 Jul 2019 06:03:12 -0400 |
parents | |
children | 09c1f97a5bcc |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/biotradis_remove_tags.xml Thu Jul 25 06:03:12 2019 -0400 @@ -0,0 +1,36 @@ +<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_tags -f $input_bam -t $tag -m $mismatches -o removed -v > $log + + ]]></command> + <inputs> + <param name="input_fastq" type="data" format="fastq" label="Fastq file" help="" /> + <param name="tag" type="text" label="Tags to remove" help="" /> + <param name="mismatches" type="integer" value ="0" label="Number of mismatches to allow when matching tag" help="(optional. default = 0)" /> + </inputs> + + <outputs> + <data name="log" format="txt" label="${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> + +</tool>