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comparison csp2_snp.xml @ 65:c2a886313008

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"planemo upload"
author rliterman
date Thu, 19 Dec 2024 14:51:58 -0500
parents 6f3b67127e44
children 90e29c1ddeca
comparison
equal deleted inserted replaced
64:6f3b67127e44 65:c2a886313008
26 export REF_FASTA_ARG=""; 26 export REF_FASTA_ARG="";
27 #elif (str($ref_fasta.ref_fasta_select) == "collection"): 27 #elif (str($ref_fasta.ref_fasta_select) == "collection"):
28 #for _, $ref_assembly in enumerate($ref_fasta.coll): 28 #for _, $ref_assembly in enumerate($ref_fasta.coll):
29 ln -sf ${ref_assembly} ./references/${ref_assembly.element_identifier}; 29 ln -sf ${ref_assembly} ./references/${ref_assembly.element_identifier};
30 #end for 30 #end for
31 export REF_FASTA_ARG="--fasta ./queries"; 31 export REF_FASTA_ARG="--fasta ./references";
32 else 32 #else
33 #for _, $ref_assembly in enumerate($ref_fasta.list): 33 #for _, $ref_assembly in enumerate($ref_fasta.list):
34 ln -sf ${ref_assembly} ./references/${ref_assembly.element_identifier}; 34 ln -sf ${ref_assembly} ./references/${ref_assembly.element_identifier};
35 #end for 35 #end for
36 export REF_FASTA_ARG="--fasta ./references"; 36 export REF_FASTA_ARG="--fasta ./references";
37 #end if 37 #end if
38 38
39 #if (str($query_reads.query_reads_select) == "none"): 39 #if (str($query_reads.query_reads_select) == "none"):
40 export QUERY_READS_ARG=""; 40 export QUERY_READS_ARG="";
41 #elif (str($query_reads.query_reads_select) == "collection"): 41 #elif (str($query_reads.query_reads_select) == "collection"):
42 #for _, $pair in enumerate($query_reads.coll): 42 #for _, $pair in enumerate($query_reads.coll):
43 ln -sf '$pair.forward' ./queries/${pair.forward.element_identifier}; 43 ln -sf ${pair.forward} ./queries/${pair.forward.element_identifier};
44 ln -sf '$pair.reverse' ./queries/${pair.reverse.element_identifier}; 44 ln -sf ${pair.reverse} ./queries/${pair.reverse.element_identifier};
45 #end for 45 #end for
46 export QUERY_READS_ARG="--reads ./queries"; 46 export QUERY_READS_ARG="--reads ./queries";
47 else 47 #else
48 #for _, $read_file in enumerate($query_reads.list): 48 #for _, $read_file in enumerate($query_reads.list):
49 ln -sf ${read_file} ./queries/${read_file.element_identifier}; 49 ln -sf ${read_file} ./queries/${read_file.element_identifier};
50 #end for 50 #end for
51 export QUERY_READS_ARG="--reads ./queries"; 51 export QUERY_READS_ARG="--reads ./queries";
52 #end if 52 #end if
53 53
54 #if (str($ref_reads.ref_reads_select) == "none"): 54 #if (str($ref_reads.ref_reads_select) == "none"):
55 export REF_READS_ARG=""; 55 export REF_READS_ARG="";
56 #elif (str($ref_reads.ref_reads_select) == "collection"): 56 #elif (str($ref_reads.ref_reads_select) == "collection"):
57 #for _, $pair in enumerate($ref_reads.coll): 57 #for _, $pair in enumerate($ref_reads.coll):
58 ln -sf '$pair.forward' ./references/${pair.forward.element_identifier}; 58 ln -sf ${pair.forward} ./references/${pair.forward.element_identifier};
59 ln -sf '$pair.reverse' ./references/${pair.reverse.element_identifier}; 59 ln -sf ${pair.reverse} ./references/${pair.reverse.element_identifier};
60 #end for 60 #end for
61 export REF_READS_ARG="--ref_reads ./references"; 61 export REF_READS_ARG="--ref_reads ./references";
62 else 62 #else
63 #for _, $read_file in enumerate($ref_reads.list): 63 #for _, $read_file in enumerate($ref_reads.list):
64 ln -sf ${read_file} ./references/${read_file.element_identifier}; 64 ln -sf ${read_file} ./references/${read_file.element_identifier};
65 #end for 65 #end for
66 export REF_READS_ARG="--ref_reads ./references"; 66 export REF_READS_ARG="--ref_reads ./references";
67 #end if 67 #end if