Mercurial > repos > rhpvorderman > data_manager_select_index_by_path
comparison data_manager/data_manager_select_index_by_path.xml @ 1:8495c49cd056 draft default tip
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 9061997af3bc94f49653ffd42f10b973578e371d
author | rhpvorderman |
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date | Mon, 16 Jul 2018 10:58:36 -0400 |
parents | 5f8d9309058b |
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0:5f8d9309058b | 1:8495c49cd056 |
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1 <tool id="data_manager_select_index_by_path" name="Select index by path manager" tool_type="manage_data" version="0.0.2"> | 1 <tool id="data_manager_select_index_by_path" name="Select index by path manager" tool_type="manage_data" version="1.0.0a1" profile="18.09"> |
2 <description>path inputer</description> | 2 <requirements> |
3 <command interpreter="python"> | 3 <!-- Away with python 2! --> |
4 path_name_value_key_manager.py | 4 <requirement type="package" version="3.5">python</requirement> |
5 <requirement type="package" version="3.12">pyyaml</requirement> | |
6 <requirement type="package" version="0.6.6">schema</requirement> | |
7 </requirements> | |
8 <description>Link to indexes on the filesystem that have already been built</description> | |
9 <command detect_errors="exit_code"><![CDATA[ | |
10 python $__tool_directory__/path_name_value_key_manager.py | |
5 --value "${value}" | 11 --value "${value}" |
6 --dbkey "${dbkey}" | 12 --dbkey "${dbkey}" |
7 --name "${name}" | 13 --name "${name}" |
8 --path "${path}" | 14 --path "${path}" |
9 --data_table_name "${data_table}" | 15 --data_table_name "${data_table_set.data_table}" |
10 --json_output_file "${json_output_file}" | 16 --json_output_file "${json_output_file}" |
11 </command> | 17 #if $data_table_set.data_table == "rnastar_index2" |
18 --extra-columns '{"with-gtf": "$data_table_set.with_gtf"}' | |
19 #end if | |
20 ]]></command> | |
12 <inputs> | 21 <inputs> |
13 <param name="value" type="text" value="" label="value field for the entry. Defaults to name if left blank." /> | 22 <param name="value" type="text" value="" label="value field for the entry. Defaults to name if left blank." /> |
14 <param name="dbkey" type="text" value="" label="dbkey field for the entry. Defaults to value if left blank." /> | 23 <param name="dbkey" type="text" value="" label="dbkey field for the entry. Defaults to value if left blank." /> |
15 <param name="name" type="text" value="" label="name field for the entry. Defaults to the file name from path if left blank." /> | 24 <param name="name" type="text" value="" label="name field for the entry. Defaults to the file name from path if left blank." /> |
16 <param name="path" type="text" value="" label="path field for the entry" /> | 25 <param name="path" type="text" value="" label="path field for the entry" /> |
17 <param name="data_table" type="select" value="" label="data table for the index"> | 26 <conditional name="data_table_set"> |
18 <option value='all_fasta'>all_fasta</option> | 27 <param name="data_table" type="select" value="" label="data table for the index"> |
19 <option value='bowtie2_indexes'>bowtie2_indexes</option> | 28 <option value='all_fasta'>all_fasta</option> |
20 <option value='bowtie_indexes'>bowtie_indexes</option> | 29 <option value='bowtie2_indexes'>bowtie2_indexes</option> |
21 <option value='bowtie_indexes_color'>bowtie_indexes_color</option> | 30 <option value='bowtie_indexes'>bowtie_indexes</option> |
22 <option value='bwa_mem_indexes'>bwa_mem_indexes</option> | 31 <option value='bowtie_indexes_color'>bowtie_indexes_color</option> |
23 <option value='bwameth_indexes'>bwameth_indexes</option> | 32 <option value='bwa_mem_indexes'>bwa_mem_indexes</option> |
24 <option value='fasta_indexes'>fasta_indexes</option> | 33 <option value='bwameth_indexes'>bwameth_indexes</option> |
25 <option value='gatk_picard_indexes'>gatk_picard_indexes</option> | 34 <option value='fasta_indexes'>fasta_indexes</option> |
26 <option value='gene_transfer'>gene_transfer</option> | 35 <option value='gatk_picard_indexes'>gatk_picard_indexes</option> |
27 <option value='hisat2_indexes'>hisat2_indexes</option> | 36 <option value='gene_transfer'>gene_transfer</option> |
28 <option value='kallisto_indexes'>kallisto_indexes</option> | 37 <option value='hisat2_indexes'>hisat2_indexes</option> |
29 <option value='picard_indexes'>picard_indexes</option> | 38 <option value='kallisto_indexes'>kallisto_indexes</option> |
30 <option value='tophat2_indexes'>tophat2_indexes</option> | 39 <option value='picard_indexes'>picard_indexes</option> |
31 </param> | 40 <option value='tophat2_indexes'>tophat2_indexes</option> |
41 <option value="rnastar_index2">rnastar_index2</option> | |
42 </param> | |
43 <when value="rnastar_index2"> | |
44 <param name="with_gtf" type="select" value="" label="Index with embedded gtf?"> | |
45 <option value="0">No</option> | |
46 <option value="1">Yes</option> | |
47 </param> | |
48 </when> | |
49 </conditional> | |
32 </inputs> | 50 </inputs> |
33 <outputs> | 51 <outputs> |
34 <data name="json_output_file" format="data_manager_json"/> | 52 <data name="json_output_file" format="data_manager_json"/> |
35 </outputs> | 53 </outputs> |
36 | |
37 <help> | 54 <help> |
38 Adds a server path to the selected data table. | 55 Adds a server path to the selected data table. |
39 | 56 |
40 The tool will check the path exists but NOT check that it holds the expected data type. | 57 The tool will check the path exists but NOT check that it holds the expected data type. |
41 | 58 |