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comparison csp2_snp.xml @ 62:0552b9528fc4

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"planemo upload"
author rliterman
date Thu, 19 Dec 2024 13:20:18 -0500
parents e7470d424809
children b87f07ac9edc
comparison
equal deleted inserted replaced
61:e7470d424809 62:0552b9528fc4
18 export QUERY_FASTA_SELECT="$query_fasta.query_fasta_select" 18 export QUERY_FASTA_SELECT="$query_fasta.query_fasta_select"
19 export QUERY_READS_SELECT="$query_reads.query_reads_select" 19 export QUERY_READS_SELECT="$query_reads.query_reads_select"
20 export REF_FASTA_SELECT="$ref_fasta.ref_fasta_select" 20 export REF_FASTA_SELECT="$ref_fasta.ref_fasta_select"
21 export REF_READS_SELECT="$ref_reads.ref_reads_select" 21 export REF_READS_SELECT="$ref_reads.ref_reads_select"
22 22
23 echo "Query Fasta: \$QUERY_FASTA_SELECT";
24 echo "Ref Fasta: \$REF_FASTA_SELECT";
25
26 echo "Query Reads: \$QUERY_READS_SELECT";
27 echo "Ref Reads: \$REF_READS_SELECT";
28
23 if [[ "\$QUERY_FASTA_SELECT" == 'collection' ]]; then 29 if [[ "\$QUERY_FASTA_SELECT" == 'collection' ]]; then
24 #set query_fasta_input=$query_fasta.coll.elements 30 #set query_fasta_input=$query_fasta.coll.elements
25 elif [[ "\$QUERY_FASTA_SELECT" == 'history' ]]; then 31 elif [[ "\$QUERY_FASTA_SELECT" == 'history' ]]; then
26 #set query_fasta_input=$query_fasta.list 32 #set query_fasta_input=$query_fasta.list
27 fi; 33 fi;
40 fi; 46 fi;
41 47
42 if [[ "\$REF_READS_SELECT" == 'collection' ]]; then 48 if [[ "\$REF_READS_SELECT" == 'collection' ]]; then
43 #set ref_reads_forward=$ref_reads.coll.forward 49 #set ref_reads_forward=$ref_reads.coll.forward
44 #set ref_reads_reverse=$ref_reads.coll.reverse 50 #set ref_reads_reverse=$ref_reads.coll.reverse
45 elif [[ "\$REF_READS_SELECT" =='history' ]]; then 51 elif [[ "\$REF_READS_SELECT" == 'history' ]]; then
46 #set ref_reads_forward=$ref_reads.list 52 #set ref_reads_forward=$ref_reads.list
47 fi; 53 fi;
48 54
49 echo "Query Fasta: \$QUERY_FASTA_SELECT"; 55 if [[ "\$QUERY_FASTA_SELECT" == 'none' ]]; then
50 echo "Ref Fasta: \$REF_FASTA_SELECT";
51
52 echo "Query Reads: \$QUERY_READS_SELECT";
53 echo "Ref Reads: \$REF_READS_SELECT";
54
55 if [[ "\$QUERY_FASTA_SELECT" == 'none']]; then
56 export QUERY_FASTA_ARG=""; 56 export QUERY_FASTA_ARG="";
57 else 57 else
58 #for query in $query_fasta_input: 58 #for query in $query_fasta_input:
59 ln -sf ${query} ./queries/${query.element_identifier}; 59 ln -sf ${query} ./queries/${query.element_identifier};
60 #end for 60 #end for
61 export QUERY_FASTA_ARG="--fasta ./queries"; 61 export QUERY_FASTA_ARG="--fasta ./queries";
62 fi; 62 fi;
63 63
64 64 if [[ "\$REF_FASTA_SELECT" == "none" ]]; then
65 if [[ "$ref_fasta.ref_fasta_select" == "none" ]]; then
66 export REF_FASTA_ARG=""; 65 export REF_FASTA_ARG="";
67 else 66 else
68 #for ref in $ref_fasta_input: 67 #for ref in $ref_fasta_input:
69 ln -sf ${ref} ./references/${ref.element_identifier}; 68 ln -sf ${ref} ./references/${ref.element_identifier};
70 #end for 69 #end for
71 export REF_FASTA_ARG="--fasta ./references"; 70 export REF_FASTA_ARG="--fasta ./references";
72 fi; 71 fi;
73 72
74 if [[ "$query_reads.query_reads_select" == "none" ]]; then 73 if [[ "\$QUERY_READS_SELECT" == "none" ]]; then
75 export QUERY_READS_ARG=""; 74 export QUERY_READS_ARG="";
76 else 75 else
77 #for query in $query_reads_forward $query_reads_reverse: 76 #for query in $query_reads_forward $query_reads_reverse:
78 ln -sf ${query} ./queries/${query.element_identifier}; 77 ln -sf ${query} ./queries/${query.element_identifier};
79 #end for 78 #end for
80 export QUERY_READS_ARG="--reads ./queries"; 79 export QUERY_READS_ARG="--reads ./queries";
81 fi; 80 fi;
82 81
83 if [[ "$ref_reads.ref_reads_select" == "none" ]]; then 82 if [[ "\$REF_READS_SELECT" == "none" ]]; then
84 export QUERY_READS_ARG=""; 83 export QUERY_READS_ARG="";
85 else 84 else
86 #for ref in $ref_reads_forward $ref_reads_reverse: 85 #for ref in $ref_reads_forward $ref_reads_reverse:
87 ln -sf ${ref} ./references/${ref.element_identifier}; 86 ln -sf ${ref} ./references/${ref.element_identifier};
88 #end for 87 #end for