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comparison csp2_screen.xml @ 45:dc4592a56011

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"planemo upload"
author rliterman
date Thu, 12 Dec 2024 14:47:33 -0500
parents 1a38b6829885
children ae20d491d871
comparison
equal deleted inserted replaced
44:1a38b6829885 45:dc4592a56011
9 9
10 mkdir ./queries ./references; 10 mkdir ./queries ./references;
11 11
12 if [ -n "$query_fasta" ] && [ "$query_fasta" != "None" ]; then 12 if [ -n "$query_fasta" ] && [ "$query_fasta" != "None" ]; then
13 #for query in $query_fasta: 13 #for query in $query_fasta:
14 ln -sf ${query} ./queries/${query.element_identifier} && 14 ln -sf ${query} ./queries/${query.element_identifier};
15 #end for 15 #end for
16 export QUERY_FASTA_ARG="--fasta ./queries" && 16 export QUERY_FASTA_ARG="--fasta ./queries";
17 else 17 else
18 export QUERY_FASTA_ARG="" && 18 export QUERY_FASTA_ARG="";
19 fi; 19 fi;
20 20
21 if [ -n "$query_reads" ] && [ "$query_reads" != "None" ]; then 21 if [ -n "$query_reads" ] && [ "$query_reads" != "None" ]; then
22 #for query in $query_reads: 22 #for query in $query_reads:
23 ln -sf ${query} ./queries/${query.element_identifier} && 23 ln -sf ${query} ./queries/${query.element_identifier};
24 #end for 24 #end for
25 export QUERY_READS_ARG="--reads ./queries" && 25 export QUERY_READS_ARG="--reads ./queries";
26 else 26 else
27 export QUERY_READS_ARG="" && 27 export QUERY_READS_ARG="";
28 fi; 28 fi;
29 29
30 if [ -n "$ref_fasta" ] && [ "$ref_fasta" != "None" ]; then 30 if [ -n "$ref_fasta" ] && [ "$ref_fasta" != "None" ]; then
31 #for ref in $ref_fasta: 31 #for ref in $ref_fasta:
32 ln -sf ${ref} ./references/${ref.element_identifier} && 32 ln -sf ${ref} ./references/${ref.element_identifier};
33 #end for 33 #end for
34 export REF_FASTA_ARG="--ref_fasta ./references" && 34 export REF_FASTA_ARG="--ref_fasta ./references";
35 else 35 else
36 export REF_FASTA_ARG="" && 36 export REF_FASTA_ARG="";
37 fi; 37 fi;
38 38
39 if [ -n "$ref_reads" ] && [ "$ref_reads" != "None" ]; then 39 if [ -n "$ref_reads" ] && [ "$ref_reads" != "None" ]; then
40 #for ref in $ref_reads: 40 #for ref in $ref_reads:
41 ln -sf ${ref} ./references/${ref.element_identifier} && 41 ln -sf ${ref} ./references/${ref.element_identifier};
42 #end for 42 #end for
43 export REF_READS_ARG="--ref_reads ./references" && 43 export REF_READS_ARG="--ref_reads ./references";
44 else 44 else
45 export REF_READS_ARG="" && 45 export REF_READS_ARG="";
46 fi; 46 fi;
47 47
48 if [ -n "$trim_name" ] && [ "$trim_name" != "None" ]; then 48 if [ -n "$trim_name" ] && [ "$trim_name" != "None" ]; then
49 export TRIM_ARG="--trim_name $trim_name" && 49 export TRIM_ARG="--trim_name $trim_name";
50 else 50 else
51 export TRIM_ARG="" && 51 export TRIM_ARG="";
52 fi; 52 fi;
53 53
54 if [ -n "$ref_id" ] && [ "$ref_id" != "None" ]; then 54 if [ -n "$ref_id" ] && [ "$ref_id" != "None" ]; then
55 export REF_ID_ARG="--ref_id $ref_id" && 55 export REF_ID_ARG="--ref_id $ref_id";
56 else 56 else
57 export REF_ID_ARG="" && 57 export REF_ID_ARG="";
58 fi; 58 fi;
59 59
60 nextflow run ${__tool_directory__}/CSP2/CSP2.nf -profile csp2_galaxy --runmode screen \$QUERY_FASTA_ARG \$REF_FASTA_ARG \$QUERY_READS_ARG \$REF_READS_ARG \$REF_ID_ARG \$TRIM_ARG --readext $readext --forward $forward --reverse $reverse --ref_readext $readext --ref_forward $forward --ref_reverse $reverse --min_cov $min_cov --min_iden $min_iden --min_len $min_len --ref_edge $ref_edge --query_edge $query_edge --dwin $dwin --wsnps $wsnps --out ./CSP2_Screen_Output > Nextflow_Log.txt 2>&1; 60 nextflow run ${__tool_directory__}/CSP2/CSP2.nf -profile csp2_galaxy --runmode screen \$QUERY_FASTA_ARG \$REF_FASTA_ARG \$QUERY_READS_ARG \$REF_READS_ARG \$REF_ID_ARG \$TRIM_ARG --readext $readext --forward $forward --reverse $reverse --ref_readext $readext --ref_forward $forward --ref_reverse $reverse --min_cov $min_cov --min_iden $min_iden --min_len $min_len --ref_edge $ref_edge --query_edge $query_edge --dwin $dwin --wsnps $wsnps --out ./CSP2_Screen_Output > Nextflow_Log.txt 2>&1;
61 cat Nextflow_Log.txt; 61 cat Nextflow_Log.txt;
62 ]]> 62 ]]>