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annotate jasminesv.xml @ 0:630e2929a131 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
author iuc
date Wed, 20 Jan 2021 19:49:40 +0000
parents
children 2b62154e39c8
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0
630e2929a131 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
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1 <?xml version="1.0"?>
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2 <tool id="jasminesv" name="JasmineSV" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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3 <description>Merge structural variants across samples</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 #if $dup_to_ins.dup_to_ins:
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13 @REF_FASTA@
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14 #end if
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15
630e2929a131 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
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16 jasmine
630e2929a131 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
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17 ## Optional params
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18 'max_dist=${max_dist}'
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19 #if float($max_dist_linear) != 0.0:
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20 'max_dist_linear=${max_dist_linear}'
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21 #end if
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22 'min_dist=${min_dist}'
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23 'kd_tree_norm=${kd_tree_norm}'
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24 'min_seq_id=${min_seq_id}'
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25 'k_jaccard=${k_jaccard}'
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26 'max_dup_length=${max_dup_length}'
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27 'min_support=${min_support}'
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28 threads=\${GALAXY_SLOTS:-4}
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29 'spec_reads=${spec_reads}'
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30 'spec_len=${spec_len}'
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31 #if $dup_to_ins.dup_to_ins:
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32 'genome_file=reference.fa'
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33 #end if
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34
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35 ## Flags:
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36 '${ignore_strand}'
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37 '${ignore_type}'
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38 #if $dup_to_ins.dup_to_ins:
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39 '${dup_to_ins}'
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40 #end if
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41 '${mark_specific}'
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42 '${pre_normalize}'
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43 '${use_edit_dist}'
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44 '${preprocess_only}'
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45 '${postprocess_only}'
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46 '${keep_var_ids}'
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47 '${use_end}'
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48 '${output_genotypes}'
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49 '${ignore_merged_inputs}'
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50 '${centroid_merging}'
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51 '${clique_merging}'
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52 '${allow_intrasample}'
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53 '${normalize_type}'
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54 '${leave_breakpoints}'
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55 '${require_first_sample}'
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56
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57 '${normalize.normalize_chrs}'
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58 #if $normalize.normalize_chrs and $normalize.chr_norm_file:
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59 'chr_norm_file=${normalize.chr_norm_file}'
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60 #end if
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61
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62 ## Required args
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63 file_list='${vcffilelist}'
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64 out_file='${out_vcf}'
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65 ]]></command>
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66 <configfiles>
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67 <configfile name="vcffilelist">#
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68 #for $vcf_file in $vcf_list:
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69 ${vcf_file}
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70 #end for
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71 </configfile>
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72 </configfiles>
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73 <inputs>
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74 <!--TODO in future versions (?)-
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75 add IrisSV support for post-processing. For now just make it accessible as a separate tool and allow users to run independently
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76 -->
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77 <!--
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78 Input files
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79 -->
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80 <param name="vcf_list" type="data" multiple="true" format="vcf" label="VCF file(s) to merge" help=""/>
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81 <!--
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82 Params
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83 -->
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84 <param argument="max_dist" type="integer" value="1000" min="0" label="The maximum distance variants can be apart when being merged" help="Setting both max_dist_linear and max_dist sets thresholds to minimum of max_dist and max_dist_linear * sv_length"/>
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85 <param argument="min_dist" type="integer" value="-1" min="-1" label="The minimum distance threshold a variant can have when using max_dist_linear" />
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86 <param argument="max_dist_linear" type="float" value="0." min="0.0" label="Make max_dist this proportion of the length of each variant" help="Setting both max_dist_linear and max_dist sets thresholds to minimum of max_dist and max_dist_linear * sv_length"/>
