view macros.xml @ 1:f7d57e56f322 draft

planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 0f3c6e906c4d32843f451990b55bfa2954235a42

<?xml version="1.0"?>
<macros>
  <xml name="requirements">
    <requirements>
      <requirement type="package" version="2.7">python</requirement>
      <yield/>
    </requirements>
  </xml>
  <token name="@URL@">
https://cpt.tamu.edu/apollo
  </token>
  <token name="@AUTH@">
@URL@
[e-mail]
\$GALAXY_WEBAPOLLO_PASSWORD
  </token>
  <xml name="auth_file">
    <param label="Apollo Authentication File"
    name="apolloCredentialsFile" type="data" format="json" />
  </xml>

  <token name="@CN_OR_GUESS@">
<![CDATA[
#if $cn_source.source_select == "auto":
    \$(cat $cn_source.cn_file | grep '^>' | head -n 1  | sed 's/\s.*//g;s/>//g')
#elif $cn_source.source_select == "auto_json":
    \$(cat $cn_source.cn_file | grep 'commonName' | head -n 1| sed 's/.*: "//g;s/".*//g')
#else
    "${cn_source.organism_cn}"
#end if
]]>
  </token>
  <xml name="cn_or_guess">
    <conditional name="cn_source">
        <param name="source_select" type="select" label="Organism Common Name Source">
            <option value="auto">Autodetect from Fasta</option>
            <option value="auto_json">Autodetect from Apollo JSON</option>
            <option value="direct">Direct Entry</option>
        </param>
        <when value="auto">
            <param name="cn_file" type="data" format="fasta" label="Organism Common Name" />
        </when>
        <when value="auto_json">
            <param name="cn_file" type="data" format="json" label="Apollo Organism File" />
        </when>
        <when value="direct">
            <param name="organism_cn" type="text" label="Organism Common Name" />
        </when>
    </conditional>
  </xml>

  <xml name="citations">
      <citations>
      </citations>
  </xml>
  <xml name="dummy">
    <param label="Dummy Inputs" name="dummy" type="data" multiple="True" optional="True">
        <help>
            With workflows that contact remote databases, it is sometimes
            necessary to have particular operations happen in a particular
            order. I.e. you would not want to try and add data to an organism
            if the organism did not yet exist in WebApollo.
            Since few of the WebApollo2 toolsuite output files which are
            used in a downstream task (e.g. the output adding an organism is
            not used elsewhere), we provide this dummy option which lets you
            select outputs to help provide context for when this task should
            execute.
        </help>
    </param>
  </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:
Eric Rasche (2016), `Galaxy wrapper <https://github.com/TAMU-CPT/galaxy-webapollo>`_
]]>
    </token>
</macros>