Mercurial > repos > charles-bernard > data_manager_build_alfa_indexes
view data_manager_build_alfa_indexes/data_manager/data_manager_build_alfa_indexes.xml @ 29:0c821f76e2e5 draft default tip
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author | charles-bernard |
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date | Thu, 21 Dec 2017 13:51:22 -0500 |
parents | 4f70c9afd89d |
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<tool id="build_alfa_indexes" name="ALFA indexes" version="0.0.1" tool_type="manage_data"> <description>build ALFA indexes from automatically downloaded gtf annotation file</description> <!-- ALFA requires bedtools suite v2.20.0 and above --> <requirements> <requirement type="package" version="2.24">bedtools</requirement> <requirement type="package" version="1.2">samtools</requirement> <requirement type="package" version="1.4">matplotlib</requirement> </requirements> <command interpreter="python">data_manager_build_alfa_indexes.py -e "${reference_source['kingdom']}" "${reference_source['species_name']}" -o "${out_file}" "$__tool_directory__"</command> <inputs> <conditional name="reference_source"> <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> <option value="ensembl" selected="True">Ensembl Genomes Websites</option> </param> <when value="ensembl"> <param name="kingdom" type="select" label="Select the ensembl website where to fetch the genome"> <option value="vertebrates" selected="True">Ensembl (Vertebrates)</option> <option value="bacteria" selected="True">Ensembl Bacteria</option> <option value="fungi" selected="True">Ensembl Fungi</option> <option value="metazoa" selected="True">Ensembl Metazoa</option> <option value="plants" selected="True">Ensembl Plants</option> <option value="protists" selected="True">Ensembl Protists</option> </param> <param name="species_name" type="text" value="Homo sapiens" label="Complete Species_Name" optional="False"> <validator type="empty_field" message="Please, enter a species name."/> </param> </when> </conditional> </inputs> <outputs> <data name="out_file" format="data_manager_json"/> </outputs> <help> <![CDATA[ **What it does** | 1. The tool asks the admin to enter a *species_name* and automatically download the last release of the corresponding gtf annotation file on Ensembl. | | 2. The tool calls ALFA.py to generate the alfa indexes from this gtf file. | | 3. Resulting indexes are stored in the child directory *alfa_indexes/* of the dir *<galaxy_data_manager_data_path>* defined in *config/galaxy.ini* | | 4. Finally, the tool adds the new entry to the table *alfa_indexes.loc*. This .loc file is where the data table *alfa_indexes* points, as defined in *config/shed_tool_data_table.conf.xml* | | 5. At the end of the process, when a user will use `alfa`_ , the built-in indexes corresponding to the *species_name* will be available .. _alfa: https://toolshed.g2.bx.psu.edu/view/charles-bernard/alfa ]]> </help> </tool>