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87 <param argument="kd_tree_norm" type="integer" value="2" min="1" label="The power to use in kd-tree distances (1 is Manhattan, 2 is Euclidean, etc.)" />
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88 <param argument="min_seq_id" type="float" value="0." min="0." label="The minimum sequence identity for two insertions to be merged" />
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89 <param argument="k_jaccard" type="integer" value="9" min="1" label="The kmer size to use when computing Jaccard similarity of insertions" />
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90 <param argument="max_dup_length" type="integer" value="10000" min="0" label="The maximum length of duplication that can be converted to an insertion" />
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91 <param argument="min_support" type="integer" value="1" min="1" label="The minimum number of callsets a variant must be in to be output" />
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92 <param argument="spec_reads" type="integer" value="10" min="1" label="The minimum number of reads a variant needs to be in the specific callset" />
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93 <param argument="spec_len" type="integer" value="30" min="1" label="The minimum length a variant needs to be in the specific callset" />
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94 <!--
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95 Flags
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96 -->
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97 <param argument="--ignore_strand" type="boolean" checked="false" truevalue="--ignore_strand" falsevalue="" label="Allow variants with different strands to be merged" />
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98 <param argument="--ignore_type" type="boolean" checked="false" truevalue="--ignore_type" falsevalue="" label="Allow variants with different types to be merged" />
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99 <conditional name="dup_to_ins">
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100 <param argument="--dup_to_ins" type="select" checked="false" label="Convert duplications to insertions for SV merging and then convert them back?" help="Requires reference genome" >
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101 <option value="--dup_to_ins">Convert duplications to insertions for SV merging and then convert them back</option>
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102 <option value="" selected="true">Don't convert duplications to insertions for SV merging</option>
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103 </param>
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104 <when value="--dup_to_ins">
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105 <expand macro="reference"/>
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106 </when>
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107 <when value=""/>
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108 </conditional>
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109 <param argument="--mark_specific" type="boolean" checked="false" truevalue="--mark_specific" falsevalue="" label="Mark calls in the original VCF files that have enough support to called specific" />
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110 <param argument="--pre_normalize" type="boolean" checked="false" truevalue="--pre_normalize" falsevalue="" label="Run type normalization before merging" />
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111 <param argument="--use_edit_dist" type="boolean" checked="false" truevalue="--use_edit_dist" falsevalue="" label="Use edit distance for comparing insertion sequences instead of Jaccard" />
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112 <param argument="--preprocess_only" type="boolean" checked="false" truevalue="--preprocess_only" falsevalue="" label="Only run the preprocessing and not the actual merging or post-processing" />
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113 <param argument="--postprocess_only" type="boolean" checked="false" truevalue="--postprocess_only" falsevalue="" label="Only run the postprocessing and not the actual merging or pre-processing" />
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114 <param argument="--keep_var_ids" type="boolean" checked="false" truevalue="--keep_var_ids" falsevalue="" label="Don't change variant IDs (should only be used if input IDs are unique across samples)" />
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115 <param argument="--use_end" type="boolean" checked="false" truevalue="--use_end" falsevalue="" label="Use the end coordinate as the second coordinate instead of the variant length" />
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116 <param argument="--output_genotypes" type="boolean" checked="false" truevalue="--output_genotypes" falsevalue="" label="Print the genotypes of the consensus variants in all of the samples they came from" />
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117 <param argument="--ignore_merged_inputs" type="boolean" checked="false" truevalue="--ignore_merged_inputs" falsevalue="" label="Ignore merging info such as support vectors which is already present in the inputs" />
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118 <param argument="--centroid_merging" type="boolean" checked="false" truevalue="--centroid_merging" falsevalue="" label="Require every group to have a centroid which is within the distance threshold of each variant" />
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119 <param argument="--clique_merging" type="boolean" checked="false" truevalue="--clique_merging" falsevalue="" label="Require every group to have each pair within in it be mergeable" />
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120 <param argument="--allow_intrasample" type="boolean" checked="false" truevalue="--allow_intrasample" falsevalue="" label="Allow variants in the same sample to be merged" />
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121 <param argument="--normalize_type" type="boolean" checked="false" truevalue="--normalize_type" falsevalue="" label="Convert all variants to INS/DEL/DUP/INV/TRA" />
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122 <param argument="--leave_breakpoints" type="boolean" checked="false" truevalue="--leave_breakpoints" falsevalue="" label="Leave breakpoints as they are even if they are inconsistent" />
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123 <param argument="--require_first_sample" type="boolean" checked="false" truevalue="--require_first_sample" falsevalue="" label="Only output merged variants which include a variant from the first sample" />
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124 <conditional name="normalize">
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125 <param argument="--normalize_chrs" type="select" checked="false" label="Whether to normalize chromosome names" help="(to NCBI standards - without 'chr' - by default)">
