Mercurial > repos > iuc > ivar_trim
view ivar_trim.xml @ 1:d37ede8589b2 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 27fa363aa1289366fd0e888709d022357533e4de"
author | iuc |
---|---|
date | Sat, 04 Apr 2020 12:37:43 -0400 |
parents | 8858fa037a15 |
children | cb903c9dc33d |
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<tool id="ivar_trim" name="ivar trim" version="@VERSION@+galaxy0"> <description>Trim reads in aligned BAM</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <expand macro="version_command" /> <command detect_errors="exit_code"><![CDATA[ ln -s '$input_bed' bed.bed && ln -s '$input_bam' sorted.bam && ivar trim -i sorted.bam -b bed.bed -m $min_len -q $min_qual -s $window_width $inc_primers -p trimmed && samtools sort -@ \${GALAXY_SLOTS:-1} -o trimmed.sorted.bam trimmed.bam && samtools index -@ \${GALAXY_SLOTS:-1} trimmed.sorted.bam ]]> </command> <inputs> <param name="input_bam" argument="-i" type="data" format="bam" label="Bam file" help="Aligned reads, to trim primers and quality"/> <param name="input_bed" argument="-b" type="data" format="bed" label="BED file with primer sequences and positions"/> <param name="min_len" argument="-m" type="integer" min="0" value="30" label="Minimum length of read to retain after trimming"/> <param name="min_qual" argument="-q" type="integer" min="0" value="20" label="Minimum quality threshold for sliding window to pass"/> <param name="window_width" argument="-s" type="integer" min="0" value="4" label="Width of sliding window"/> <param name="inc_primers" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="false" label="Include reads with no primers"/> </inputs> <outputs> <data name="output_bam" format="bam" label="${tool.name} on ${on_string} Trimmed bam" from_work_dir="trimmed.sorted.bam"/> </outputs> <tests> <!-- #1: SARS-Cov data--> <test> <param name="input_bam" value="covid19/PC00101P_sub.sorted.bam" /> <param name="input_bed" value="covid19/ARTIC-V1.bed" /> <param name="inc_primers" value="true" /> <output name="output_bam" file="covid19/PC00101P_sub.sorted.bam" compare="sim_size" delta="300000"/> </test> <!-- #1: Zika data--> <test> <param name="input_bam" value="zika/Z52_a.sorted.bam" /> <param name="input_bed" value="zika/db/zika_primers.bed" /> <output name="output_bam" file="zika/Z52_a.trimmed.sorted.bam" compare="sim_size" delta="100000"/> </test> <test> <param name="input_bam" value="zika/Z52_b.sorted.bam" /> <param name="input_bed" value="zika/db/zika_primers.bed" /> <output name="output_bam" file="zika/Z52_b.trimmed.sorted.bam" compare="sim_size" delta="100000"/> </test> </tests> <help><![CDATA[ iVar uses primer positions supplied in a BED file to soft clip primer sequences from an aligned and sorted BAM file. Following this, the reads are trimmed based on a quality threshold(Default: 20). To do the quality trimming, iVar uses a sliding window approach(Default: 4). The windows slides from the 5' end to the 3' end and if at any point the average base quality in the window falls below the threshold, the remaining read is soft clipped. If after trimming, the length of the read is greater than the minimum length specified(Default: 30), the read is written to the new trimmed BAM file Documentation can be found at `<https://andersen-lab.github.io/ivar/html/manualpage.html>`_. ]]> </help> <expand macro="citations" /> </tool>