Mercurial > repos > iuc > colibread_discosnp_rad

comparison discosnp_RAD.xml @ 3:2af5a5ca9c87 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 0ed02865f048ad7471ea79509c0e23162bc29166"
author iuc
date Mon, 17 Aug 2020 10:37:37 -0400
parents 9ee3bf979757
children 923df36f6592
comparison
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2:9ee3bf979757 3:2af5a5ca9c87
23 CONNECTOR_DIR=`dirname \$CONNECTOR_PATH` && 23 CONNECTOR_DIR=`dirname \$CONNECTOR_PATH` &&
24 24
25 run_discoSnpRad.sh 25 run_discoSnpRad.sh
26 @discosnp_inputs@ 26 @discosnp_inputs@
27 -S "\$CONNECTOR_DIR" 27 -S "\$CONNECTOR_DIR"
28 --max_size_cluster ${max_size_cluster}
28 -a ${a} 29 -a ${a}
30 ${high_precision}
31 --max_missing ${max_missing}
32 --min_rank ${min_rank}
33
34 --max_threads \${GALAXY_SLOTS:-1}
29 35
30 ]]></command> 36 ]]></command>
31 37
32 <inputs> 38 <inputs>
33 39
34 <expand macro="discosnp_inputs" /> 40 <expand macro="discosnp_inputs" />
35 41
36 <param argument="-b" type="select" label="Branching strategy"> 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)." />
37 <option value="1">forbid SNPs for wich the two paths are branching</option>
38 <option value="2">No limitation on branching</option>
39 </param>
40 43
41 <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"/> 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"/>
45
46 <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"/>
49
50 <param argument="--min_rank" type="float" label="Remove variants whose rank is smaller than this threshold" value="0.4"/>
42 51
43 <expand macro="discosnp_options" /> 52 <expand macro="discosnp_options" />
44 53
45 </inputs> 54 </inputs>
46 55
47 <outputs> 56 <outputs>
48 <data name="vcf" from_work_dir="*_coherent_sorted_with_clusters.vcf" format="vcf" label="VCF with ${tool.name} on $on_string"/> 57 <data name="vcf" from_work_dir="discoRad_*_clustered.vcf" format="vcf" label="VCF with ${tool.name} on $on_string"/>
49 <data name="fasta" from_work_dir="discoRad_*_coherent.fa" format="fasta" label="Fasta 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"/>
50 </outputs> 59 </outputs>
51 60
52 <tests> 61 <tests>
53 <test> 62 <test>
54 <conditional name="input_type_options"> 63 <conditional name="input_type_options">
57 </conditional> 66 </conditional>
58 <param name="D" value="0"/> 67 <param name="D" value="0"/>
59 <param name="P" value="4"/> 68 <param name="P" value="4"/>
60 <param name="k" value="31"/> 69 <param name="k" value="31"/>
61 <param name="b" value="2"/> 70 <param name="b" value="2"/>
71 <param name="max_size_cluster" value="50"/>
72 <param name="max_missing" value="0.95"/>
73 <param name="min_rank" value="0.0"/>
62 <output name="fasta" file="discosnpRAD/fasta.fa"/> 74 <output name="fasta" file="discosnpRAD/fasta.fa"/>
63 <output name="vcf"> 75 <output name="vcf">
64 <assert_contents> 76 <assert_contents>
65 <has_n_lines n="8"/> 77 <has_n_lines n="31"/>
66 <has_text text="Ty=SNP;Rk=0;UL=23;UR=39;CL=.;CR=.;Genome=.;Sd=."/> 78 <has_text text="Ty=SNP;Rk=0.0;UL=23;UR=39;CL=23;CR=39;Genome=.;Sd=.;Cluster=0;ClSize=2"/>
67 <has_text text="0/1:84:604,15,604:42,42:0,0"/> 79 <has_text text="0/1:84:604,15,604:42,42:0,0"/>
68 </assert_contents> 80 </assert_contents>
69 </output> 81 </output>
82 <assert_command>
83 <has_text text="--max_size_cluster 50"/>
84 <has_text text="--max_missing 0.95"/>
85 <has_text text="--min_rank 0.0"/>
86 </assert_command>
70 </test> 87 </test>
71 </tests> 88 </tests>
72 89
73 <help><![CDATA[ 90 <help><![CDATA[
74 91