Mercurial > repos > iuc > colibread_discosnp_rad

comparison discosnp_RAD.xml @ 4:923df36f6592 draft

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"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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3:2af5a5ca9c87 4:923df36f6592
1 <?xml version='1.0' encoding='utf-8'?> 1 <tool id="discosnp_rad" name="DiscoSnpRAD" version="@DISCOSNP_VERSION@+galaxy0" profile="@PROFILE@">
2 <tool profile="16.04" id="discosnp_rad" name="DiscoSnpRAD" version="@DISCOSNP_VERSION@">
3 <description>discovering polymorphism from raw unassembled RADSeq NGS reads.</description> 2 <description>discovering polymorphism from raw unassembled RADSeq NGS reads.</description>
4 <macros> 3 <macros>
5 <import>macros.xml</import> 4 <import>macros.xml</import>
6 </macros> 5 </macros>
7 <expand macro="discosnp_requirements" /> 6 <expand macro="discosnp_requirements" />
8 <command><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
9 ## simple option 8 #if str($input_type_options.input_type) == "single"
10 #if str( $input_type_options.input_type) == "single" 9 @discosnp_single_for@
11 @discosnp_single_reads@ 10 @single_reads@
12 ## paired option 11 @discosnp_single_end_for@
13 #else if str( $input_type_options.input_type) == "paired" 12 #else if str($input_type_options.input_type) == "paired"
14 @discosnp_paired_reads@ 13 @discosnp_paired_for@
15 ## mix option 14 @paired_reads@
15 @discosnp_paired_end_for@
16 #else 16 #else
17 @discosnp_single_reads@ 17 @discosnp_single_for@
18 @discosnp_paired_reads@ 18 @single_reads@
19 @discosnp_single_end_for@
20 @discosnp_paired_for@
21 @paired_reads@
22 @discosnp_paired_end_for@
19 #end if 23 #end if
20
21 ## get the absolute path for short_reads_connector
22 CONNECTOR_PATH=`which short_read_connector.sh` && 24 CONNECTOR_PATH=`which short_read_connector.sh` &&
23 CONNECTOR_DIR=`dirname \$CONNECTOR_PATH` && 25 CONNECTOR_DIR=`dirname \$CONNECTOR_PATH` &&
24
25 run_discoSnpRad.sh 26 run_discoSnpRad.sh
26 @discosnp_inputs@ 27 @discosnp_inputs@
27 -S "\$CONNECTOR_DIR" 28 -S "\$CONNECTOR_DIR"
28 --max_size_cluster ${max_size_cluster} 29 --max_size_cluster ${max_size_cluster}
29 -a ${a} 30 -a ${a}
30 ${high_precision} 31 ${high_precision}
31 --max_missing ${max_missing} 32 --max_missing ${max_missing}
32 --min_rank ${min_rank} 33 --min_rank ${min_rank}
33
34 --max_threads \${GALAXY_SLOTS:-1} 34 --max_threads \${GALAXY_SLOTS:-1}
35
36 ]]></command> 35 ]]></command>
37
38 <inputs> 36 <inputs>
39
40 <expand macro="discosnp_inputs" /> 37 <expand macro="discosnp_inputs" />
41
42 <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)." /> 38 <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)." />
43
44 <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"/> 39 <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"/>
45
46 <param argument="--max_size_cluster" type="integer" label="Discards cluster of variants containing more than this number of variants." value="150"/> 40 <param argument="--max_size_cluster" type="integer" label="Discards cluster of variants containing more than this number of variants." value="150"/>
47
48 <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"/> 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"/>
49
50 <param argument="--min_rank" type="float" label="Remove variants whose rank is smaller than this threshold" value="0.4"/> 42 <param argument="--min_rank" type="float" label="Remove variants whose rank is smaller than this threshold" value="0.4"/>
51
52 <expand macro="discosnp_options" /> 43 <expand macro="discosnp_options" />
53
54 </inputs> 44 </inputs>
55
56 <outputs> 45 <outputs>
57 <data name="vcf" from_work_dir="discoRad_*_clustered.vcf" format="vcf" label="VCF with ${tool.name} on $on_string"/> 46 <data name="vcf" from_work_dir="discoRad_*_clustered.vcf" format="vcf" label="VCF with ${tool.name} on $on_string"/>
58 <data name="fasta" from_work_dir="discoRad_*_raw.fa" format="fasta" label="Fasta with ${tool.name} on $on_string"/> 47 <data name="fasta" from_work_dir="discoRad_*_raw.fa" format="fasta" label="Fasta with ${tool.name} on $on_string"/>
59 </outputs> 48 </outputs>
60
61 <tests> 49 <tests>
62 <test> 50 <test>
63 <conditional name="input_type_options"> 51 <conditional name="input_type_options">
64 <param name="input_type" value="single"/> 52 <param name="input_type" value="single"/>
65 <param name="list_reads" value="discosnpRAD/loci_reads" ftype="fasta" /> 53 <param name="list_reads" value="discosnpRAD/loci_reads.gz" ftype="fasta.gz" />
66 </conditional> 54 </conditional>
67 <param name="D" value="0"/> 55 <param name="D" value="0"/>
68 <param name="P" value="4"/> 56 <param name="P" value="4"/>
69 <param name="k" value="31"/> 57 <param name="k" value="31"/>
70 <param name="b" value="2"/> 58 <param name="b" value="2"/>
84 <has_text text="--max_missing 0.95"/> 72 <has_text text="--max_missing 0.95"/>
85 <has_text text="--min_rank 0.0"/> 73 <has_text text="--min_rank 0.0"/>
86 </assert_command> 74 </assert_command>
87 </test> 75 </test>
88 </tests> 76 </tests>
89
90 <help><![CDATA[ 77 <help><![CDATA[
91 78
92 **Description** 79 **Description**
93 80
94 Software discoSnp is designed for discovering Single Nucleotide Polymorphism (SNP) from raw set(s) of reads obtained with Next Generation Sequencers (NGS). 81 Software discoSnp is designed for discovering Single Nucleotide Polymorphism (SNP) from raw set(s) of reads obtained with Next Generation Sequencers (NGS).