Mercurial > repos > rhpvorderman > data_manager_select_index_by_path

comparison data_manager/data_manager_select_index_by_path.xml @ 1:8495c49cd056 draft default tip

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planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 9061997af3bc94f49653ffd42f10b973578e371d
author rhpvorderman
date Mon, 16 Jul 2018 10:58:36 -0400
parents 5f8d9309058b
children
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0:5f8d9309058b 1:8495c49cd056
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