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comparison csp2_snp.xml @ 57:c8dfcb29d91b

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"planemo upload"
author rliterman
date Thu, 19 Dec 2024 11:22:22 -0500
parents c8ca27626fa9
children c8676ac8c6b7
comparison
equal deleted inserted replaced
56:c8ca27626fa9 57:c8dfcb29d91b
6 </requirements> 6 </requirements>
7 <version_command>nextflow -version</version_command> 7 <version_command>nextflow -version</version_command>
8 <command detect_errors="aggressive"><![CDATA[ 8 <command detect_errors="aggressive"><![CDATA[
9 mkdir ./queries ./references; 9 mkdir ./queries ./references;
10 10
11 if [[ "$query_fasta.query_fasta_select" == "none" ]]; then 11 export QUERY_FASTA_SELECT="${query_fasta.query_fasta_select}"
12 export QUERY_READS_SELECT="${query_reads.query_reads_select}"
13 export REF_FASTA_SELECT="${ref_fasta.ref_fasta_select}"
14 export REF_READS_SELECT="${ref_reads.ref_reads_select}"
15
16 if [[ "\$QUERY_FASTA_SELECT" == "none" ]]; then
12 export QUERY_FASTA_ARG=""; 17 export QUERY_FASTA_ARG="";
13 elif [[ "$query_fasta.query_fasta_select" == "history" ]]; then 18 elif [[ "\$QUERY_FASTA_SELECT" == "history" ]]; then
14 #for query in $query_fasta.list: 19 #for query in $query_fasta.list:
15 ln -sf ${query} ./queries/${query.element_identifier}; 20 ln -sf ${query} ./queries/${query.element_identifier};
16 #end for 21 #end for
17 export QUERY_FASTA_ARG="--fasta ./queries"; 22 export QUERY_FASTA_ARG="--fasta ./queries";
18 else 23 else
20 ln -sf ${query} ./queries/${query.element_identifier}; 25 ln -sf ${query} ./queries/${query.element_identifier};
21 #end for 26 #end for
22 export QUERY_FASTA_ARG="--fasta ./queries"; 27 export QUERY_FASTA_ARG="--fasta ./queries";
23 fi; 28 fi;
24 29
25 if [[ "$ref_fasta.ref_fasta_select" == "none" ]]; then 30 if [[ "\$REF_FASTA_SELECT" == "none" ]]; then
26 export REF_FASTA_ARG=""; 31 export REF_FASTA_ARG="";
27 elif [[ "$ref_fasta.ref_fasta_select" == "history" ]]; then 32 elif [[ "\$REF_FASTA_SELECT" == "history" ]]; then
28 #for ref in $ref_fasta.list: 33 #for ref in $ref_fasta.list:
29 ln -sf ${ref} ./references/${ref.element_identifier}; 34 ln -sf ${ref} ./references/${ref.element_identifier};
30 #end for 35 #end for
31 export REF_FASTA_ARG="--ref_fasta ./references"; 36 export REF_FASTA_ARG="--ref_fasta ./references";
32 else 37 else
34 ln -sf ${ref} ./references/${ref.element_identifier}; 39 ln -sf ${ref} ./references/${ref.element_identifier};
35 #end for 40 #end for
36 export REF_FASTA_ARG="--ref_fasta ./references"; 41 export REF_FASTA_ARG="--ref_fasta ./references";
37 fi; 42 fi;
38 43
39 if [[ "$query_reads.query_reads_select" == "none" ]]; then 44 if [[ "\$QUERY_READS_SELECT" == "none" ]]; then
40 export QUERY_READS_ARG=""; 45 export QUERY_READS_ARG="";
41 elif [[ "$query_reads.query_reads_select" == "history" ]]; then 46 elif [[ "\$QUERY_READS_SELECT" == "history" ]]; then
42 #for query in $query_reads.list: 47 #for query in $query_reads.list:
43 ln -sf ${query} ./queries/${query.element_identifier}; 48 ln -sf ${query} ./queries/${query.element_identifier};
44 #end for 49 #end for
45 export QUERY_READS_ARG="--reads ./queries"; 50 export QUERY_READS_ARG="--reads ./queries";
46 else 51 else
51 ln -sf ${query} ./queries/${query.element_identifier}; 56 ln -sf ${query} ./queries/${query.element_identifier};
52 #end for 57 #end for
53 export QUERY_READS_ARG="--reads ./queries"; 58 export QUERY_READS_ARG="--reads ./queries";
54 fi; 59 fi;
55 60
56 if [[ "$ref_reads.ref_reads_select" == "none" ]]; then 61 if [[ "\$REF_READS_SELECT" == "none" ]]; then
57 export REF_READS_ARG=""; 62 export REF_READS_ARG="";
58 elif [[ "$ref_reads.ref_reads_select" == "history" ]]; then 63 elif [[ "\$REF_READS_SELECT" == "history" ]]; then
59 #for ref in $ref_reads.list: 64 #for ref in $ref_reads.list:
60 ln -sf ${ref} ./references/${ref.element_identifier}; 65 ln -sf ${ref} ./references/${ref.element_identifier};
61 #end for 66 #end for
62 export REF_READS_ARG="--ref_reads ./references"; 67 export REF_READS_ARG="--ref_reads ./references";
63 else 68 else