comparison export.xml @ 16:c3251541cf2b draft

"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 1f9a5502a7423c78d862e81537b7646c9f4da5d9"

15:b503fe85f261

python '$__tool_directory__/export.py'

@ORG_CN_OR_GUESS@

--gff '$gff_out'
--fasta_pep '$fasta_pep'
--fasta_cds '$fasta_cds'
--fasta_cdna '$fasta_cdna'
--vcf '$vcf_out'
--json '$json_out'

'$__user_email__'

]]></command>
  <inputs>
    <expand macro="cn_or_guess" />
  </inputs>
  <outputs>
    <data format="gff3" name="gff_out" label="Annotations from Apollo"/>
    <data format="fasta" name="fasta_pep" label="Peptide sequences from Apollo"/>
    <data format="fasta" name="fasta_cds" label="CDS sequences from Apollo"/>

16:c3251541cf2b

python '$__tool_directory__/export.py'

@ORG_CN_OR_GUESS@

--gff '$gff_out'
$gff_with_fasta
--fasta_pep '$fasta_pep'
--fasta_cds '$fasta_cds'
--fasta_cdna '$fasta_cdna'
--vcf '$vcf_out'
--json '$json_out'
$die

'$__user_email__'

]]></command>
  <inputs>
    <expand macro="cn_or_guess" />
    <param name="gff_with_fasta" type="boolean" truevalue="--gff_with_fasta" falsevalue="" label="Include fasta in the GFF3 file" help="The fasta is available separately in the cDNA sequence file, but some tools might prefer it included in the GFF3 file."/>
    <param name="die" type="boolean" truevalue="--die" falsevalue="" label="Fail hard if any portion of the export fails" help="By default it will just print a warning message, this causes any error to be fatal."/>
  </inputs>
  <outputs>
    <data format="gff3" name="gff_out" label="Annotations from Apollo"/>
    <data format="fasta" name="fasta_pep" label="Peptide sequences from Apollo"/>
    <data format="fasta" name="fasta_cds" label="CDS sequences from Apollo"/>