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annotate 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
parents
children 1d4f065fa0ef
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30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
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1 <?xml version="1.0"?>
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2 <tool id="irissv" name="Iris" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
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3 <description>Refine insertion sequences</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7
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8 <expand macro="requirements"/>
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9 <expand macro="version_command"/>
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10
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11 <command detect_errors="exit_code"><![CDATA[
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12 @REF_FASTA@
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13
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14 iris
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15 genome_in=reference.fa
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16 vcf_in='${in_vcf}'
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17 reads_in='${in_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 -->
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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" />
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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" />
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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" />
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47 <param argument="min_ins_length" type="integer" value="30" min="1" label="The min length allowed for a refined insertion sequence" />
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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" />
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49 <param argument="max_out_length" type="integer" value="100000" min="0" label="The max length of variant which will be output" />
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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" />
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51
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52 <param name="aligner" type="select">
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53 <option value="" selected="true">Use minimap2 for mapping</option>
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54 <option value="--pacbio" selected="true">Use minimap2 for mapping in PacBio mode</option>
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55 <option value="--hifi">Use minimap2 in hifi mode</option>
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56 </param>
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57 <param argument="--rerunracon" type="boolean" truevalue="--rerunracon" falsevalue="" checked="false" label="Use racon twice for consensus finding" />
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58 <!--
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59 Flags
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60 -->
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61 <param argument="--also_deletions" type="boolean" truevalue="also_deletions" falsevalue="" checked="false" label="also try to refine deletion positions/lengths"/>
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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"/>
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63 </inputs>
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64 <outputs>
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65 <!-- standard -->
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66 <data name="out_vcf" format="vcf" label="${tool.name} on ${on_string}: Result"/>
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67 <!--log_out param doesn't seem to produce output for some reason, commenting out.-->
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68 <!-- <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log">
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69 <filter>output_log</filter>
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70 </data> -->
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71 </outputs>
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72 <tests>
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73 <!-- #1 default -->
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74 <test expect_num_outputs="1">
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75 <conditional name="reference_source">
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76 <param name="reference_source_selector" value="history"/>
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77 <param name="ref_file" ftype="fasta" value="genome.fa"/>
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78 </conditional>
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79 <param name="in_vcf" value="sniffles.vcf"/>
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80 <param name="in_bam" value="iris.bam"/>
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81 <output name="out_vcf" file="test_out.vcf"/>
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82 </test>
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83 <test expect_num_outputs="1">
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84 <conditional name="reference_source">
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85 <param name="reference_source_selector" value="cached"/>
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86 <param name="ref_file" value="iris"/>
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87 </conditional>
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88 <param name="in_vcf" value="sniffles.vcf"/>
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89 <param name="in_bam" value="iris.bam"/>
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90 <output name="out_vcf" file="test_out.vcf"/>
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91 </test>
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92 </tests>
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93 <help><![CDATA[
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94 .. class:: infomark
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95
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
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96 **What it does**
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97
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98 @WID@
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99
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100
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101 **Input**
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102
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103 - FASTA file containing the reference genome
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104
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105 - VCF file with variant calls & supporting reads determined by Sniffles
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106
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107 - BAM file containing the reads
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108
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
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109 **Output**
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110
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111 - VCF file with refined insertion sequences
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112
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113 **References**
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114
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115 @REFERENCES@
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116 ]]></help>
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117 <expand macro="citations"/>
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118 </tool>