Mercurial > repos > iuc > colibread_discosnp_rad
comparison discosnp_RAD.xml @ 4:923df36f6592 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
author | iuc |
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date | Thu, 06 May 2021 12:43:46 +0000 |
parents | 2af5a5ca9c87 |
children | 74ed1718ef58 |
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3:2af5a5ca9c87 | 4:923df36f6592 |
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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). |