Mercurial > repos > thanhlv > galru
view galru.xml @ 0:685f2f21f160 draft
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author | thanhlv |
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date | Tue, 02 Jun 2020 10:07:09 -0400 |
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children | f435723251c3 |
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<tool id="galru" name="galru" version="@VERSION@"> <description>Long read spoligotyping for Mycobacterium tuberculosis</description> <macros> <token name="@VERSION@">1.0.0</token> </macros> <requirements> <requirement type="package" version="@VERSION@">galru</requirement> </requirements> <version_command>galru --version</version_command> <command detect_errors="exit_code"><![CDATA[ galru --technology $technology #if str($cas_input.cas_select) == "history": --cas_fasta '$cas_input.cas_file' #end if --gene_start_offset $gene_start_offset --min_mapping_quality $min_mapping_quality --qcov_margin $qcov_margin --min_bitscore $min_bitscore --min_identity $min_identity --threads \${GALAXY_SLOTS:-4} $extended $debug $verbose --output_file $output $fastq ]]> </command> <inputs> <param name="fastq" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" label="Uncorrected long reads"/> <conditional name="cas_input"> <param name="cas_select" type="select" label="CAS file"> <option selected="true" value="bundle">Use bundled CAS file</option> <option value="history">Use a fasta file in the history</option> </param> <when value="history"> <param name="cas_file" type="data" format="fasta,fasta.gz" label="Select a CAS file"/> </when> </conditional> <param name="technology" type="select" optional="false" label="Sequencing technology"> <option value="map-ont">map-ont</option> <option value="map-pb">map-pb</option> <option value="ava-ont">ava-ont</option> <option value="ava-pb">ava-pb</option> </param> <param name="extended" argument="--extended_results" type="boolean" truevalue="--extended_results" falsevalue="" checked="false" label="Output extended results" /> <param name="gene_start_offset" argument="--gene_start_offset" type="integer" min="0" value="30" label="Only count CRISPR reads which cover this base"/> <param name="min_mapping_quality" argument="--min_mapping_quality" type="integer" min="0" value="10" label="Minimum mapping quality score"/> <param name="qcov_margin" argument="--qcov_margin" type="integer" min="0" value="100" label="Maximum perc coverage difference between CRISPR and read"/> <param name="min_bitscore" argument="--min_bitscore" type="integer" min="0" value="38" label="Minimum blast bitscore"/> <param name="min_identity" argument="--min_identity" type="integer" min="0" value="95" label="Minimum blast identity"/> <param name="debug" type="boolean" truevalue="--debug" falsevalue="" checked="false" label="Turn on debugging" /> <param name="verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="false" label="Turn on verbose output" /> </inputs> <outputs> <data name="output" format="tabular" label="${tool.name} on ${on_string} Output"/> <data name="log" format="text" label="${tool.name} on ${on_string} Log"> <filter>debug is True</filter> </data> </outputs> <help><![CDATA[ Documentation can be found at `<https://github.com/quadram-institute-bioscience/galru>`_. ]]> </help> <citations> <citation type="doi">10.1101/2020.05.31.126490v1</citation> </citations> </tool>