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comparison csp2_screen.xml @ 43:32ee1ce20411

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"planemo upload"
author rliterman
date Thu, 12 Dec 2024 14:22:33 -0500
parents bbbf36187d87
children 1a38b6829885
comparison
equal deleted inserted replaced
42:bbbf36187d87 43:32ee1ce20411
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 ${query} \$CSP2_DIR/queries/${query.element_identifier} && 23 ln -sf ${query} \$CSP2_DIR/queries/${query.element_identifier} &&
24 #end for 24 #end for
25 export QUERY_READS_ARG="--reads \$CSP2_DIR/queries" && 25 export QUERY_READS_ARG="--reads \$CSP2_DIR/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 ${ref} \$CSP2_DIR/references/${ref.element_identifier} && 32 ln -sf ${ref} \$CSP2_DIR/references/${ref.element_identifier} &&
33 #end for 33 #end for
34 export REF_FASTA_ARG="--ref_fasta \$CSP2_DIR/references" && 34 export REF_FASTA_ARG="--ref_fasta \$CSP2_DIR/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 ${ref} \$CSP2_DIR/references/${ref.element_identifier} && 41 ln -sf ${ref} \$CSP2_DIR/references/${ref.element_identifier} &&
42 #end for 42 #end for
43 export REF_READS_ARG="--ref_reads \$CSP2_DIR/references" && 43 export REF_READS_ARG="--ref_reads \$CSP2_DIR/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 ]]>
63 </command> 63 </command>