view feature_load_gff.xml @ 4:3a36c33f7a49 draft

planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit d21999bb3e142fd972a3338b70216989a257d5b1

<?xml version="1.0"?>
<tool id="feature_load_gff" name="Chado load gff" version="@WRAPPER_VERSION@.0">
    <description></description>
    <macros>
    	 <import>macros.xml</import>
    </macros>
    <code file="chado.py"/>
    <expand macro="requirements"/>
    <command detect_errors="aggressive"><![CDATA[
@AUTH@

chakin feature load_gff
'$gff'
'$analysis_id'
'$organism'

#if $landmark_type:
  --landmark_type '$landmark_type'
#end if
#if $re_protein:
  --re_protein '$re_protein'
#end if
#if $re_protein_capture:
  --re_protein_capture '$re_protein_capture'
#end if
#if $fasta:
  --fasta '$fasta'
#end if
#if $no_seq_compute:
  $no_seq_compute
#end if
#if $add_only:
  $add_only
#end if

--quiet

 > $results
    ]]></command>
  	<inputs>
          <!-- arguments -->
      	<param name="gff" label="Gff" argument="gff" type="data" format="gff" help="Path to the Fasta file to load" />
      	<param argument="--analysis_id"
      		type="select"
      		dynamic_options="list_analyses()"
      		label="Analysis" />
          <param argument="--organism"
                 type="select"
                 dynamic_options="list_organisms()"
                 label="Organism" />

          <!-- options -->
      	<param name="landmark_type" label="Landmark Type" argument="landmark_type" type="text" help="Type of the landmarks (will speed up loading if provided, e.g. contig, should be a term of the Sequence ontology)" />
      	<param name="re_protein_capture" label="Regex protein capture" argument="re_protein_capture" type="text" help="Regular expression to capture groups in mRNA name to use in 'Regex protein' (e.g. '^(.*?)-R([A-Z]+)$', default='^(.*?)$' )">
            <expand macro="sanitized"/>
        </param>
      	<param name="re_protein" label="Regex protein" argument="re_protein" type="text" help="Replacement string for the protein name using capturing groups defined in 'Regex protein capture' (e.g. '\1-P\2')">
            <expand macro="sanitized"/>
        </param>
      	<param name="fasta" label="Fasta" argument="fasta" type="data" format="fasta" help="A Fasta containing sequences for some features. When creating a feature, if its sequence is in this fasta file it will be loaded. Otherwise for mRNA and polypeptides it will be computed from the genome sequence (if available), otherwise it will be left empty." optional="true" />
      	<param name="no_seq_compute" label="Allow computing missing sequences" argument="no_seq_compute" type="boolean" truevalue="" falsevalue="--no_seq_compute" help="Enable the computation of mRNA and polypeptides sequences based on genome sequence and positions." />
      	<param name="add_only" label="Add only" argument="add_only" type="boolean" truevalue="--add_only" falsevalue="" help="Use this flag if you're not updating existing features, but just adding new features to the selected analysis and organism. It will speedup loading, and reduce memory usage, but might produce errors in case of already existing feature." />

        <expand macro="wait_for"/>
  	</inputs>
  	<outputs>
  		  <data format="txt" name="results"/>
  	</outputs>
  	<help>
Load features from a gff file

@HELP@
  	</help>
</tool>