Mercurial > repos > iuc > colibread_discosnp_rad
diff discosnp_RAD.xml @ 4:923df36f6592 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
author | iuc |
---|---|
date | Thu, 06 May 2021 12:43:46 +0000 |
parents | 2af5a5ca9c87 |
children | 74ed1718ef58 |
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--- a/discosnp_RAD.xml Mon Aug 17 10:37:37 2020 -0400 +++ b/discosnp_RAD.xml Thu May 06 12:43:46 2021 +0000 @@ -1,27 +1,28 @@ -<?xml version='1.0' encoding='utf-8'?> -<tool profile="16.04" id="discosnp_rad" name="DiscoSnpRAD" version="@DISCOSNP_VERSION@"> +<tool id="discosnp_rad" name="DiscoSnpRAD" version="@DISCOSNP_VERSION@+galaxy0" profile="@PROFILE@"> <description>discovering polymorphism from raw unassembled RADSeq NGS reads.</description> <macros> <import>macros.xml</import> </macros> <expand macro="discosnp_requirements" /> - <command><![CDATA[ - ## simple option - #if str( $input_type_options.input_type) == "single" - @discosnp_single_reads@ - ## paired option - #else if str( $input_type_options.input_type) == "paired" - @discosnp_paired_reads@ - ## mix option + <command detect_errors="exit_code"><![CDATA[ + #if str($input_type_options.input_type) == "single" + @discosnp_single_for@ + @single_reads@ + @discosnp_single_end_for@ + #else if str($input_type_options.input_type) == "paired" + @discosnp_paired_for@ + @paired_reads@ + @discosnp_paired_end_for@ #else - @discosnp_single_reads@ - @discosnp_paired_reads@ + @discosnp_single_for@ + @single_reads@ + @discosnp_single_end_for@ + @discosnp_paired_for@ + @paired_reads@ + @discosnp_paired_end_for@ #end if - - ## get the absolute path for short_reads_connector CONNECTOR_PATH=`which short_read_connector.sh` && CONNECTOR_DIR=`dirname \$CONNECTOR_PATH` && - run_discoSnpRad.sh @discosnp_inputs@ -S "\$CONNECTOR_DIR" @@ -30,39 +31,26 @@ ${high_precision} --max_missing ${max_missing} --min_rank ${min_rank} - --max_threads \${GALAXY_SLOTS:-1} - ]]></command> - <inputs> - <expand macro="discosnp_inputs" /> - <param argument="--high_precision" type="boolean" checked="false" truevalue="--high_precision" falsevalue="" label="Lower recall / higher precision mode." help="With this parameter no symmetrical crossroads may be traversed during bubble detection (by default up to 5 symmetrical crossroads may be traversed during bubble detection)." /> - <param argument="-a" type="integer" label="Maximal size of ambiguity of INDELs" value="20" help="INDELS whose ambiguity is higher than this value are not output"/> - <param argument="--max_size_cluster" type="integer" label="Discards cluster of variants containing more than this number of variants." value="150"/> - <param argument="--max_missing" type="float" label="Remove variants with more than this proportion of missing values" value="0.95" help="Default 0.95, removes variants detected in 5% and less populations"/> - <param argument="--min_rank" type="float" label="Remove variants whose rank is smaller than this threshold" value="0.4"/> - <expand macro="discosnp_options" /> - </inputs> - <outputs> <data name="vcf" from_work_dir="discoRad_*_clustered.vcf" format="vcf" label="VCF with ${tool.name} on $on_string"/> <data name="fasta" from_work_dir="discoRad_*_raw.fa" format="fasta" label="Fasta with ${tool.name} on $on_string"/> </outputs> - <tests> <test> <conditional name="input_type_options"> <param name="input_type" value="single"/> - <param name="list_reads" value="discosnpRAD/loci_reads" ftype="fasta" /> + <param name="list_reads" value="discosnpRAD/loci_reads.gz" ftype="fasta.gz" /> </conditional> <param name="D" value="0"/> <param name="P" value="4"/> @@ -86,7 +74,6 @@ </assert_command> </test> </tests> - <help><![CDATA[ **Description**