Mercurial > repos > iuc > chewbbaca_createschema
diff 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 |
|---|---|
| date | Fri, 07 Jun 2024 14:27:26 +0000 |
| parents | 4e61ec4fd5f5 |
| children |
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--- a/CreateSchema.xml Sat May 11 22:50:19 2024 +0000 +++ b/CreateSchema.xml Fri Jun 07 14:27:26 2024 +0000 @@ -5,9 +5,11 @@ </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ + #import re mkdir 'input' && #for $file in $input_file - ln -sf '$file' 'input/${file.element_identifier}' && + #set escaped_element_identifier = re.sub('[^\w\-]', '_', str($file.element_identifier)) + ln -sf '$file' 'input/${escaped_element_identifier}.${file.ext}' && #end for chewBBACA.py CreateSchema #if $training_file: @@ -62,6 +64,16 @@ </output> </test> <test expect_num_outputs="1"> + <param name="input_file" value="GCA_000007265.1_ASM726v1_genomic"/> + <output name="schema"> + <assert_contents> + <has_archive_member path="schema_seed/.*\.fasta" n="204"/> + <has_archive_member path="schema_seed/short/.*\.fasta" n="102"/> + <has_archive_member path="schema_seed/\.schema_config"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> <param name="input_file" value="GCA_000007265.1_ASM726v1_genomic.fna"/> <param name="training_file" value="Streptococcus_agalactiae.trn"/> <output name="schema"> @@ -77,7 +89,7 @@ <param name="cds_input" value="true"/> <output name="schema"> <assert_contents> - <has_archive_member path="schema_seed/CDS-Str-agalactiae-protein1.fasta"/> + <has_archive_member path="schema_seed/CDS-Str-agalactiae-fasta-protein1.fasta"/> </assert_contents> </output> </test>