Mercurial > repos > biocomp-ibens > data_manager_build_alfa_indexes
comparison 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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| -1:000000000000 | 0:f68a60c3d768 |
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| 1 <tool id="build_alfa_indexes" name="ALFA indexes" version="0.0.1" tool_type="manage_data"> | |
| 2 <description>build ALFA indexes from automatically downloaded gtf annotation file</description> | |
| 3 <!-- ALFA requires bedtools suite v2.20.0 and above --> | |
| 4 <requirements> | |
| 5 <requirement type="package" version="2.24">bedtools</requirement> | |
| 6 <requirement type="package" version="1.2">samtools</requirement> | |
| 7 <requirement type="package" version="1.4">matplotlib</requirement> | |
| 8 </requirements> | |
| 9 | |
| 10 <command interpreter="python">data_manager_build_alfa_indexes.py -e "${reference_source['kingdom']}" "${reference_source['species_name']}" -o "${out_file}" "$__tool_directory__"</command> | |
| 11 | |
| 12 <inputs> | |
| 13 <conditional name="reference_source"> | |
| 14 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> | |
| 15 <option value="ensembl" selected="True">Ensembl Genomes Websites</option> | |
| 16 </param> | |
| 17 <when value="ensembl"> | |
| 18 <param name="kingdom" type="select" label="Select the ensembl website where to fetch the genome"> | |
| 19 <option value="vertebrates" selected="True">Ensembl (Vertebrates)</option> | |
| 20 <option value="bacteria" selected="True">Ensembl Bacteria</option> | |
| 21 <option value="fungi" selected="True">Ensembl Fungi</option> | |
| 22 <option value="metazoa" selected="True">Ensembl Metazoa</option> | |
| 23 <option value="plants" selected="True">Ensembl Plants</option> | |
| 24 <option value="protists" selected="True">Ensembl Protists</option> | |
| 25 </param> | |
| 26 <param name="species_name" type="text" value="Homo sapiens" label="Complete Species_Name" optional="False"> | |
| 27 <validator type="empty_field" message="Please, enter a species name."/> | |
| 28 </param> | |
| 29 </when> | |
| 30 </conditional> | |
| 31 </inputs> | |
| 32 | |
| 33 <outputs> | |
| 34 <data name="out_file" format="data_manager_json"/> | |
| 35 </outputs> | |
| 36 | |
| 37 <help> | |
| 38 <![CDATA[ | |
| 39 **What it does** | |
| 40 | |
| 41 | |
| 42 | 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. | |
| 43 | | |
| 44 | 2. The tool calls ALFA.py to generate the alfa indexes from this gtf file. | |
| 45 | | |
| 46 | 3. Resulting indexes are stored in the child directory *alfa_indexes/* of the dir *<galaxy_data_manager_data_path>* defined in *config/galaxy.ini* | |
| 47 | | |
| 48 | 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* | |
| 49 | | |
| 50 | 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 | |
| 51 | |
| 52 .. _alfa: https://toolshed.g2.bx.psu.edu/view/charles-bernard/alfa | |
| 53 | |
| 54 ]]> | |
| 55 </help> | |
| 56 | |
| 57 </tool> |