Mercurial > repos > thanhlv > galru
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galru.xml Tue Jun 02 10:07:09 2020 -0400 @@ -0,0 +1,70 @@ +<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>