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comparison panta.xml @ 2:137d00a9a598 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 55ba2c9616d6567fe7e6a798103c28885ca754dd
author iuc
date Mon, 13 Oct 2025 07:59:25 +0000
parents b50893534705
children 1de68b7a1e3f
comparison
equal deleted inserted replaced
1:b50893534705 2:137d00a9a598
11 #set input_directory = 'input_directory' 11 #set input_directory = 'input_directory'
12 mkdir $input_directory && 12 mkdir $input_directory &&
13 13
14 #if $input_type.input_type_selector == "gff": 14 #if $input_type.input_type_selector == "gff":
15 #for gff in $input_type.input_gff 15 #for gff in $input_type.input_gff
16 #set identifier = re.sub('[^\s\w\-\\.]','_',str($gff.element_identifier)) 16 #set $filename = '%s.gff' % re.sub('[^\w_-]', '_', str($gff.element_identifier))
17 ln -fs '$gff' '$input_directory/$identifier' && 17 cp '$gff' '$input_directory/$filename' &&
18 #end for 18 #end for
19 #elif $input_type.input_type_selector == "tsv": 19 #elif $input_type.input_type_selector == "tsv":
20 #set identifier = re.sub('[^\s\w\-\\.]','_',str($input_type.input_tsv.element_identifier)) 20 #set $filename = '%s.tsv' % re.sub('[^\w_-]', '_', str($input_type.input_tsv.element_identifier))
21 ln -fs '$input_type.input_tsv' '$input_directory/$identifier' && 21 cp '$input_type.input_tsv' '$input_directory/$filename' &&
22 #end if 22 #end if
23 23
24 #if $mode.select_mode == "main": 24 #if $mode.select_mode == "main":
25 panta main 25 panta main
26 #if $input_type.input_type_selector == "gff": 26 #if $input_type.input_type_selector == "gff":
400 <has_n_lines n="6" delta='3'/> 400 <has_n_lines n="6" delta='3'/>
401 </assert_contents> 401 </assert_contents>
402 </output> 402 </output>
403 <output name="core_gene_alignment" ftype="txt"> 403 <output name="core_gene_alignment" ftype="txt">
404 <assert_contents> 404 <assert_contents>
405 <has_n_lines n="96690" delta='3'/> 405 <has_n_lines n="96130" delta='3'/>
406 </assert_contents> 406 </assert_contents>
407 </output> 407 </output>
408 <output name="pan_genome_reference" ftype="txt"> 408 <output name="pan_genome_reference" ftype="txt">
409 <assert_contents> 409 <assert_contents>
410 <has_text text="AAAGGCGTTTGGTATATAACGATGCCAG"/> 410 <has_text text="AAAGGCGTTTGGTATATAACGATGCCAG"/>