Commit db64b323 authored by Mariam's avatar Mariam

Added the rest of the steps in the reporter module to the galaxy tool

parent 068275ae
<tool id="snvphyl_reporter" name="Snvphyl Reporter" version="1.1">
<description>Runs Snvphyl reporter</description>
<requirements>
<requirement type="package" version="1.3.7">snvphyl</requirement>
<requirement type="package" version="1.3.5">snvphyl</requirement>
</requirements>
<command interpreter="perl">
/\$VCF2PSEUDO/reporter.pl --step bam_quality_data --output $output
#for $f in $input.keys#
--bam "$f=$input[$f]"
#end for
/\$VCF2PSEUDO/reporter.pl --output $output
#if $job_type.type == "bam_quality"
--step bam_quality_data
#if $job_type.json
--json $job_type.json
#end if
#for $f in $job_type.input.keys#
--bam "$f=$job_type.input[$f]"
#end for
#else if $job_type.type == "filter_stats"
#if $job_type.json
--json $job_type.json
#end if
--step record_filter_stats
--pseudo $job_type.pseudo
#else if $job_type.type == "reference_info"
#if $job_type.json
--json $job_type.json
#end if
--step record_reference_info
--ref-file $job_type.ref_file
--ref-sequencer $job_type.sequencer --ref-source $job_type.source
--plasmids $job_type.plasmid --genus $job_type.genus
--species $job_type.species --serotype $job_type.serotype
#else if $job_type.type == "file_sizes"
#if $job_type.json
--json $job_type.json
#end if
--step record_file_sizes
--file-type $job_type.format
#for $f in $job_type.sizes.keys#
--file-sizes "$f=$job_type.sizes[$f]"
#end for
#else if $job_type.type == "run_parameters"
#if $job_type.json
--json $job_type.json
#end if
--step record_run_parameters
--masked-positions $job_type.masked
--run-id $job_type.run_id
--freebayes-params '$job_type.freebayes'
--min-coverage $job_type.min_cov
--max-coverage $job_type.max_cov
--processors $job_type.processors
--smalt-index '$job_type.smalt_index'
--smalt-map '$job_type.smalt_map'
--trim-clean '$job_type.trim_clean'
--vcf2core-cpus $job_type.core_cpus
#for $f in $job_type.fastqs.keys#
--read-file "$f=$job_type.fastqs[$f]"
#end for
#end if
</command>
<inputs>
<param name="input" type="data_collection" lable="Bam files Collection" help="Please enter a list collection of bam files" optional="false" collection_type="list" />
<conditional name="job_type">
<param name="type" type="select" label="Job Type">
<option value="bam_quality">Bam Quality Data</option>
<option value="filter_stats">Record Filter Stats</option>
<option value="reference_info">Record Reference Info</option>
<option value="file_sizes">Record File Sizes</option>
<option value="run_parameters">Record Run Parameters</option>
</param>
<when value="bam_quality">
<param name="json" type="data" label="JSON File (optional)" help="The JSON file containing reporter data for the run." optional="true" />
<param name="input" type="data_collection" label="Bam files Collection" help="Please enter a list collection of bam files" optional="false" collection_type="list" />
</when>
<when value="filter_stats">
<param name="json" type="data" label="JSON File (optional)" help="The JSON file containing reporter data for the run." optional="true" />
<param name="pseudo" type="data" format="txt" label="Pseudoalign positions file" help="Please enter the psuedoalign-positions.tsv file" optional="false" />
</when>
<when value="reference_info">
<param name="json" type="data" label="JSON File (optional)" help="The JSON file containing reporter data for the run." optional="true" />
<param name="ref_file" type="data" format="fasta" label="Reference fasta file" optional="false" />
<param name="sequencer" type="text" label="Sequencer type" help="The type of sequencer used to generate the reference reads." optional="true" />
<param name="source" type="text" label="Source" help="The lab/site/team that the reference sequence was retrieved from." optional="true" />
<param name="plasmid" type="boolean" label="Plasmid present" help="Are plasmids present int the reference sequence?" truevalue="yes" falsevalue="no" />
<param name="genus" type="text" label="Genus" help="The genus of the reference orgamism." optional="true" />
<param name="species" type="text" label="Species" help="The species of the reference organism." optional="true" />
<param name="serotype" type="text" label="Serotype" help="The serotype of the reference orgamism." optional="true" />
</when>
<when value="file_sizes">
<param name="json" type="data" label="JSON File (optional)" help="The JSON file containing reporter data for the run." optional="true" />
<param name="format" type="text" label="File Format" help="The file format of the input files." optional="false" />
<param name="sizes" type="data_collection" label="Files Collection" help="The list of files to be analyzed." optional="false" collection_type="list" />
</when>
<when value="run_parameters">
<param name="json" type="data" label="JSON File (optional)" help="The JSON file containing reporter data for the run." optional="true" />
<param name="fastqs" type="data_collection" label="Fastq Files Collection" help="The list of fastq files to be analyzed." optional="false" collection_type="list" />
<param name="masked" type="data" format="txt" label="Masked Positions File" optional="true"/>
<param name="run_id" type="text" label="Run ID" optional="true" />
<param name="freebayes" type="text" label="Freebays parameters" help="The freebayes parameters string" optional="true" />
<param name="min_cov" type="integer" value="15" label="Minimum coverage" optional="true" />
<param name="max_cov" type="integer" value="200" label="Maximum coverage" optional="true" />
<param name="processors" type="integer" value="1" label="Processors" help="The number of processors used for parallelization" />
<param name="smalt_index" type="text" label="Smalt Index" help="The parameter string for smalt_index." optional="true" />
<param name="smalt_map" type="text" label="Smalt Map" help="The parameter string for smalt_map." optional="true" />
<param name="trim_clean" type="text" label="Trim Clean" help="The parameter string for trim_clean." optional="true" />
<param name="core_cpus" type="integer" value="1" label="VCF2Core CPUs" help="The number of CPUs used for vcf2core stage." optional="true" />
</when>
</conditional>
</inputs>
<outputs>
......
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