Mercurial > repos > iuc > chewbbaca_createschema
comparison CreateSchema.xml @ 2:6a8df4d75f3a draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 501c1cb91f4b91ec93e6df6e555323bbe8e2b703
author | iuc |
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date | Fri, 07 Jun 2024 14:27:26 +0000 |
parents | 4e61ec4fd5f5 |
children |
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1:220e2f7ff8bb | 2:6a8df4d75f3a |
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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> |