diff export.xml @ 19:4ba339eb4f73 draft

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

--- a/export.xml	Tue Jun 08 09:10:52 2021 +0000
+++ b/export.xml	Fri Dec 10 09:44:53 2021 +0000
@@ -13,17 +13,21 @@
 @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"/>