Mercurial > repos > iuc > ivar_trim
view ivar_trim.xml @ 3:5d6ed46cc101 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 47276c84cd0cd40084b7ccdf2e22c620ee1c10f6"
author | iuc |
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date | Fri, 05 Jun 2020 04:12:52 -0400 |
parents | cb903c9dc33d |
children | db536ad45f28 |
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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[ #if $primer.source == "history" ln -s '$primer.input_bed' bed.bed && #else ln -s '$primer.cached_bed.fields.path' bed.bed && #end if ln -s '$input_bam' sorted.bam && ivar trim -i sorted.bam -b bed.bed -m $min_len -q $min_qual -s $window_width $inc_primers -p trimmed && samtools sort -@ \${GALAXY_SLOTS:-1} -o trimmed.sorted.bam trimmed.bam ]]> </command> <inputs> <param name="input_bam" argument="-i" type="data" format="bam" label="Bam file" help="Aligned reads, to trim primers and quality"/> <conditional name="primer"> <param label="Source of primer information" name="source" type="select"> <option value="history" selected="true">History</option> <option value="cached">Built-in</option> </param> <when value="history"> <param name="input_bed" argument="-b" type="data" format="bed" label="BED file with primer sequences and positions"/> </when> <when value="cached"> <param name="cached_bed" type="select" label="Primer scheme name" help="Select primer scheme bed file from a list"> <options from_data_table="primer_scheme_bedfiles"> <filter type="sort_by" column="1" /> <validator type="no_options" message="No primer schemes are available" /> </options> </param> </when> </conditional> <param name="min_len" argument="-m" type="integer" min="0" value="30" label="Minimum length of read to retain after trimming"/> <param name="min_qual" argument="-q" type="integer" min="0" value="20" label="Minimum quality threshold for sliding window to pass"/> <param name="window_width" argument="-s" type="integer" min="0" value="4" label="Width of sliding window"/> <param name="inc_primers" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="false" label="Include reads with no primers"/> </inputs> <outputs> <data name="output_bam" format="bam" label="${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> <conditional name="primer"> <param name="source" value="history" /> <param name="input_bed" value="zika/db/zika_primers.bed" /> </conditional> <param name="input_bam" value="zika/Z52_a.sorted.bam" /> <output name="output_bam" file="zika/Z52_a.trimmed.sorted.bam" compare="sim_size" delta="100000"/> </test> <test> <conditional name="primer"> <param name="source" value="history" /> <param name="input_bed" value="zika/db/zika_primers.bed" /> </conditional> <param name="input_bam" value="zika/Z52_b.sorted.bam" /> <output name="output_bam" file="zika/Z52_b.trimmed.sorted.bam" compare="sim_size" delta="100000"/> </test> <test> <conditional name="primer"> <param name="source" value="cached" /> <param name="cached_bed" value="SARS-CoV-2-ARTICv1" /> </conditional> <param name="input_bam" value="sars-cov-2/sars_cov2_untrimmed.bam" ftype="bam" /> <output name="output_bam" file="sars-cov-2/sars_cov2_trimmed.bam" /> </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>