Mercurial > repos > gga > chado_feature_load_fasta
view feature_load_fasta.xml @ 5:5b482826e065 draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit f0d2ad8e0257148a570ed59f07618ce7403c5583
author | gga |
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date | Fri, 31 Aug 2018 02:59:35 -0400 |
parents | 48cad01fd762 |
children | 0e2c2d7d080f |
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<?xml version="1.0"?> <tool id="feature_load_fasta" name="Chado load fasta" version="@WRAPPER_VERSION@.0"> <description></description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <code file="chado.py"/> <command detect_errors="aggressive"><![CDATA[ @AUTH@ chakin feature load_fasta '$fasta' '$organism' #if $sequence_type: --sequence_type '$sequence_type' #end if #if $analysis_id: --analysis_id '$analysis_id' #end if #if $re_name: --re_name '$re_name' #end if #if $re_uniquename: --re_uniquename '$re_uniquename' #end if #if $match_on_name: $match_on_name #end if $update #if $ext_db.db: --db '${ext_db.db}' #end if #if $ext_db.re_db_accession: --re_db_accession '${ext_db.re_db_accession}' #end if #if str($relationships.rel_type) != "none": --rel_type '${relationships.rel_type}' --re_parent '${relationships.rel_subject_re}' --parent_type '${relationships.rel_subject_type}' #end if | jq -S . > $results ]]></command> <inputs> <!-- arguments --> <param name="fasta" label="Fasta" argument="fasta" type="data" format="fasta" help="Path to the Fasta file to load" /> <param argument="--organism" type="select" dynamic_options="list_organisms()" label="Organism" /> <!-- options --> <param argument="--analysis_id" type="select" dynamic_options="list_analyses()" label="Analysis" /> <param name="sequence_type" label="Sequence Type" type="text" value="contig" help="this should be a Sequence Ontology term"/> <param name="re_name" label="Name regular expression" argument="re_name" type="text" help="Regular expression to extract the feature name from the fasta sequence id (first capturing group will be used)." optional="true" /> <param name="re_uniquename" label="Uniquename regular expression" argument="re_uniquename" type="text" help="Regular expression to extract the feature name from the fasta sequence id (first capturing group will be used)." optional="true" /> <param name="match_on_name" label="Match on name" argument="match_on_name" type="boolean" truevalue="--match_on_name" falsevalue="" help="Match existing features using their name instead of their uniquename" /> <param name="update" label="Update" argument="update" type="boolean" truevalue="--update" falsevalue="" help="Update existing feature with new sequence instead of throwing an error" /> <conditional name="relationships"> <param name="rel_type" argument="--rel_type" type="select" label="Relationship type" help="Use this when inserting features that should be associated to other already existing features"> <option value="none" selected="true">No relationship</option> <option value="part_of">Part of (for CDS sequences)</option> <option value="derives_from">Derives from (for peptide sequences)</option> </param> <when value="none"/> <when value="part_of"> <expand macro="feature_rel" /> </when> <when value="derives_from"> <expand macro="feature_rel" /> </when> </conditional> <section name="ext_db" title="Cross references to external database"> <param name="db" label="Db" argument="db" type="integer" help="External database to cross reference to." optional="true" /><!-- FIXME get this from db --> <param name="re_db_accession" label="Regex external db accession" argument="re_db_accession" type="text" help="Regular expression to extract an external database accession from the fasta sequence id (first capturing group will be used)." optional="true"> <expand macro="sanitized"/> </param> </section> <expand macro="wait_for"/> </inputs> <outputs> <data format="json" name="results"/> </outputs> <help> Load features from a fasta file @HELP@ </help> </tool>