Mercurial > repos > mvdbeek > bam_readtagger
view normalize_readsizes.xml @ 81:a446ab055307 draft default tip
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1abb25638cbf5e86c70b59de6453c7c045c2364f"
author | mvdbeek |
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date | Sun, 26 Apr 2020 07:59:19 -0400 |
parents | c42dd2551c9c |
children |
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<tool id="normalize_readsizes" name="Normalize readsizes" version="0.5.25"> <description>of multiple fastq files</description> <requirements> <requirement type="package" version="0.5.25">readtagger</requirement> </requirements> <version_command>normalize_readsizes --version</version_command> <command detect_errors="aggressive"><![CDATA[ #for $i, $element in enumerate($input): ln -fs '$element' '${i}.${element.ext}' && #end for normalize_readsizes #for $i, $element in enumerate($input): -i '${i}.${element.ext}' -o '${i}.out.${element.ext}' #end for #for $i, $element in enumerate($output): && mv '${i}.out.${element.ext}' '$element' #end for ]]></command> <inputs> <param name="input" type="data_collection" collection_type="list" label="Select collection of fastq datasets to normalize" format="fastqsanger,fastqsanger.gz"/> </inputs> <outputs> <collection name="output" type="list" structured_like="input" inherit_format="true"/> </outputs> <tests> <test> <param name="input"> <collection type="list"> <element name="a" value="long_reads_a.fastq" /> <element name="b" value="long_reads_b.fastq" /> </collection> </param> <param name="insert_reference" value="transposon"/> <output_collection name="output"> <element name="a" value="long_reads_a_normalized.fastq" ftype="fastqsanger"/> <element name="b" value="long_reads_b_normalized.fastq" ftype="fastqsanger"/> </output_collection> </test> </tests> <help><![CDATA[ Normalizes read size distributions across a collection of fastq files so that the read size distribution is the same across all datasets. ]]></help> </tool>