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comparison data_manager/bowtie2_index_builder.xml @ 6:bb050998cee2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
author iuc
date Thu, 09 May 2019 16:15:27 -0400
parents 8a892275932f
children 224f1598642a
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5:8a892275932f 6:bb050998cee2
1 <tool id="bowtie2_index_builder_data_manager" name="Bowtie2 index" tool_type="manage_data" version="2.3.0"> 1 <tool id="bowtie2_index_builder_data_manager" name="Bowtie2 index" tool_type="manage_data" version="@WRAPPER_VERSION@" profile="18.09">
2 <description>builder</description> 2 <description>builder</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.3.0">bowtie2</requirement> 4 <requirement type="package" version="@WRAPPER_VERSION@">bowtie2</requirement>
5 </requirements> 5 </requirements>
6 <macros>
7 <token name="@WRAPPER_VERSION@">2.3.4.3</token>
8 </macros>
6 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
7 python '$__tool_directory__/bowtie2_index_builder.py' 10 python '$__tool_directory__/bowtie2_index_builder.py'
8 '${out_file}' 11 '${out_file}'
9 --fasta_filename '${all_fasta_source.fields.path}' 12 --fasta_filename '${all_fasta_source.fields.path}'
10 --fasta_dbkey '${all_fasta_source.fields.dbkey}' 13 --fasta_dbkey '${all_fasta_source.fields.dbkey}'
20 <param name="tophat2" type="boolean" truevalue="--data_table_name tophat2_indexes" falsevalue="" checked="True" label="Also make available for TopHat" help="Adds values to tophat2_indexes tool data table" /> 23 <param name="tophat2" type="boolean" truevalue="--data_table_name tophat2_indexes" falsevalue="" checked="True" label="Also make available for TopHat" help="Adds values to tophat2_indexes tool data table" />
21 </inputs> 24 </inputs>
22 <outputs> 25 <outputs>
23 <data name="out_file" format="data_manager_json"/> 26 <data name="out_file" format="data_manager_json"/>
24 </outputs> 27 </outputs>
28 <tests>
29 <test>
30 <param name="all_fasta_source" value="phiX174"/>
31 <output name="out_file" value="bowtie2_data_manager.json"/>
32 </test>
33 </tests>
25 34
26 <help> 35 <help>
27 .. class:: infomark 36 .. class:: infomark
28 37
29 **Notice:** If you leave name, description, or id blank, it will be generated automatically. 38 **Notice:** If you leave name, description, or id blank, it will be generated automatically.