<?xml version="1.0"?>
<macros>
  <token name="@WRAPPER_VERSION@">4.2.3</token>

  <xml name="requirements">
    <requirements>
      <requirement type="package" version="4.2.3">apollo</requirement>
      <yield/>
    </requirements>
  </xml>
  <token name="@DATA_DIR@">\$GALAXY_SHARED_DIR</token>
  <token name="@EXT_URL@">
"\$GALAXY_WEBAPOLLO_EXT_URL"
  </token>
  <token name="@URL@">
"\$GALAXY_WEBAPOLLO_URL"
  </token>

  <token name="@AUTH@"><![CDATA[
      if [ -z "\$ARROW_GLOBAL_CONFIG_PATH" ]; then
        echo "__default: local" > '.auth.yml' &&
        echo "local:" >> '.auth.yml' &&
        echo "    url: \"\$GALAXY_WEBAPOLLO_URL\"" >> '.auth.yml' &&
        echo "    username: \"\$GALAXY_WEBAPOLLO_USER\"" >> '.auth.yml' &&
        echo "    password: \"\$GALAXY_WEBAPOLLO_PASSWORD\"" >> '.auth.yml' &&

        export ARROW_GLOBAL_CONFIG_PATH='.auth.yml'
      ; fi &&
  ]]></token>

  <token name="@ORG_OR_GUESS@">
<![CDATA[
#if $org_source.source_select == "auto_json":
    --org_json '${org_source.org_file}'
#elif $org_source.source_select == "select":
    --org_id '${org_source.org_select}'
#else:
    --org_raw '${org_source.org_raw}'
#end if
]]>
  </token>
  <token name="@ORG_CN_OR_GUESS@">
<![CDATA[
@ORG_OR_GUESS@

#if $cn_source.source_select == "auto":
    #if str($cn_source.cn_file) != "None":
        --seq_fasta '$cn_source.cn_file'
    #end if
#else
    #if $cn_source.source_select != "all" and len($cn_source.refseqs) > 0:
        --seq_raw
        #for $item in $cn_source.refseqs:
            '${item.refseq}'
        #end for
    #end if
#end if
]]>
  </token>
  <xml name="org_or_guess">
    <conditional name="org_source">
        <param name="source_select" type="select" label="Organism Common Name Source">
            <option value="select">Select</option>
            <option value="direct">Direct Entry</option>
            <option value="auto_json">Autodetect from Apollo JSON</option>
        </param>
        <when value="select">
            <param name="org_select" type="select" dynamic_options="galaxy_list_orgs(__trans__)" label="Organism" />
        </when>
        <when value="direct">
            <param name="org_raw" type="text" label="Organism Common Name" optional="False" />
        </when>
        <when value="auto_json">
            <param name="org_file" type="data" format="json" label="Apollo Organism File" help="Will only fetch first organism" />
        </when>
    </conditional>
  </xml>
  <xml name="cn_or_guess">
    <expand macro="org_or_guess" />
    <conditional name="cn_source">
        <param name="source_select" type="select" label="Organism Sequence(s) Source">
            <option value="all">All Refseqs</option>
            <option value="direct">Direct Entry</option>
            <option value="auto">Autodetect from Fasta</option>
        </param>
        <when value="all">
        </when>
        <when value="auto">
            <param name="cn_file" type="data" format="fasta" label="Reference sequence(s)" optional="true"/>
        </when>
        <when value="direct">
            <repeat name="refseqs" title="Reference Sequences" help="These are used to identify sequences within an organism that you wish to extract">
                <param name="refseq" type="text" label="Reference sequence(s)" />
            </repeat>
        </when>
    </conditional>
  </xml>

  <xml name="citations">
      <citations>
        <citation type="doi">10.1371/journal.pcbi.1006790</citation>
      </citations>
  </xml>
  <xml name="gff3_input">
    <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/>
  </xml>
  <token name="@GENOME_SELECTOR_PRE@">
#if $reference_genome.reference_genome_source == 'history':
    ln -s '$reference_genome.genome_fasta' genomeref.fa;
#end if
  </token>
  <token name="@GENOME_SELECTOR@">
#if $reference_genome.reference_genome_source == 'cached':
    '${reference_genome.fasta_indexes.fields.path}'
#elif $reference_genome.reference_genome_source == 'history':
    genomeref.fa
#end if
  </token>
<token name="@REFERENCES@">
<![CDATA[
------

**Citation**

If you use this tool in Galaxy, please cite:
Helena Rasche, Anthony Bretaudeau, and Mateo Boudet (2019), `Galaxy Apollo Tools <https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo>`_
]]>
    </token>
</macros>