Mercurial > repos > greg > cfsan_snp_pipeline_snp_matrix
comparison cfsan_snp_pipeline_snp_matrix.xml @ 3:f959d99d1758 draft default tip
Uploaded
| author | greg |
|---|---|
| date | Thu, 23 Nov 2023 19:02:52 +0000 |
| parents | f3485a9e51a3 |
| children |
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| 2:610251aac6ef | 3:f959d99d1758 |
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| 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 #if str($reference_cond.reference_source) == 'cached' | 8 #if str($reference_cond.reference_source) == 'cached' |
| 9 set reference = '$reference_cond.reference.fields.path' | 9 #set reference = $reference_cond.reference.fields.path |
| 10 #else: | 10 #else: |
| 11 set reference = '$reference_cond.reference' | 11 #set reference = $reference_cond.reference |
| 12 #end if | 12 #end if |
| 13 | 13 |
| 14 python '$__tool_directory__/snp_wind.py' ./ -p 'consensus.fasta' | 14 python '$__tool_directory__/snp_wind.py' ./ -p 'consensus.fasta' |
| 15 #for $fa in sorted($input_fasta_collection, key=lambda f: f.element_identifier): | 15 #for $fa in sorted($input_fasta_collection, key=lambda f: f.element_identifier): |
| 16 -n '$fa.element_identifier' -f '$fa' | 16 -n '$fa.element_identifier' -f '$fa' |