Mercurial > repos > rhpvorderman > data_manager_select_index_by_path
diff 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 |
|---|---|
| date | Mon, 16 Jul 2018 10:58:36 -0400 |
| parents | 5f8d9309058b |
| children |
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--- a/data_manager/data_manager_select_index_by_path.xml Mon Sep 25 03:35:26 2017 -0400 +++ b/data_manager/data_manager_select_index_by_path.xml Mon Jul 16 10:58:36 2018 -0400 @@ -1,39 +1,56 @@ -<tool id="data_manager_select_index_by_path" name="Select index by path manager" tool_type="manage_data" version="0.0.2"> - <description>path inputer</description> - <command interpreter="python"> - path_name_value_key_manager.py +<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"> + <requirements> + <!-- Away with python 2! --> + <requirement type="package" version="3.5">python</requirement> + <requirement type="package" version="3.12">pyyaml</requirement> + <requirement type="package" version="0.6.6">schema</requirement> + </requirements> + <description>Link to indexes on the filesystem that have already been built</description> + <command detect_errors="exit_code"><![CDATA[ + python $__tool_directory__/path_name_value_key_manager.py --value "${value}" --dbkey "${dbkey}" --name "${name}" --path "${path}" - --data_table_name "${data_table}" + --data_table_name "${data_table_set.data_table}" --json_output_file "${json_output_file}" - </command> + #if $data_table_set.data_table == "rnastar_index2" + --extra-columns '{"with-gtf": "$data_table_set.with_gtf"}' + #end if + ]]></command> <inputs> <param name="value" type="text" value="" label="value field for the entry. Defaults to name if left blank." /> <param name="dbkey" type="text" value="" label="dbkey field for the entry. Defaults to value if left blank." /> <param name="name" type="text" value="" label="name field for the entry. Defaults to the file name from path if left blank." /> <param name="path" type="text" value="" label="path field for the entry" /> - <param name="data_table" type="select" value="" label="data table for the index"> - <option value='all_fasta'>all_fasta</option> - <option value='bowtie2_indexes'>bowtie2_indexes</option> - <option value='bowtie_indexes'>bowtie_indexes</option> - <option value='bowtie_indexes_color'>bowtie_indexes_color</option> - <option value='bwa_mem_indexes'>bwa_mem_indexes</option> - <option value='bwameth_indexes'>bwameth_indexes</option> - <option value='fasta_indexes'>fasta_indexes</option> - <option value='gatk_picard_indexes'>gatk_picard_indexes</option> - <option value='gene_transfer'>gene_transfer</option> - <option value='hisat2_indexes'>hisat2_indexes</option> - <option value='kallisto_indexes'>kallisto_indexes</option> - <option value='picard_indexes'>picard_indexes</option> - <option value='tophat2_indexes'>tophat2_indexes</option> - </param> + <conditional name="data_table_set"> + <param name="data_table" type="select" value="" label="data table for the index"> + <option value='all_fasta'>all_fasta</option> + <option value='bowtie2_indexes'>bowtie2_indexes</option> + <option value='bowtie_indexes'>bowtie_indexes</option> + <option value='bowtie_indexes_color'>bowtie_indexes_color</option> + <option value='bwa_mem_indexes'>bwa_mem_indexes</option> + <option value='bwameth_indexes'>bwameth_indexes</option> + <option value='fasta_indexes'>fasta_indexes</option> + <option value='gatk_picard_indexes'>gatk_picard_indexes</option> + <option value='gene_transfer'>gene_transfer</option> + <option value='hisat2_indexes'>hisat2_indexes</option> + <option value='kallisto_indexes'>kallisto_indexes</option> + <option value='picard_indexes'>picard_indexes</option> + <option value='tophat2_indexes'>tophat2_indexes</option> + <option value="rnastar_index2">rnastar_index2</option> + </param> + <when value="rnastar_index2"> + <param name="with_gtf" type="select" value="" label="Index with embedded gtf?"> + <option value="0">No</option> + <option value="1">Yes</option> + </param> + </when> + </conditional> </inputs> <outputs> <data name="json_output_file" format="data_manager_json"/> </outputs> - <help> Adds a server path to the selected data table.