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comparison data_manager/hisat2_index_builder.xml @ 8:e4f36467bb51 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit e5971e34b23280f7c3d6291a03325b6dd47e3fdd
author iuc
date Sat, 16 Aug 2025 14:36:15 +0000
parents 8eac26f44d29
children
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7:d74c740bdb25 8:e4f36467bb51
1 <tool id="hisat2_index_builder_data_manager" name="HISAT2 index" tool_type="manage_data" version="2.1.0" profile="19.05"> 1 <tool id="hisat2_index_builder_data_manager" name="HISAT2 index" tool_type="manage_data" version="@WRAPPER_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
2 <description>builder</description> 2 <description>builder</description>
3 <macros>
4 <token name="@WRAPPER_VERSION@">2.2.1</token>
5 <token name="@VERSION_SUFFIX@">1</token>
6 </macros>
3 <requirements> 7 <requirements>
4 <requirement type="package" version="2.1.0">hisat2</requirement> 8 <requirement type="package" version="@WRAPPER_VERSION@">hisat2</requirement>
5 </requirements> 9 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 #set $value = $sequence_id or $all_fasta_source.fields.dbkey
12 #set $fasta_file_name = str($all_fasta_source.fields.path).split('/')[-1]
7 #if $advanced.adv_param_select == 'yes' and $advanced.gtf_input: 13 #if $advanced.adv_param_select == 'yes' and $advanced.gtf_input:
8 ln -s '${advanced.gtf_input}' gtf_file.gtf && 14 ln -s '${advanced.gtf_input}' gtf_file.gtf &&
9 hisat2_extract_splice_sites.py gtf_file.gtf > splice_sites.txt && 15 hisat2_extract_splice_sites.py gtf_file.gtf > splice_sites.txt &&
10 hisat2_extract_exons.py gtf_file.gtf > exon.txt && 16 hisat2_extract_exons.py gtf_file.gtf > exon.txt &&
11 #end if 17 #end if
15 hisat2_extract_snps_haplotypes_VCF.py '${all_fasta_source.fields.path}' snps.tabular extracted && 21 hisat2_extract_snps_haplotypes_VCF.py '${all_fasta_source.fields.path}' snps.tabular extracted &&
16 #else 22 #else
17 hisat2_extract_snps_haplotypes_UCSC.py '${all_fasta_source.fields.path}' snps.tabular extracted && 23 hisat2_extract_snps_haplotypes_UCSC.py '${all_fasta_source.fields.path}' snps.tabular extracted &&
18 #end if 24 #end if
19 #end if 25 #end if
20 python '$__tool_directory__/hisat2_index_builder.py' --output '${out_file}' 26
21 --fasta_filename '${all_fasta_source.fields.path}' 27 mkdir -p '${out_file.extra_files_path}' &&
22 --fasta_dbkey '${all_fasta_source.fields.dbkey}' 28 ln -s '${all_fasta_source.fields.path}' '${out_file.extra_files_path}/${fasta_file_name}' &&
23 --fasta_description '${all_fasta_source.fields.name}' 29 working="\$(pwd)" &&
24 --data_table_name hisat2_indexes 30 cd '${out_file.extra_files_path}' &&
25 --indexer_options "-p \${GALAXY_SLOTS:-1} 31
32 hisat2-build -p "\${GALAXY_SLOTS:-1}"
26 #if $advanced.adv_param_select == 'yes': 33 #if $advanced.adv_param_select == 'yes':
27 --noauto 34 --noauto
28 #if $advanced.snps: 35 #if $advanced.snps:
29 --snps "`pwd`/extracted.snp" 36 --snp "\${working}/extracted.snp"
30 --haplotype "`pwd`/extracted.haplotype" 37 --haplotype "\${working}/extracted.haplotype"
31 #end if 38 #end if
32 #if $advanced.gtf_input: 39 #if $advanced.gtf_input:
33 --ss "`pwd`/splice_sites.txt" 40 --ss "\${working}/splice_sites.txt"
34 --exon "`pwd`/exon.txt" 41 --exon "\${working}/exon.txt"
35 #end if 42 #end if
36 --bmax $advanced.bmax 43 --bmax $advanced.bmax
37 --bmaxdivn $advanced.bmaxdivn 44 --bmaxdivn $advanced.bmaxdivn
38 --dcv $advanced.dcv 45 --dcv $advanced.dcv
39 --offrate $advanced.offrate 46 --offrate $advanced.offrate
40 #end if 47 #end if
41 " 48 '${fasta_file_name}' '${value}' &&
49 rm '${out_file.extra_files_path}/${fasta_file_name}' &&
50
51 cp '$dmjson' '$out_file'
42 ]]> 52 ]]>
43 </command> 53 </command>
54 <configfiles>
55 <configfile name="dmjson"><![CDATA[#slurp
56 #set $fasta_file_name = str($all_fasta_source.fields.path).split('/')[-1]
57 #set $value = $sequence_id or $all_fasta_source.fields.dbkey
58 #set $name = $sequence_name or $all_fasta_source.fields.name
59 {
60 "data_tables":{
61 "hisat2_indexes":[
62 {
63 "value": "${value}",
64 "dbkey": "${all_fasta_source.fields.dbkey}",
65 "name": "${name}",
66 "path": "${value}"
67 }
68 ]
69 }
70 }
71 ]]></configfile>
72 </configfiles>
44 <inputs> 73 <inputs>
45 <param label="Source FASTA Sequence" name="all_fasta_source" type="select"> 74 <param label="Source FASTA Sequence" name="all_fasta_source" type="select">
46 <options from_data_table="all_fasta" /> 75 <options from_data_table="all_fasta" />
47 </param> 76 </param>
48 <conditional name="advanced" label="Advanced parameters"> 77 <conditional name="advanced" label="Advanced parameters">
67 <data name="out_file" format="data_manager_json" /> 96 <data name="out_file" format="data_manager_json" />
68 </outputs> 97 </outputs>
69 <tests> 98 <tests>
70 <test> 99 <test>
71 <param name="all_fasta_source" value="phiX174"/> 100 <param name="all_fasta_source" value="phiX174"/>
72 <output name="out_file" file="hisat2_data_manager.json"/> 101 <output name="out_file" file="hisat2_data_manager.1.json"/>
102 </test>
103 <test>
104 <param name="all_fasta_source" value="phiX174"/>
105 <param name="sequence_name" value="Galeocerdo cuvier"/>
106 <param name="sequence_id" value="tigHai1"/>
107 <param name="advanced|adv_param_select" value="yes"/>
108 <param name="advanced|bmax" value="3"/>
109 <param name="advanced|bmaxdivn" value="3"/>
110 <param name="advanced|dcv" value="4"/>
111 <param name="advanced|offrate" value="5"/>
112 <output name="out_file" file="hisat2_data_manager.2.json"/>
73 </test> 113 </test>
74 </tests> 114 </tests>
75 <help> 115 <help>
76 <![CDATA[ 116 <![CDATA[
77 .. class:: infomark 117 .. class:: infomark