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comparison data_manager/bowtie2_index_builder.xml @ 12:6754002631cd draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit e5971e34b23280f7c3d6291a03325b6dd47e3fdd
author iuc
date Sat, 16 Aug 2025 14:35:19 +0000
parents 39865c64a4e1
children
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11:39865c64a4e1 12:6754002631cd
1 <tool id="bowtie2_index_builder_data_manager" name="Bowtie2 index" tool_type="manage_data" version="@WRAPPER_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0"> 1 <tool id="bowtie2_index_builder_data_manager" name="Bowtie2 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@">2.5.4</token> 4 <token name="@WRAPPER_VERSION@">2.5.4</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@">bowtie2</requirement> 8 <requirement type="package" version="@WRAPPER_VERSION@">bowtie2</requirement>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
12 #set $fasta_file_name = str($all_fasta_source.fields.path).split('/')[-1] 12 #set $fasta_file_name = str($all_fasta_source.fields.path).split('/')[-1]
13 mkdir -p '${out_file.extra_files_path}' && 13 mkdir -p '${out_file.extra_files_path}' &&
14 ln -s '${all_fasta_source.fields.path}' '${out_file.extra_files_path}/${fasta_file_name}' && 14 ln -s '${all_fasta_source.fields.path}' '${out_file.extra_files_path}/${fasta_file_name}' &&
15 cd '${out_file.extra_files_path}' && 15 cd '${out_file.extra_files_path}' &&
16 bowtie2-build --threads \${GALAXY_SLOTS:-1} '${out_file.extra_files_path}/${fasta_file_name}' '${value}' && 16 bowtie2-build --threads \${GALAXY_SLOTS:-1} '${out_file.extra_files_path}/${fasta_file_name}' '${value}' &&
17 rm '${out_file.extra_files_path}/${fasta_file_name}' &&
17 cp '$dmjson' '$out_file' 18 cp '$dmjson' '$out_file'
18 ]]></command> 19 ]]></command>
19 <configfiles> 20 <configfiles>
20 <configfile name="dmjson"><![CDATA[#slurp 21 <configfile name="dmjson"><![CDATA[#slurp
21 #set $fasta_file_name = str($all_fasta_source.fields.path).split('/')[-1] 22 #set $fasta_file_name = str($all_fasta_source.fields.path).split('/')[-1]
26 "bowtie2_indexes":[ 27 "bowtie2_indexes":[
27 { 28 {
28 "value": "${value}", 29 "value": "${value}",
29 "dbkey": "${all_fasta_source.fields.dbkey}", 30 "dbkey": "${all_fasta_source.fields.dbkey}",
30 "name": "${name}", 31 "name": "${name}",
31 "path": "${fasta_file_name}" 32 "path": "${value}"
32 } 33 }
33 #if $tophat2: 34 #if $tophat2:
34 ], 35 ],
35 "tophat2_indexes":[ 36 "tophat2_indexes":[
36 { 37 {
37 "value": "${value}", 38 "value": "${value}",
38 "dbkey": "${all_fasta_source.fields.dbkey}", 39 "dbkey": "${all_fasta_source.fields.dbkey}",
39 "name": "${name}", 40 "name": "${name}",
40 "path": "${fasta_file_name}" 41 "path": "${value}"
41 } 42 }
42 #end if 43 #end if
43 ] 44 ]
44 } 45 }
45 } 46 }