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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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3242dbeea69c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 00d6705a08a9d9cc9093846b730c4dec247cf5e7
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1 <tool id="irissv" name="Iris" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
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2 <description>Refine insertion sequences</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="version_command"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 @REF_FASTA@
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10
2
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11 ln -s '$in_bam' reads.bam &&
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12 ln -s '$in_bam.metadata.bam_index' 'reads.bam.bai' &&
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13
0
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14 iris
1
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15 genome_in=reference
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16 vcf_in='${in_vcf}'
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17 reads_in='reads.bam'
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18 vcf_out='${out_vcf}'
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19 threads=\${GALAXY_SLOTS:-4}
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20 padding_before='${padding_before}'
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21 padding_after='${padding_after}'
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22 genome_buffer='${genome_buffer}'
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23 min_ins_length='${min_ins_length}'
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24 max_ins_dist='${max_ins_dist}'
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25 max_out_length='${max_out_length}'
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26 max_len_change='${max_len_change}'
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27 '${aligner}'
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28 '${rerunracon}'
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29 '${also_deletions}'
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30 '${keep_long_variants}'
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31 ]]></command>
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32 <inputs>
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33 <!--
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34 Required arguments
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35 -->
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36 <expand macro="reference"/>
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37 <param name="in_vcf" type="data" format="vcf" label="The VCF file with variant calls/supporting reads"/>
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38 <param name="in_bam" type="data" format="bam" label="The BAM file containing the reads"/>
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39 <!--log_out param doesn't seem to produce output for some reason, commenting out.-->
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40 <!-- <param name="output_log" type="boolean" label="Output log file?" checked="true"/> -->
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41 <!--
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42 Optional arguments
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43 -->
3
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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"/>
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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"/>
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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"/>
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47 <param argument="min_ins_length" type="integer" min="1" value="30" label="The min length allowed for a refined insertion sequence"/>
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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"/>
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49 <param argument="max_out_length" type="integer" min="0" value="100000" label="The max length of variant which will be output"/>
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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"/>
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51 <param name="aligner" type="select">
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52 <option value="" selected="true">Use minimap2 for mapping</option>
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53 <option value="--pacbio" selected="true">Use minimap2 for mapping in PacBio mode</option>
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54 <option value="--hifi">Use minimap2 in hifi mode</option>
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55 </param>
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56 <param argument="--rerunracon" type="boolean" truevalue="--rerunracon" falsevalue="" checked="false" label="Use racon twice for consensus finding"/>
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57 <!--
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58 Flags
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59 -->
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60 <param argument="--also_deletions" type="boolean" truevalue="also_deletions" falsevalue="" checked="false" label="also try to refine deletion positions/lengths"/>
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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"/>
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62 </inputs>
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63 <outputs>
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64 <!-- standard -->
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65 <data name="out_vcf" format="vcf" label="${tool.name} on ${on_string}: Result"/>
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66 <!--log_out param doesn't seem to produce output for some reason, commenting out.-->
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67 <!-- <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log">
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68 <filter>output_log</filter>
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69 </data> -->
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70 </outputs>
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71 <tests>
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72 <!-- #1 default -->
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73 <test expect_num_outputs="1">
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74 <conditional name="reference_source">
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75 <param name="reference_source_selector" value="history"/>
3
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76 <param name="ref_file" value="genome.fa.gz" ftype="fasta.gz"/>
0
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77 </conditional>
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78 <param name="in_vcf" value="sniffles.vcf"/>
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79 <param name="in_bam" value="iris.bam"/>
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80 <output name="out_vcf" file="test_out.vcf"/>
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81 </test>
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82 <test expect_num_outputs="1">
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83 <conditional name="reference_source">
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84 <param name="reference_source_selector" value="cached"/>
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85 <param name="ref_file" value="iris"/>
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86 </conditional>
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87 <param name="in_vcf" value="sniffles.vcf"/>
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88 <param name="in_bam" value="iris.bam"/>
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89 <output name="out_vcf" file="test_out.vcf"/>
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90 </test>
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91 </tests>
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92 <help><![CDATA[
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93 .. class:: infomark
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94
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
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95 **What it does**
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96
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97 @WID@
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98
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
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99
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100 **Input**
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101
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102 - FASTA file containing the reference genome
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103
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104 - VCF file with variant calls & supporting reads determined by Sniffles
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105
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106 - BAM file containing the reads
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107
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
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108 **Output**
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109
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110 - VCF file with refined insertion sequences
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111
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112 **References**
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113
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114 @REFERENCES@
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115 ]]></help>
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116 <expand macro="citations"/>
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117 </tool>