Mercurial > repos > iuc > chewbbaca_createschema

comparison CreateSchema.xml @ 2:6a8df4d75f3a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 501c1cb91f4b91ec93e6df6e555323bbe8e2b703
author iuc
date Fri, 07 Jun 2024 14:27:26 +0000
parents 4e61ec4fd5f5
children ae1374a5ecdf
comparison
equal deleted inserted replaced
1:220e2f7ff8bb 2:6a8df4d75f3a
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 #import re
8 mkdir 'input' && 9 mkdir 'input' &&
9 #for $file in $input_file 10 #for $file in $input_file
10 ln -sf '$file' 'input/${file.element_identifier}' && 11 #set escaped_element_identifier = re.sub('[^\w\-]', '_', str($file.element_identifier))
12 ln -sf '$file' 'input/${escaped_element_identifier}.${file.ext}' &&
11 #end for 13 #end for
12 chewBBACA.py CreateSchema 14 chewBBACA.py CreateSchema
13 #if $training_file: 15 #if $training_file:
14 --ptf '$training_file' 16 --ptf '$training_file'
15 #end if 17 #end if
60 <has_archive_member path="schema_seed/\.schema_config"/> 62 <has_archive_member path="schema_seed/\.schema_config"/>
61 </assert_contents> 63 </assert_contents>
62 </output> 64 </output>
63 </test> 65 </test>
64 <test expect_num_outputs="1"> 66 <test expect_num_outputs="1">
67 <param name="input_file" value="GCA_000007265.1_ASM726v1_genomic"/>
68 <output name="schema">
69 <assert_contents>
70 <has_archive_member path="schema_seed/.*\.fasta" n="204"/>
71 <has_archive_member path="schema_seed/short/.*\.fasta" n="102"/>
72 <has_archive_member path="schema_seed/\.schema_config"/>
73 </assert_contents>
74 </output>
75 </test>
76 <test expect_num_outputs="1">
65 <param name="input_file" value="GCA_000007265.1_ASM726v1_genomic.fna"/> 77 <param name="input_file" value="GCA_000007265.1_ASM726v1_genomic.fna"/>
66 <param name="training_file" value="Streptococcus_agalactiae.trn"/> 78 <param name="training_file" value="Streptococcus_agalactiae.trn"/>
67 <output name="schema"> 79 <output name="schema">
68 <assert_contents> 80 <assert_contents>
69 <has_archive_member path="schema_seed/.*\.fasta" n="198"/> 81 <has_archive_member path="schema_seed/.*\.fasta" n="198"/>
75 <test expect_num_outputs="1"> 87 <test expect_num_outputs="1">
76 <param name="input_file" value="CDS_Str_agalactiae.fasta"/> 88 <param name="input_file" value="CDS_Str_agalactiae.fasta"/>
77 <param name="cds_input" value="true"/> 89 <param name="cds_input" value="true"/>
78 <output name="schema"> 90 <output name="schema">
79 <assert_contents> 91 <assert_contents>
80 <has_archive_member path="schema_seed/CDS-Str-agalactiae-protein1.fasta"/> 92 <has_archive_member path="schema_seed/CDS-Str-agalactiae-fasta-protein1.fasta"/>
81 </assert_contents> 93 </assert_contents>
82 </output> 94 </output>
83 </test> 95 </test>
84 </tests> 96 </tests>
85 <help> 97 <help>