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comparison irissv.xml @ 3:3242dbeea69c draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 00d6705a08a9d9cc9093846b730c4dec247cf5e7
author iuc
date Sat, 18 May 2024 20:34:13 +0000
parents b4b6b660293a
children
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2:b4b6b660293a 3:3242dbeea69c
1 <tool id="irissv" name="Iris" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@"> 1 <tool id="irissv" name="Iris" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
2 <description>Refine insertion sequences</description> 2 <description>Refine insertion sequences</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6
7 <expand macro="requirements"/> 6 <expand macro="requirements"/>
8 <expand macro="version_command"/> 7 <expand macro="version_command"/>
9
10 <command detect_errors="aggressive"><![CDATA[ 8 <command detect_errors="aggressive"><![CDATA[
11 @REF_FASTA@ 9 @REF_FASTA@
12 10
13 ln -s '$in_bam' reads.bam && 11 ln -s '$in_bam' reads.bam &&
14 ln -s '$in_bam.metadata.bam_index' 'reads.bam.bai' && 12 ln -s '$in_bam.metadata.bam_index' 'reads.bam.bai' &&
41 <!--log_out param doesn't seem to produce output for some reason, commenting out.--> 39 <!--log_out param doesn't seem to produce output for some reason, commenting out.-->
42 <!-- <param name="output_log" type="boolean" label="Output log file?" checked="true"/> --> 40 <!-- <param name="output_log" type="boolean" label="Output log file?" checked="true"/> -->
43 <!-- 41 <!--
44 Optional arguments 42 Optional arguments
45 --> 43 -->
46 <param argument="padding_before" type="integer" value="1" min="1" label="The number of bases to output before the variant in REF/ALT fields" /> 44 <param argument="padding_before" type="integer" min="1" value="1" label="The number of bases to output before the variant in REF/ALT fields"/>
47 <param argument="padding_after" type="integer" value="0" min="0" label="The number of bases to output after the variant in REF/ALT fields" /> 45 <param argument="padding_after" type="integer" min="0" value="0" label="The number of bases to output after the variant in REF/ALT fields"/>
48 <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" /> 46 <param argument="genome_buffer" type="integer" min="1" value="100000" label="The genome region on each side of the SV to align assembled reads to"/>
49 <param argument="min_ins_length" type="integer" value="30" min="1" label="The min length allowed for a refined insertion sequence" /> 47 <param argument="min_ins_length" type="integer" min="1" value="30" label="The min length allowed for a refined insertion sequence"/>
50 <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" /> 48 <param argument="max_ins_dist" type="integer" min="0" value="100" label="The max distance a refined insertion call can be from its old position"/>
51 <param argument="max_out_length" type="integer" value="100000" min="0" label="The max length of variant which will be output" /> 49 <param argument="max_out_length" type="integer" min="0" value="100000" label="The max length of variant which will be output"/>
52 <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" /> 50 <param argument="max_len_change" type="float" min="0.0" value="0.25" label="The max proportion by which a variant's length can change"/>
53
54 <param name="aligner" type="select"> 51 <param name="aligner" type="select">
55 <option value="" selected="true">Use minimap2 for mapping</option> 52 <option value="" selected="true">Use minimap2 for mapping</option>
56 <option value="--pacbio" selected="true">Use minimap2 for mapping in PacBio mode</option> 53 <option value="--pacbio" selected="true">Use minimap2 for mapping in PacBio mode</option>
57 <option value="--hifi">Use minimap2 in hifi mode</option> 54 <option value="--hifi">Use minimap2 in hifi mode</option>
58 </param> 55 </param>
59 <param argument="--rerunracon" type="boolean" truevalue="--rerunracon" falsevalue="" checked="false" label="Use racon twice for consensus finding" /> 56 <param argument="--rerunracon" type="boolean" truevalue="--rerunracon" falsevalue="" checked="false" label="Use racon twice for consensus finding"/>
60 <!-- 57 <!--
61 Flags 58 Flags
62 --> 59 -->
63 <param argument="--also_deletions" type="boolean" truevalue="also_deletions" falsevalue="" checked="false" label="also try to refine deletion positions/lengths"/> 60 <param argument="--also_deletions" type="boolean" truevalue="also_deletions" falsevalue="" checked="false" label="also try to refine deletion positions/lengths"/>
64 <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"/> 61 <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"/>
74 <tests> 71 <tests>
75 <!-- #1 default --> 72 <!-- #1 default -->
76 <test expect_num_outputs="1"> 73 <test expect_num_outputs="1">
77 <conditional name="reference_source"> 74 <conditional name="reference_source">
78 <param name="reference_source_selector" value="history"/> 75 <param name="reference_source_selector" value="history"/>
79 <param name="ref_file" ftype="fasta.gz" value="genome.fa.gz"/> 76 <param name="ref_file" value="genome.fa.gz" ftype="fasta.gz"/>
80 </conditional> 77 </conditional>
81 <param name="in_vcf" value="sniffles.vcf"/> 78 <param name="in_vcf" value="sniffles.vcf"/>
82 <param name="in_bam" value="iris.bam"/> 79 <param name="in_bam" value="iris.bam"/>
83 <output name="out_vcf" file="test_out.vcf"/> 80 <output name="out_vcf" file="test_out.vcf"/>
84 </test> 81 </test>