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comparison csp2_snp.xml @ 64:6f3b67127e44

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"planemo upload"
author rliterman
date Thu, 19 Dec 2024 14:35:57 -0500
parents b87f07ac9edc
children c2a886313008
comparison
equal deleted inserted replaced
63:b87f07ac9edc 64:6f3b67127e44
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_FASTA_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"):
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_FASTA_ARG="--ref_reads ./references"; 66 export REF_READS_ARG="--ref_reads ./references";
67 #end if 67 #end if
68 68
69 if [ -n "$trim_name" ] && [ "$trim_name" != "None" ]; then 69 if [ -n "$trim_name" ] && [ "$trim_name" != "None" ]; then
70 export TRIM_ARG="--trim_name $trim_name"; 70 export TRIM_ARG="--trim_name $trim_name";
71 else 71 else