Mercurial > repos > gga > apollo_delete_features

comparison delete_features.xml @ 13:21a8cad7dfa5 draft

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"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 7bf18c69becc57152efdadedf7ebd0bcfa382a15"
author gga
date Mon, 29 Jun 2020 09:12:19 -0400
parents df0e4eb2dfa5
children
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12:90c7d1d29b15 13:21a8cad7dfa5
12 #if str($ask_one) == "yes": 12 #if str($ask_one) == "yes":
13 ## Nope, still don't trust them to not be dumb (or malicious), so we backup first. 13 ## Nope, still don't trust them to not be dumb (or malicious), so we backup first.
14 python '$__tool_directory__/export.py' 14 python '$__tool_directory__/export.py'
15 @ORG_OR_GUESS@ 15 @ORG_OR_GUESS@
16 --gff '$gff_out' 16 --gff '$gff_out'
17 --fasta_pep '$fasta_pep' 17 --fasta_pep '$fasta_pep'
18 --fasta_cds '$fasta_cds' 18 --fasta_cds '$fasta_cds'
19 --fasta_cdna '$fasta_cdna' 19 --fasta_cdna '$fasta_cdna'
20 --vcf '$vcf_out' 20 --vcf '$vcf_out'
21 --json '$json_out' 21 --json '$json_out'
22 '$__user_email__' 22 '$__user_email__'
23 23
24 && 24 &&
25 25
68 68
69 <output name="gff_out"> 69 <output name="gff_out">
70 <assert_contents> 70 <assert_contents>
71 <has_text text="##sequence-region Merlin 1 172788" /> 71 <has_text text="##sequence-region Merlin 1 172788" />
72 <has_text text="owner=admin@local.host;" /> 72 <has_text text="owner=admin@local.host;" />
73 <has_text text="Name=cds-not-under-exon" />
74 </assert_contents> 73 </assert_contents>
75 </output> 74 </output>
76 <output name="fasta_pep" file="export/pep.fa" lines_diff="12"/> 75 <output name="fasta_pep" file="export/pep.fa" lines_diff="12"/>
77 <output name="fasta_cds" file="export/cds.fa" lines_diff="12"/> 76 <output name="fasta_cds" file="export/cds.fa" lines_diff="12"/>
78 <output name="fasta_cdna" file="export/cdna.fa" lines_diff="12"/> 77 <output name="fasta_cdna" file="export/cdna.fa" lines_diff="12"/>