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comparison data_manager/bowtie_index_builder.xml @ 7:a601bb53be5f draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 57d05675396f0b44265fb4dbc8f9f891c6073219
author iuc
date Thu, 05 Dec 2024 06:47:05 +0000
parents a230fefc187a
children
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6:bee4e8729ce7 7:a601bb53be5f
1 <tool id="bowtie_index_builder_data_manager" name="Bowtie index" tool_type="manage_data" version="1.2.0"> 1 <tool id="bowtie_index_builder_data_manager" name="Bowtie 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@">1.3.1</token>
5 <token name="@VERSION_SUFFIX@">0</token>
6 </macros>
3 <requirements> 7 <requirements>
4 <requirement type="package" version="1.2.0">bowtie</requirement> 8 <requirement type="package" version="@WRAPPER_VERSION@">bowtie</requirement>
5 </requirements> 9 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
7 python '$__tool_directory__/bowtie_index_builder.py' 11 #set $fasta_file_name = str($all_fasta_source.fields.path).split('/')[-1]
8 '${out_file}' 12 mkdir -p '${out_file.extra_files_path}' &&
9 --fasta_filename '${all_fasta_source.fields.path}' 13 ln -s '${all_fasta_source.fields.path}' '${out_file.extra_files_path}/${fasta_file_name}' &&
10 --fasta_dbkey '${all_fasta_source.fields.dbkey}' 14 bowtie-build '${out_file.extra_files_path}/${fasta_file_name}' '${out_file.extra_files_path}/${fasta_file_name}' &&
11 --fasta_description '${all_fasta_source.fields.name}' 15 cp '$dmjson' '$out_file'
12 --data_table_name bowtie_indexes 16 ]]>
13 ]]></command> 17 </command>
18 <configfiles>
19 <configfile name="dmjson"><![CDATA[#slurp
20 #set $fasta_file_name = str($all_fasta_source.fields.path).split('/')[-1]
21 #set $value = $sequence_id or $all_fasta_source.fields.dbkey
22 #set $name = $sequence_name or $all_fasta_source.fields.name
23 {
24 "data_tables":{
25 "bowtie_indexes":[
26 {
27 "value": "${value}",
28 "dbkey": "${all_fasta_source.fields.dbkey}",
29 "name": "${name}",
30 "path": "${fasta_file_name}"
31 }
32 ]
33 }
34 }
35 ]]></configfile>
36 </configfiles>
14 <inputs> 37 <inputs>
15 <param name="all_fasta_source" type="select" label="Source FASTA Sequence"> 38 <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
16 <options from_data_table="all_fasta"/> 39 <options from_data_table="all_fasta"/>
17 </param> 40 </param>
18 <param name="sequence_name" type="text" value="" label="Name of sequence" help="Leave blank to use all_fasta name" /> 41 <param name="sequence_name" type="text" value="" label="Name of sequence" help="Leave blank to use all_fasta name" />
19 <param name="sequence_id" type="text" value="" label="ID for sequence" help="Leave blank to use all_fasta id" /> 42 <param name="sequence_id" type="text" value="" label="ID for sequence" help="Leave blank to use all_fasta id" />
20 </inputs> 43 </inputs>
21 <outputs> 44 <outputs>
22 <data name="out_file" format="data_manager_json"/> 45 <data name="out_file" format="data_manager_json"/>
23 </outputs> 46 </outputs>
47 <tests>
48 <test>
49 <param name="all_fasta_source" value="phiX174"/>
50 <output name="out_file" file="bowtie_data_manager.1.json"/>
51 </test>
52 <test>
53 <param name="all_fasta_source" value="phiX174"/>
54 <param name="sequence_name" value="Galeocerdo cuvier"/>
55 <param name="sequence_id" value="tigHai1"/>
56 <output name="out_file" file="bowtie_data_manager.2.json"/>
57 </test>
58 </tests>
24 <help><![CDATA[ 59 <help><![CDATA[
25 .. class:: infomark 60 .. class:: infomark
26 61
27 **Notice:** If you leave name, description, or id blank, it will be generated automatically. 62 **Notice:** If you leave name, description, or id blank, it will be generated automatically.
28 ]]></help> 63 ]]></help>