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comparison csp2_snp.xml @ 61:e7470d424809

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"planemo upload"
author rliterman
date Thu, 19 Dec 2024 13:02:58 -0500
parents 5378cd1e3a39
children 0552b9528fc4
comparison
equal deleted inserted replaced
60:5378cd1e3a39 61:e7470d424809
13 #set query_reads_forward="" 13 #set query_reads_forward=""
14 #set query_reads_reverse="" 14 #set query_reads_reverse=""
15 #set ref_reads_forward="" 15 #set ref_reads_forward=""
16 #set ref_reads_reverse="" 16 #set ref_reads_reverse=""
17 17
18 #if "$query_fasta.query_fasta_select" == 'collection' 18 export QUERY_FASTA_SELECT="$query_fasta.query_fasta_select"
19 export QUERY_READS_SELECT="$query_reads.query_reads_select"
20 export REF_FASTA_SELECT="$ref_fasta.ref_fasta_select"
21 export REF_READS_SELECT="$ref_reads.ref_reads_select"
22
23 if [[ "\$QUERY_FASTA_SELECT" == 'collection' ]]; then
19 #set query_fasta_input=$query_fasta.coll.elements 24 #set query_fasta_input=$query_fasta.coll.elements
20 #elseif "$query_fasta.query_fasta_select" == 'history' 25 elif [[ "\$QUERY_FASTA_SELECT" == 'history' ]]; then
21 #set query_fasta_input=$query_fasta.list 26 #set query_fasta_input=$query_fasta.list
22 #end if 27 fi;
23 28
24 #if "$ref_fasta.ref_fasta_select" == 'collection' 29 if [[ "\$REF_FASTA_SELECT" == 'collection' ]]; then
25 #set ref_fasta_input=$ref_fasta.coll.elements 30 #set ref_fasta_input=$ref_fasta.coll.elements
26 #elseif "$ref_fasta.ref_fasta_select" == 'history' 31 elif [[ "\$REF_FASTA_SELECT" == 'history' ]]; then
27 #set ref_fasta_input=$ref_fasta.list 32 #set ref_fasta_input=$ref_fasta.list
28 #end if 33 fi;
29 34
30 #if "$query_reads.query_reads_select" == 'collection' 35 if [[ "\$QUERY_READS_SELECT" == 'collection' ]]; then
31 #set query_reads_forward=$query_reads.coll.forward 36 #set query_reads_forward=$query_reads.coll.forward
32 #set query_reads_reverse=$query_reads.coll.reverse 37 #set query_reads_reverse=$query_reads.coll.reverse
33 #elseif "$query_reads.query_reads_select" == 'history' 38 elif [[ "\$QUERY_READS_SELECT" == 'history' ]]; then
34 #set query_reads_forward=$query_reads.list 39 #set query_reads_forward=$query_reads.list
35 #end if 40 fi;
36 41
37 #if "$ref_reads.ref_reads_select" == 'collection' 42 if [[ "\$REF_READS_SELECT" == 'collection' ]]; then
38 #set ref_reads_forward=$ref_reads.coll.forward 43 #set ref_reads_forward=$ref_reads.coll.forward
39 #set ref_reads_reverse=$ref_reads.coll.reverse 44 #set ref_reads_reverse=$ref_reads.coll.reverse
40 #elseif "$ref_reads.ref_reads_select" == 'history' 45 elif [[ "\$REF_READS_SELECT" =='history' ]]; then
41 #set ref_reads_forward=$ref_reads.list 46 #set ref_reads_forward=$ref_reads.list
42 #end if 47 fi;
43 48
44 if [[ "$query_fasta.query_fasta_select" == "none" ]]; then 49 echo "Query Fasta: \$QUERY_FASTA_SELECT";
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
45 export QUERY_FASTA_ARG=""; 56 export QUERY_FASTA_ARG="";
46 else 57 else
47 #for query in $query_fasta_input: 58 #for query in $query_fasta_input:
48 ln -sf ${query} ./queries/${query.element_identifier}; 59 ln -sf ${query} ./queries/${query.element_identifier};
49 #end for 60 #end for