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comparison 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
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children 2b62154e39c8
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1 <?xml version="1.0"?>
2 <tool id="jasminesv" name="JasmineSV" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
3 <description>Merge structural variants across samples</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 #if $dup_to_ins.dup_to_ins:
13 @REF_FASTA@
14 #end if
15
16 jasmine
17 ## Optional params
18 'max_dist=${max_dist}'
19 #if float($max_dist_linear) != 0.0:
20 'max_dist_linear=${max_dist_linear}'
21 #end if
22 'min_dist=${min_dist}'
23 'kd_tree_norm=${kd_tree_norm}'
24 'min_seq_id=${min_seq_id}'
25 'k_jaccard=${k_jaccard}'
26 'max_dup_length=${max_dup_length}'
27 'min_support=${min_support}'
28 threads=\${GALAXY_SLOTS:-4}
29 'spec_reads=${spec_reads}'
30 'spec_len=${spec_len}'
31 #if $dup_to_ins.dup_to_ins:
32 'genome_file=reference.fa'
33 #end if
34
35 ## Flags:
36 '${ignore_strand}'
37 '${ignore_type}'
38 #if $dup_to_ins.dup_to_ins:
39 '${dup_to_ins}'
40 #end if
41 '${mark_specific}'
42 '${pre_normalize}'
43 '${use_edit_dist}'
44 '${preprocess_only}'
45 '${postprocess_only}'
46 '${keep_var_ids}'
47 '${use_end}'
48 '${output_genotypes}'
49 '${ignore_merged_inputs}'
50 '${centroid_merging}'
51 '${clique_merging}'
52 '${allow_intrasample}'
53 '${normalize_type}'
54 '${leave_breakpoints}'
55 '${require_first_sample}'
56
57 '${normalize.normalize_chrs}'
58 #if $normalize.normalize_chrs and $normalize.chr_norm_file:
59 'chr_norm_file=${normalize.chr_norm_file}'
60 #end if
61
62 ## Required args
63 file_list='${vcffilelist}'
64 out_file='${out_vcf}'
65 ]]></command>
66 <configfiles>
67 <configfile name="vcffilelist">#
68 #for $vcf_file in $vcf_list:
69 ${vcf_file}
70 #end for
71 </configfile>
72 </configfiles>
73 <inputs>
74 <!--TODO in future versions (?)-
75 add IrisSV support for post-processing. For now just make it accessible as a separate tool and allow users to run independently
76 -->
77 <!--
78 Input files
79 -->
80 <param name="vcf_list" type="data" multiple="true" format="vcf" label="VCF file(s) to merge" help=""/>
81 <!--
82 Params
83 -->
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"/>
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" />
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"/>
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.)" />
88 <param argument="min_seq_id" type="float" value="0." min="0." label="The minimum sequence identity for two insertions to be merged" />
89 <param argument="k_jaccard" type="integer" value="9" min="1" label="The kmer size to use when computing Jaccard similarity of insertions" />
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" />
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" />
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" />
93 <param argument="spec_len" type="integer" value="30" min="1" label="The minimum length a variant needs to be in the specific callset" />
94 <!--
95 Flags
96 -->
97 <param argument="--ignore_strand" type="boolean" checked="false" truevalue="--ignore_strand" falsevalue="" label="Allow variants with different strands to be merged" />
98 <param argument="--ignore_type" type="boolean" checked="false" truevalue="--ignore_type" falsevalue="" label="Allow variants with different types to be merged" />
99 <conditional name="dup_to_ins">
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" >
101 <option value="--dup_to_ins">Convert duplications to insertions for SV merging and then convert them back</option>
102 <option value="" selected="true">Don't convert duplications to insertions for SV merging</option>
103 </param>
104 <when value="--dup_to_ins">
105 <expand macro="reference"/>
106 </when>
107 <when value=""/>
108 </conditional>
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" />
110 <param argument="--pre_normalize" type="boolean" checked="false" truevalue="--pre_normalize" falsevalue="" label="Run type normalization before merging" />
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" />
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" />
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" />
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)" />
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" />
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" />
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" />
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" />
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" />
120 <param argument="--allow_intrasample" type="boolean" checked="false" truevalue="--allow_intrasample" falsevalue="" label="Allow variants in the same sample to be merged" />
121 <param argument="--normalize_type" type="boolean" checked="false" truevalue="--normalize_type" falsevalue="" label="Convert all variants to INS/DEL/DUP/INV/TRA" />
122 <param argument="--leave_breakpoints" type="boolean" checked="false" truevalue="--leave_breakpoints" falsevalue="" label="Leave breakpoints as they are even if they are inconsistent" />
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" />
124 <conditional name="normalize">
125 <param argument="--normalize_chrs" type="select" checked="false" label="Whether to normalize chromosome names" help="(to NCBI standards - without 'chr' - by default)">
126 <option value="--normalize_chrs">Normalize chromosome names</option>
127 <option value="" selected="true">Don't normalize chromosome names</option>
128 </param>
129 <when value="--normalize_chrs">
130 <param name="chr_norm_file" type="data" format="txt,tsv" value="" label="A file containing chromosome name mappings" optional="true"/>
131 </when>
132 <when value=""/>
133 </conditional>
134 </inputs>
135 <outputs>
136 <!-- standard -->
137 <data name="out_vcf" format="vcf" label="${tool.name} on ${on_string}: Result"/>
138 </outputs>
139 <tests>
140 <!-- #1 default -->
141 <test expect_num_outputs="1">
142 <param name="vcf_list" value="a.vcf,b.vcf" ftype="vcf"/>
143 <output name="out_vcf" file="out1.vcf"/>
144 </test>
145 <test expect_num_outputs="1">
146 <param name="vcf_list" value="c.vcf,d.vcf" ftype="vcf"/>
147 <conditional name="normalize">
148 <param name="normalize_chrs" value="--normalize_chrs"/>
149 <param name="chr_norm_file" value="chr_norm_file.txt"/>
150 </conditional>
151 <output name="out_vcf" file="out1.vcf"/>
152 </test>
153 <test expect_num_outputs="1">
154 <param name="vcf_list" value="a.vcf,b.vcf" ftype="vcf"/>
155 <conditional name="dup_to_ins">
156 <param name="dup_to_ins" value="--dup_to_ins"/>
157 <conditional name="reference_source">
158 <param name="reference_source_selector" value="history"/>
159 <param name="ref_file" ftype="fasta" value="genome.fa"/>
160 </conditional>
161 </conditional>
162 <output name="out_vcf" file="out1.vcf"/>
163 </test>
164 <test expect_num_outputs="1">
165 <param name="vcf_list" value="a.vcf,b.vcf" ftype="vcf"/>
166 <conditional name="dup_to_ins">
167 <param name="dup_to_ins" value="--dup_to_ins"/>
168 <conditional name="reference_source">
169 <param name="reference_source_selector" value="cached"/>
170 <param name="ref_file" value="jasmine"/>
171 </conditional>
172 </conditional>
173 <output name="out_vcf" file="out1.vcf"/>
174 </test>
175
176 </tests>
177 <help><![CDATA[
178 .. class:: infomark
179
180 **What it does**
181
182 @WID@
183
184 **Input**
185
186 - Multiple VCF files to be merged
187
188 **Output**
189
190 - Merged Variants (VCF)
191
192 **References**
193
194 @REFERENCES@
195 ]]></help>
196 <expand macro="citations"/>
197 </tool>