Mercurial > repos > iuc > colibread_discosnp_rad

comparison discosnp_RAD.xml @ 5:74ed1718ef58 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 747394d19e88a569a5154615e366ea0401c820dd
author iuc
date Sat, 05 Oct 2024 19:55:43 +0000
parents 923df36f6592
children
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4:923df36f6592 5:74ed1718ef58
1 <tool id="discosnp_rad" name="DiscoSnpRAD" version="@DISCOSNP_VERSION@+galaxy0" profile="@PROFILE@"> 1 <tool id="discosnp_rad" name="DiscoSnpRAD" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
2 <description>discovering polymorphism from raw unassembled RADSeq NGS reads.</description> 2 <description>discovering polymorphism from raw unassembled RADSeq NGS reads.</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">2.5.4</token>
4 <import>macros.xml</import> 5 <import>macros.xml</import>
5 </macros> 6 </macros>
6 <expand macro="discosnp_requirements" /> 7 <expand macro="discosnp_requirements" />
7 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
8 #if str($input_type_options.input_type) == "single" 9 #if str($input_type_options.input_type) == "single"
41 <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"/> 42 <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"/>
42 <param argument="--min_rank" type="float" label="Remove variants whose rank is smaller than this threshold" value="0.4"/> 43 <param argument="--min_rank" type="float" label="Remove variants whose rank is smaller than this threshold" value="0.4"/>
43 <expand macro="discosnp_options" /> 44 <expand macro="discosnp_options" />
44 </inputs> 45 </inputs>
45 <outputs> 46 <outputs>
46 <data name="vcf" from_work_dir="discoRad_*_clustered.vcf" format="vcf" label="VCF with ${tool.name} on $on_string"/> 47 <data name="vcf" from_work_dir="discoRad_*_clustered.vcf" format="vcf" label="${tool.name} on ${on_string}: VCF"/>
47 <data name="fasta" from_work_dir="discoRad_*_raw.fa" format="fasta" label="Fasta with ${tool.name} on $on_string"/> 48 <data name="fasta" from_work_dir="discoRad_*_raw.fa" format="fasta" label="${tool.name} on ${on_string}: FASTA"/>
48 </outputs> 49 </outputs>
49 <tests> 50 <tests>
50 <test> 51 <test>
51 <conditional name="input_type_options"> 52 <conditional name="input_type_options">
52 <param name="input_type" value="single"/> 53 <param name="input_type" value="single"/>
53 <param name="list_reads" value="discosnpRAD/loci_reads.gz" ftype="fasta.gz" /> 54 <param name="list_reads" value="discosnpRAD/loci_reads.gz" ftype="fasta.gz" />
54 </conditional> 55 </conditional>
55 <param name="D" value="0"/> 56 <param name="D" value="0"/>
56 <param name="P" value="4"/> 57 <param name="P" value="4"/>
57 <param name="k" value="31"/> 58 <param name="k" value="31"/>
58 <param name="b" value="2"/>
59 <param name="max_size_cluster" value="50"/> 59 <param name="max_size_cluster" value="50"/>
60 <param name="max_missing" value="0.95"/> 60 <param name="max_missing" value="0.95"/>
61 <param name="min_rank" value="0.0"/> 61 <param name="min_rank" value="0.0"/>
62 <output name="fasta" file="discosnpRAD/fasta.fa"/> 62 <output name="fasta" file="discosnpRAD/fasta.fa"/>
63 <output name="vcf"> 63 <output name="vcf">