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comparison irissv.xml @ 0:30fc9f2bcbe4 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
author iuc
date Tue, 19 Jan 2021 20:30:21 +0000
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children 1d4f065fa0ef
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-1:000000000000 0:30fc9f2bcbe4
1 <?xml version="1.0"?>
2 <tool id="irissv" name="Iris" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
3 <description>Refine insertion sequences</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7
8 <expand macro="requirements"/>
9 <expand macro="version_command"/>
10
11 <command detect_errors="exit_code"><![CDATA[
12 @REF_FASTA@
13
14 iris
15 genome_in=reference.fa
16 vcf_in='${in_vcf}'
17 reads_in='${in_bam}'
18 vcf_out='${out_vcf}'
19 threads=\${GALAXY_SLOTS:-4}
20 padding_before='${padding_before}'
21 padding_after='${padding_after}'
22 genome_buffer='${genome_buffer}'
23 min_ins_length='${min_ins_length}'
24 max_ins_dist='${max_ins_dist}'
25 max_out_length='${max_out_length}'
26 max_len_change='${max_len_change}'
27 '${aligner}'
28 '${rerunracon}'
29 '${also_deletions}'
30 '${keep_long_variants}'
31 ]]></command>
32 <inputs>
33 <!--
34 Required arguments
35 -->
36 <expand macro="reference"/>
37 <param name="in_vcf" type="data" format="vcf" label="The VCF file with variant calls/supporting reads"/>
38 <param name="in_bam" type="data" format="bam" label="The BAM file containing the reads"/>
39 <!--log_out param doesn't seem to produce output for some reason, commenting out.-->
40 <!-- <param name="output_log" type="boolean" label="Output log file?" checked="true"/> -->
41 <!--
42 Optional arguments
43 -->
44 <param argument="padding_before" type="integer" value="1" min="1" label="The number of bases to output before the variant in REF/ALT fields" />
45 <param argument="padding_after" type="integer" value="0" min="0" label="The number of bases to output after the variant in REF/ALT fields" />
46 <param argument="genome_buffer" type="integer" value="100000" min="1" label="The genome region on each side of the SV to align assembled reads to" />
47 <param argument="min_ins_length" type="integer" value="30" min="1" label="The min length allowed for a refined insertion sequence" />
48 <param argument="max_ins_dist" type="integer" value="100" min="0" label="The max distance a refined insertion call can be from its old position" />
49 <param argument="max_out_length" type="integer" value="100000" min="0" label="The max length of variant which will be output" />
50 <param argument="max_len_change" type="float" value="0.25" min="0.0" label="The max proportion by which a variant's length can change" />
51
52 <param name="aligner" type="select">
53 <option value="" selected="true">Use minimap2 for mapping</option>
54 <option value="--pacbio" selected="true">Use minimap2 for mapping in PacBio mode</option>
55 <option value="--hifi">Use minimap2 in hifi mode</option>
56 </param>
57 <param argument="--rerunracon" type="boolean" truevalue="--rerunracon" falsevalue="" checked="false" label="Use racon twice for consensus finding" />
58 <!--
59 Flags
60 -->
61 <param argument="--also_deletions" type="boolean" truevalue="also_deletions" falsevalue="" checked="false" label="also try to refine deletion positions/lengths"/>
62 <param argument="--keep_long_variants" type="boolean" truevalue="--keep_long_variants" falsevalue="" checked="false" label="output original VCF line for very long variants instead of ignoring them"/>
63 </inputs>
64 <outputs>
65 <!-- standard -->
66 <data name="out_vcf" format="vcf" label="${tool.name} on ${on_string}: Result"/>
67 <!--log_out param doesn't seem to produce output for some reason, commenting out.-->
68 <!-- <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log">
69 <filter>output_log</filter>
70 </data> -->
71 </outputs>
72 <tests>
73 <!-- #1 default -->
74 <test expect_num_outputs="1">
75 <conditional name="reference_source">
76 <param name="reference_source_selector" value="history"/>
77 <param name="ref_file" ftype="fasta" value="genome.fa"/>
78 </conditional>
79 <param name="in_vcf" value="sniffles.vcf"/>
80 <param name="in_bam" value="iris.bam"/>
81 <output name="out_vcf" file="test_out.vcf"/>
82 </test>
83 <test expect_num_outputs="1">
84 <conditional name="reference_source">
85 <param name="reference_source_selector" value="cached"/>
86 <param name="ref_file" value="iris"/>
87 </conditional>
88 <param name="in_vcf" value="sniffles.vcf"/>
89 <param name="in_bam" value="iris.bam"/>
90 <output name="out_vcf" file="test_out.vcf"/>
91 </test>
92 </tests>
93 <help><![CDATA[
94 .. class:: infomark
95
96 **What it does**
97
98 @WID@
99
100
101 **Input**
102
103 - FASTA file containing the reference genome
104
105 - VCF file with variant calls & supporting reads determined by Sniffles
106
107 - BAM file containing the reads
108
109 **Output**
110
111 - VCF file with refined insertion sequences
112
113 **References**
114
115 @REFERENCES@
116 ]]></help>
117 <expand macro="citations"/>
118 </tool>