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comparison virheat.xml @ 3:b5411b5e8259 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 8f495733edea9287f6392a893c9429fd16b1cb1d
author iuc
date Mon, 26 Aug 2024 18:10:25 +0000
parents 927e55d1aa97
children
comparison
equal deleted inserted replaced
2:927e55d1aa97 3:b5411b5e8259
9 </macros> 9 </macros>
10 <expand macro="biotools"/> 10 <expand macro="biotools"/>
11 <expand macro="requirements"/> 11 <expand macro="requirements"/>
12 <expand macro="version"/> 12 <expand macro="version"/>
13 <command detect_errors="exit_code"><![CDATA[ 13 <command detect_errors="exit_code"><![CDATA[
14 #import re 14
15 #set $vcfs_dir = 'vcfs_dir/'
16 mkdir -p $vcfs_dir &&
17 mkdir -p ./output_dir && 15 mkdir -p ./output_dir &&
18 #set $outfile = 'tmp_output.' + str($advanced.output_type) 16 #set $outfile = 'tmp_output.' + str($advanced.output_type)
19 #for $input_file in $sinputs
20 #set $file_path = $vcfs_dir + re.sub('[^\s\w\-\\.]', '_', str($input_file.element_identifier))
21 ln -s '$input_file' '$file_path' &&
22 #end for
23 #set $output_dir = 'output_dir/' 17 #set $output_dir = 'output_dir/'
18 bash vcfs_to_dir.sh &&
24 virheat 19 virheat
25 '$vcfs_dir' 20 'vcfs_dir/'
26 '$output_dir' 21 '$output_dir'
27 --name '$outfile' 22 --name '$outfile'
23 -r '$ref_id'
28 #if $genome_data.choice == 'length' 24 #if $genome_data.choice == 'length'
29 -l $genome_data.genome_length 25 -l $genome_data.genome_length
30 #else 26 #else
31 -g '$genome_data.gff3_file' 27 -g '$genome_data.gff3_file'
32 #if $genome_data.annotations 28 #if $genome_data.annotations
53 #else 49 #else
54 '${sc.scores_file.element_identifier}' 50 '${sc.scores_file.element_identifier}'
55 #end if 51 #end if
56 #end for 52 #end for
57 ]]></command> 53 ]]></command>
54 <configfiles>
55 <configfile filename="vcfs_to_dir.sh"><![CDATA[
56 mkdir -p 'vcfs_dir/' &&
57 #for $input_file in $sinputs
58 #set $sample_id = $input_file.element_identifier.replace("'", '_').replace('/', '_')
59 #set $file_path = 'vcfs_dir/' + $sample_id
60 #if not $file_path.endswith('.vcf'):
61 #set $file_path = $file_path + '.vcf'
62 #end if
63 ln -s '$input_file' '$file_path' &&
64 #end for
65 echo "VCF files are placed in vcfs_dir/."
66 ]]></configfile>
67 </configfiles>
58 <inputs> 68 <inputs>
59 <param name="sinputs" type="data_collection" format="vcf" label="Variant lists data" help="Select at least two datasets (or a dataset collection) with variant lists. Datasets are expected to represent individual samples and dataset names will be used as sample identifiers." multiple="true" collection_type="list" /> 69 <param name="sinputs" type="data_collection" format="vcf" label="Variant lists data" help="Select at least two datasets (or a dataset collection) with variant lists. Datasets are expected to represent individual samples and dataset names will be used as sample identifiers." multiple="true" collection_type="list" />
60 <conditional name="genome_data"> 70 <conditional name="genome_data">
61 <param name="choice" type="select" 71 <param name="choice" type="select"
62 label="Data for genomic annotation"> 72 label="Data for genomic annotation">
71 <repeat name="annotations" title="Annotations" help="Add annotations from the GFF3 file to display. If no annotations are added, 'gene' will be used by default."> 81 <repeat name="annotations" title="Annotations" help="Add annotations from the GFF3 file to display. If no annotations are added, 'gene' will be used by default.">
72 <param name="ann" type="text" value="gene" optional="false" label="Annotation name"/> 82 <param name="ann" type="text" value="gene" optional="false" label="Annotation name"/>
73 </repeat> 83 </repeat>
74 </when> 84 </when>
75 </conditional> 85 </conditional>
86 <param name="ref_id" argument="-r" type="text" optional="false" label="Reference identifier" help="Specify the ref id and generate plots for vcf with multiple refs, e.g. segmented viruses."/>
76 <param name="varfreq" argument="-t" type="float" min="0" max="1" value="0" optional="true" label="Variant Frequency Threshold" help="Only plot variants with an intrasample frequency above this threshold in at least one sample." /> 87 <param name="varfreq" argument="-t" type="float" min="0" max="1" value="0" optional="true" label="Variant Frequency Threshold" help="Only plot variants with an intrasample frequency above this threshold in at least one sample." />
77 <param argument="--delete" type="boolean" truevalue="--delete" falsevalue="--no-delete" checked="true" label="Delete mutations that are present in all samples and their maximum frequency divergence is smaller than 0.5"/> 88 <param argument="--delete" type="boolean" truevalue="--delete" falsevalue="--no-delete" checked="true" label="Delete mutations that are present in all samples and their maximum frequency divergence is smaller than 0.5"/>
78 <param name="delete_n" argument="-n" type="integer" min="0" value="0" label="Do not show mutations that occur n times or less"/> 89 <param name="delete_n" argument="-n" type="integer" min="0" value="0" label="Do not show mutations that occur n times or less"/>
79 <conditional name="zoom"> 90 <conditional name="zoom">
80 <param name="choice" type="select" label="Restrict the plot to a specific genomic region"> 91 <param name="choice" type="select" label="Restrict the plot to a specific genomic region">