Mercurial > repos > mvdbeek > bam_readtagger
diff normalize_readsizes.xml @ 70:f383ca1c5033 draft
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
author | mvdbeek |
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date | Tue, 05 Nov 2019 05:06:18 -0500 |
parents | |
children | b090e190c813 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/normalize_readsizes.xml Tue Nov 05 05:06:18 2019 -0500 @@ -0,0 +1,45 @@ +<tool id="normalize_readsizes" name="Normalize readsizes" version="0.5.17"> + <description>of multiple fastq files</description> + <requirements> + <requirement type="package" version="0.5.17">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>