Mercurial > repos > biocomp-ibens > data_manager_build_alfa_indexes
diff data_manager_build_alfa_indexes/data_manager/data_manager_build_alfa_indexes.xml @ 0:f68a60c3d768 draft default tip
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author | biocomp-ibens |
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date | Wed, 16 May 2018 09:56:43 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager_build_alfa_indexes/data_manager/data_manager_build_alfa_indexes.xml Wed May 16 09:56:43 2018 -0400 @@ -0,0 +1,57 @@ +<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>