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126 <option value="--normalize_chrs">Normalize chromosome names</option>
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127 <option value="" selected="true">Don't normalize chromosome names</option>
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128 </param>
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129 <when value="--normalize_chrs">
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130 <param name="chr_norm_file" type="data" format="txt,tsv" value="" label="A file containing chromosome name mappings" optional="true"/>
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131 </when>
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132 <when value=""/>
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133 </conditional>
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134 </inputs>
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135 <outputs>
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136 <!-- standard -->
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137 <data name="out_vcf" format="vcf" label="${tool.name} on ${on_string}: Result"/>
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138 </outputs>
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139 <tests>
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140 <!-- #1 default -->
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141 <test expect_num_outputs="1">
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142 <param name="vcf_list" value="a.vcf,b.vcf" ftype="vcf"/>
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143 <output name="out_vcf" file="out1.vcf"/>
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144 </test>
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145 <test expect_num_outputs="1">
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146 <param name="vcf_list" value="c.vcf,d.vcf" ftype="vcf"/>
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147 <conditional name="normalize">
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148 <param name="normalize_chrs" value="--normalize_chrs"/>
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149 <param name="chr_norm_file" value="chr_norm_file.txt"/>
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150 </conditional>
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151 <output name="out_vcf" file="out1.vcf"/>
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152 </test>
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153 <test expect_num_outputs="1">
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154 <param name="vcf_list" value="a.vcf,b.vcf" ftype="vcf"/>
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155 <conditional name="dup_to_ins">
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156 <param name="dup_to_ins" value="--dup_to_ins"/>
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157 <conditional name="reference_source">
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158 <param name="reference_source_selector" value="history"/>
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159 <param name="ref_file" ftype="fasta" value="genome.fa"/>
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160 </conditional>
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161 </conditional>
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162 <output name="out_vcf" file="out1.vcf"/>
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163 </test>
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164 <test expect_num_outputs="1">
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165 <param name="vcf_list" value="a.vcf,b.vcf" ftype="vcf"/>
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166 <conditional name="dup_to_ins">
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167 <param name="dup_to_ins" value="--dup_to_ins"/>
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168 <conditional name="reference_source">
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169 <param name="reference_source_selector" value="cached"/>
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170 <param name="ref_file" value="jasmine"/>
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171 </conditional>
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172 </conditional>
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173 <output name="out_vcf" file="out1.vcf"/>
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174 </test>
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175
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176 </tests>
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177 <help><![CDATA[
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178 .. class:: infomark
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179
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180 **What it does**
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181
630e2929a131 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
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182 @WID@
630e2929a131 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
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183
630e2929a131 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
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184 **Input**
630e2929a131 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
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185
630e2929a131 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
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186 - Multiple VCF files to be merged
630e2929a131 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
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187
630e2929a131 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
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188 **Output**
630e2929a131 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
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189
630e2929a131 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
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190 - Merged Variants (VCF)
630e2929a131 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
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191
630e2929a131 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
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192 **References**
630e2929a131 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
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193
630e2929a131 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
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194 @REFERENCES@
630e2929a131 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
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195 ]]></help>
630e2929a131 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
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196 <expand macro="citations"/>
630e2929a131 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
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197 </tool>