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comparison data_manager/bowtie_index_builder.xml @ 9:b3f54bd230de 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 e5971e34b23280f7c3d6291a03325b6dd47e3fdd
author iuc
date Sat, 16 Aug 2025 14:35:33 +0000
parents 9c91b5015dd3
children
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8:9c91b5015dd3 9:b3f54bd230de
1 <tool id="bowtie_index_builder_data_manager" name="Bowtie index" tool_type="manage_data" version="@WRAPPER_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0"> 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> 3 <macros>
4 <token name="@WRAPPER_VERSION@">1.3.1</token> 4 <token name="@WRAPPER_VERSION@">1.3.1</token>
5 <token name="@VERSION_SUFFIX@">0</token> 5 <token name="@VERSION_SUFFIX@">1</token>
6 </macros> 6 </macros>
7 <requirements> 7 <requirements>
8 <requirement type="package" version="@WRAPPER_VERSION@">bowtie</requirement> 8 <requirement type="package" version="@WRAPPER_VERSION@">bowtie</requirement>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 #set $fasta_file_name = str($all_fasta_source.fields.path).split('/')[-1] 11 #set $fasta_file_name = str($all_fasta_source.fields.path).split('/')[-1]
12 mkdir -p '${out_file.extra_files_path}' && 12 mkdir -p '${out_file.extra_files_path}' &&
13 ln -s '${all_fasta_source.fields.path}' '${out_file.extra_files_path}/${fasta_file_name}' && 13 ln -s '${all_fasta_source.fields.path}' '${out_file.extra_files_path}/${fasta_file_name}' &&
14 bowtie-build '${out_file.extra_files_path}/${fasta_file_name}' '${out_file.extra_files_path}/${fasta_file_name}' && 14 bowtie-build '${out_file.extra_files_path}/${fasta_file_name}' '${out_file.extra_files_path}/${fasta_file_name}' &&
15 rm '${out_file.extra_files_path}/${fasta_file_name}' &&
15 cp '$dmjson' '$out_file' 16 cp '$dmjson' '$out_file'
16 ]]> 17 ]]>
17 </command> 18 </command>
18 <configfiles> 19 <configfiles>
19 <configfile name="dmjson"><![CDATA[#slurp 20 <configfile name="dmjson"><![CDATA[#slurp