Mercurial > repos > rliterman > csp2

comparison csp2_snp.xml @ 56:c8ca27626fa9

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"planemo upload"
author rliterman
date Thu, 19 Dec 2024 10:56:32 -0500
parents 629a4fe7bb13
children c8dfcb29d91b
comparison
equal deleted inserted replaced
55:629a4fe7bb13 56:c8ca27626fa9
14 #for query in $query_fasta.list: 14 #for query in $query_fasta.list:
15 ln -sf ${query} ./queries/${query.element_identifier}; 15 ln -sf ${query} ./queries/${query.element_identifier};
16 #end for 16 #end for
17 export QUERY_FASTA_ARG="--fasta ./queries"; 17 export QUERY_FASTA_ARG="--fasta ./queries";
18 else 18 else
19 #for query in $query_fasta.elements: 19 #for query in $query_fasta.coll.elements:
20 ln -sf ${query} ./queries/${query.element_identifier}; 20 ln -sf ${query} ./queries/${query.element_identifier};
21 #end for 21 #end for
22 export QUERY_FASTA_ARG="--fasta ./queries"; 22 export QUERY_FASTA_ARG="--fasta ./queries";
23 fi; 23 fi;
24 24
28 #for ref in $ref_fasta.list: 28 #for ref in $ref_fasta.list:
29 ln -sf ${ref} ./references/${ref.element_identifier}; 29 ln -sf ${ref} ./references/${ref.element_identifier};
30 #end for 30 #end for
31 export REF_FASTA_ARG="--ref_fasta ./references"; 31 export REF_FASTA_ARG="--ref_fasta ./references";
32 else 32 else
33 #for ref in $ref_fasta.elements: 33 #for ref in $ref_fasta.coll.elements:
34 ln -sf ${ref} ./references/${ref.element_identifier}; 34 ln -sf ${ref} ./references/${ref.element_identifier};
35 #end for 35 #end for
36 export REF_FASTA_ARG="--ref_fasta ./references"; 36 export REF_FASTA_ARG="--ref_fasta ./references";
37 fi; 37 fi;
38 38