Mercurial > repos > mvdbeek > bam_readtagger
comparison normalize_readsizes.xml @ 70:f383ca1c5033 draft
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
| author | mvdbeek |
|---|---|
| date | Tue, 05 Nov 2019 05:06:18 -0500 |
| parents | |
| children | b090e190c813 |
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| 69:97411db5f752 | 70:f383ca1c5033 |
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| 1 <tool id="normalize_readsizes" name="Normalize readsizes" version="0.5.17"> | |
| 2 <description>of multiple fastq files</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="0.5.17">readtagger</requirement> | |
| 5 </requirements> | |
| 6 <version_command>normalize_readsizes --version</version_command> | |
| 7 <command detect_errors="aggressive"><![CDATA[ | |
| 8 #for $i, $element in enumerate($input): | |
| 9 ln -fs '$element' '${i}.${element.ext}' && | |
| 10 #end for | |
| 11 normalize_readsizes | |
| 12 #for $i, $element in enumerate($input): | |
| 13 -i '${i}.${element.ext}' | |
| 14 -o '${i}.out.${element.ext}' | |
| 15 #end for | |
| 16 #for $i, $element in enumerate($output): | |
| 17 && mv '${i}.out.${element.ext}' '$element' | |
| 18 #end for | |
| 19 ]]></command> | |
| 20 <inputs> | |
| 21 <param name="input" type="data_collection" collection_type="list" label="Select collection of fastq datasets to normalize" format="fastqsanger,fastqsanger.gz"/> | |
| 22 </inputs> | |
| 23 <outputs> | |
| 24 <collection name="output" type="list" structured_like="input" inherit_format="true"/> | |
| 25 </outputs> | |
| 26 <tests> | |
| 27 <test> | |
| 28 <param name="input"> | |
| 29 <collection type="list"> | |
| 30 <element name="a" value="long_reads_a.fastq" /> | |
| 31 <element name="b" value="long_reads_b.fastq" /> | |
| 32 </collection> | |
| 33 </param> | |
| 34 <param name="insert_reference" value="transposon"/> | |
| 35 <output_collection name="output"> | |
| 36 <element name="a" value="long_reads_a_normalized.fastq" ftype="fastqsanger"/> | |
| 37 <element name="b" value="long_reads_b_normalized.fastq" ftype="fastqsanger"/> | |
| 38 </output_collection> | |
| 39 </test> | |
| 40 </tests> | |
| 41 <help><![CDATA[ | |
| 42 Normalizes read size distributions across a collection of fastq files so that the read size distribution is the same | |
| 43 across all datasets. | |
| 44 ]]></help> | |
| 45 </tool> |