Mercurial > repos > devteam > data_manager_bowtie2_index_builder
comparison data_manager/bowtie2_index_builder.xml @ 13:8bf75f813413 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 57d05675396f0b44265fb4dbc8f9f891c6073219
author | iuc |
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date | Thu, 05 Dec 2024 06:46:58 +0000 |
parents | 2699da480b0b |
children |
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12:16230154ee87 | 13:8bf75f813413 |
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1 <tool id="bowtie2_index_builder_data_manager" name="Bowtie2 index" tool_type="manage_data" version="@WRAPPER_VERSION@+galaxy0" profile="18.09"> | 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> | |
4 <token name="@WRAPPER_VERSION@">2.5.4</token> | |
5 <token name="@VERSION_SUFFIX@">0</token> | |
6 </macros> | |
3 <requirements> | 7 <requirements> |
4 <requirement type="package" version="@WRAPPER_VERSION@">bowtie2</requirement> | 8 <requirement type="package" version="@WRAPPER_VERSION@">bowtie2</requirement> |
5 </requirements> | 9 </requirements> |
6 <macros> | |
7 <token name="@WRAPPER_VERSION@">2.4.4</token> | |
8 </macros> | |
9 <command detect_errors="exit_code"><![CDATA[ | 10 <command detect_errors="exit_code"><![CDATA[ |
10 python '$__tool_directory__/bowtie2_index_builder.py' | 11 #set $value = $sequence_id or $all_fasta_source.fields.dbkey |
11 '${out_file}' | 12 #set $fasta_file_name = str($all_fasta_source.fields.path).split('/')[-1] |
12 --fasta_filename '${all_fasta_source.fields.path}' | 13 mkdir -p '${out_file.extra_files_path}' && |
13 --fasta_dbkey '${all_fasta_source.fields.dbkey}' | 14 ln -s '${all_fasta_source.fields.path}' '${out_file.extra_files_path}/${fasta_file_name}' && |
14 --fasta_description '${all_fasta_source.fields.name}' | 15 cd '${out_file.extra_files_path}' && |
15 --data_table_name bowtie2_indexes ${tophat2} | 16 bowtie2-build --threads \${GALAXY_SLOTS:-1} '${out_file.extra_files_path}/${fasta_file_name}' '${value}' && |
17 cp '$dmjson' '$out_file' | |
16 ]]></command> | 18 ]]></command> |
19 <configfiles> | |
20 <configfile name="dmjson"><![CDATA[#slurp | |
21 #set $fasta_file_name = str($all_fasta_source.fields.path).split('/')[-1] | |
22 #set $value = $sequence_id or $all_fasta_source.fields.dbkey | |
23 #set $name = $sequence_name or $all_fasta_source.fields.name | |
24 { | |
25 "data_tables":{ | |
26 "bowtie2_indexes":[ | |
27 { | |
28 "value": "${value}", | |
29 "dbkey": "${all_fasta_source.fields.dbkey}", | |
30 "name": "${name}", | |
31 "path": "${fasta_file_name}" | |
32 } | |
33 #if $tophat2: | |
34 ], | |
35 "tophat2_indexes":[ | |
36 { | |
37 "value": "${value}", | |
38 "dbkey": "${all_fasta_source.fields.dbkey}", | |
39 "name": "${name}", | |
40 "path": "${fasta_file_name}" | |
41 } | |
42 #end if | |
43 ] | |
44 } | |
45 } | |
46 ]]></configfile> | |
47 </configfiles> | |
17 <inputs> | 48 <inputs> |
18 <param name="all_fasta_source" type="select" label="Source FASTA Sequence"> | 49 <param name="all_fasta_source" type="select" label="Source FASTA Sequence"> |
19 <options from_data_table="all_fasta"/> | 50 <options from_data_table="all_fasta"/> |
20 </param> | 51 </param> |
21 <param name="sequence_name" type="text" value="" label="Name of sequence" /> | 52 <param name="sequence_name" type="text" value="" label="Name of sequence" /> |
22 <param name="sequence_id" type="text" value="" label="ID for sequence" /> | 53 <param name="sequence_id" type="text" value="" label="ID for sequence" /> |
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" /> | 54 <param name="tophat2" type="boolean" checked="True" label="Also make available for TopHat" help="Adds values to tophat2_indexes tool data table" /> |
24 </inputs> | 55 </inputs> |
25 <outputs> | 56 <outputs> |
26 <data name="out_file" format="data_manager_json"/> | 57 <data name="out_file" format="data_manager_json"/> |
27 </outputs> | 58 </outputs> |
28 <tests> | 59 <tests> |
29 <test> | 60 <test> |
30 <param name="all_fasta_source" value="phiX174"/> | 61 <param name="all_fasta_source" value="phiX174"/> |
31 <output name="out_file" value="bowtie2_data_manager.json"/> | 62 <output name="out_file" value="bowtie2_data_manager.1.json"/> |
63 </test> | |
64 <test> | |
65 <param name="all_fasta_source" value="phiX174"/> | |
66 <param name="sequence_name" value="Galeocerdo cuvier"/> | |
67 <param name="sequence_id" value="tigHai1"/> | |
68 <param name="tophat2" value="False"/> | |
69 <output name="out_file" file="bowtie2_data_manager.2.json"/> | |
32 </test> | 70 </test> |
33 </tests> | 71 </tests> |
34 | 72 |
35 <help> | 73 <help> |
36 .. class:: infomark | 74 .. class:: infomark |