annotate feature_load_fasta.xml @ 23:0df99f0fc35e draft default tip

planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 20d8d84d66eb27f870cadb94a02c97806090df24

<?xml version="1.0"?>
<tool id="feature_load_fasta" name="Chado load fasta" version="@WRAPPER_VERSION@">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <code file="chado.py"/>
    <command detect_errors="aggressive"><![CDATA[
@START_PSQL@ &&

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

$match_on_name

$do_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'

@ZIP_PSQL@
    ]]></command>
    <inputs>
        <expand macro="psql_target"/>
        <!-- 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">
            <expand macro="sanitized"/>
        </param>
        <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">
            <expand macro="sanitized"/>
        </param>
        <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="do_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"/>
        <data format="postgresql" name="outfile" from_work_dir="postgresql_out.tar.bz2" label="${tool.name} on ${on_string}">
    			<filter>psql_target['method'] == "pgtools"</filter>
    		</data>
    </outputs>
    <help>
Load features from a fasta file

@HELP@
    </help>
</tool>