Mercurial > repos > iuc > data_manager_mothur_toolsuite
diff data_manager/data_manager_fetch_mothur_reference_data.xml @ 0:ab7a7e798c34 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
author | iuc |
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date | Mon, 06 Nov 2017 06:21:50 -0500 |
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children | aec831b54a5b |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/data_manager_fetch_mothur_reference_data.xml Mon Nov 06 06:21:50 2017 -0500 @@ -0,0 +1,132 @@ +<?xml version="1.0"?> +<tool id="data_manager_fetch_mothur_reference_data" name="Fetch Mothur toolsuite reference data" version="0.1.3" tool_type="manage_data"> + <description>Fetch and install reference data for Mothur</description> + <requirements> + <requirement type="package" version="2.7">python</requirement> + </requirements> + <command><![CDATA[ + python '$__tool_directory__/fetch_mothur_reference_data.py' + --source=$data_source.data_source_selector + #if str( $data_source.data_source_selector ) == "mothur_website" + --datasets '${data_source.ref_data}' + #elif str( $data_source.data_source_selector ) == "filesystem_paths" + --description '${data_source.description}' + --paths '${data_source.paths}' + #if $data_source.create_symlink + --link + #end if + #end if + '${out_file}' + ]]></command> + <inputs> + <conditional name="data_source"> + <param name="data_source_selector" type="select" + label="Choose the source for the reference data"> + <option value="mothur_website">Mothur website</option> + <option value="filesystem_paths">Filesystem paths</option> + </param> + <when value="mothur_website"> + <param name="ref_data" type="select" display="checkboxes" multiple="true" + label="Reference dataset to install"> + <option value="lookup_titanium">GS FLX Titanium lookup files</option> + <option value="lookup_gsflx">GSFLX lookup files</option> + <option value="lookup_gs20">GS20 lookup files</option> + <option value="RDP_v16">RDP reference files (training set version 16)</option> + <option value="RDP_v14">RDP reference files (training set version 14)</option> + <option value="RDP_v10">RDP reference files (training set version 10)</option> + <option value="RDP_v9">RDP reference files (training set version 9)</option> + <option value="RDP_v7">RDP reference files (training set version 7)</option> + <option value="RDP_v6">RDP reference files (training set version 6)</option> + <option value="silva_release_128">SILVA reference files (release 128)</option> + <option value="silva_release_123">SILVA reference files (release 123)</option> + <option value="silva_release_119">SILVA reference files (release 119)</option> + <option value="silva_release_102">SILVA reference files (release 102)</option> + <option value="greengenes_August2013">Greengenes reference taxonomy and alignment v13.8 (August 2013)</option> + <option value="greengenes_May2013">Greengenes reference taxonomy and alignment v13.5 (May 2013)</option> + <option value="greengenes_old">Greengenes reference taxonomy and alignment (pre-May 2013)</option> + <option value="greengenes_gold_alignment">Greengenes gold alignment</option> + <option value="secondary_structure_maps_silva">SILVA secondary structure maps</option> + <option value="secondary_structure_maps_greengenes">Greengenes secondary structure maps</option> + </param> + </when> + <when value="filesystem_paths"> + <param name="description" type="text" value="" size="50" + label="Description of the data" optional="False" /> + <param name="paths" type="text" value="" area="True" size="10x50" + label="Paths to upload" optional="False" + help="Upload all files pasted in the box. The (recursive) contents of any pasted directories will be added as well." /> + <param type="boolean" name="create_symlink" truevalue="create_symlink" + falsevalue="copy_file" + label="Create symlinks to data instead of copying into Galaxy" checked="on" /> + </when> + </conditional> + </inputs> + <outputs> + <data name="out_file" format="data_manager_json" /> + </outputs> + <tests> + <test> + <param name="data_sourece|ref_data" value="lookup_titanium"/> + <output name="out_file"> + <assert_contents> + <has_text text="GS FLX Titanium" /> + <has_text text="LookUp_Titanium.pat" /> + </assert_contents> + </output> + </test> + </tests> + <help> +.. class:: infomark + +**What it does** + +This tool fetches reference data used by the mothur_toolsuite set of Galaxy tools, +and populates the appropriate data tables. + +The reference data can be imported directly from the Mothur website, or from files +in a server directory. + +Files are added to the following data tables based on file extension: + + * **mothur_lookup**: for .pat files + * **mothur_aligndb**: for .fasta files + * **mothur_map**: for .map files + * **mothur_taxonomy**: for .tax files + +------ + +**Importing from Mothur website** + +Reference data sets provided by the Mothur developers can be downloaded from the +Mothur website. See the following pages to get more information about each dataset: + + * Lookup data: http://www.mothur.org/wiki/Lookup_files + * RDP reference data: http://www.mothur.org/wiki/RDP_reference_files + * Silva data: http://www.mothur.org/wiki/Silva_reference_files + * Greengenes data: http://www.mothur.org/wiki/Greengenes-formatted_databases + * Secondary structure maps: http://www.mothur.org/wiki/Secondary_structure_map + +**Importing from file system paths** + +If reference data is already on the server filesystem then use this option to +import it into the Mothur data tables. The appropriate data tables are determined +based on the file extensions. + +Optionally a description can be added which will appear next to the base of the +reference file name in the data table entry. + +------ + +.. class:: warningmark + +**A note on Lane masks** + +Lane mask data is also available via the Mothur website (files ending in ".filter"): + + * http://www.mothur.org/wiki/Lane_mask + +but as these data are not currently used in the toolsuite, they cannot be imported +using this data manager. + + </help> +</tool>