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comparison csp2_snp.xml @ 53:a21f63856acf

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"planemo upload"
author rliterman
date Thu, 19 Dec 2024 08:53:33 -0500
parents 44cbdce84814
children d0a7dd5c900e
comparison
equal deleted inserted replaced
52:44cbdce84814 53:a21f63856acf
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 [ -n "$query_fasta" ] && [ "$query_fasta" != "None" ]; then 11 if [ -n "$query_fasta" ] && [ "$query_fasta" != "None" ]; then
12 #for query in $query_fasta: 12 if [ -n "$query_fasta__collection_type" ]; then
13 #for query in $query_fasta_ELEMENTS:
13 ln -sf ${query} ./queries/${query.element_identifier}; 14 ln -sf ${query} ./queries/${query.element_identifier};
14 #end for 15 #end for
16 else
17 #for query in $query_fasta:
18 ln -sf ${query} ./queries/${query.element_identifier};
19 #end for
15 export QUERY_FASTA_ARG="--fasta ./queries"; 20 export QUERY_FASTA_ARG="--fasta ./queries";
16 else 21 else
17 export QUERY_FASTA_ARG=""; 22 export QUERY_FASTA_ARG="";
18 fi; 23 fi;
19 24
20 if [ -n "$query_reads" ] && [ "$query_reads" != "None" ]; then 25 if [ -n "$query_reads" ] && [ "$query_reads" != "None" ]; then
21 #for query in $query_reads: 26 if [ -n "$query_reads__collection_type" ]; then
22 ln -sf ${query} ./queries/${query.element_identifier}; 27 #for query in $query_reads_ELEMENTS:
23 #end for 28 ln -sf ${query} ./queries/${query.element_identifier};
24 export QUERY_READS_ARG="--reads ./queries"; 29 #end for
30 else
31 #for query in $query_reads:
32 ln -sf ${query} ./queries/${query.element_identifier};
33 #end for
34 export QUERY_READS_ARG="--reads ./queries";
25 else 35 else
26 export QUERY_READS_ARG=""; 36 export QUERY_READS_ARG="";
27 fi; 37 fi;
28 38
29 if [ -n "$ref_fasta" ] && [ "$ref_fasta" != "None" ]; then 39 if [ -n "$ref_fasta" ] && [ "$ref_fasta" != "None" ]; then
30 #for ref in $ref_fasta: 40 if [ -n "$ref_fasta__collection_type" ]; then
31 ln -sf ${ref} ./references/${ref.element_identifier}; 41 #for ref in $ref_fasta_ELEMENTS:
32 #end for 42 ln -sf ${ref} ./references/${ref.element_identifier};
43 #end for
44 else
45 #for ref in $ref_fasta:
46 ln -sf ${ref} ./references/${ref.element_identifier};
47 #end for
33 export REF_FASTA_ARG="--ref_fasta ./references"; 48 export REF_FASTA_ARG="--ref_fasta ./references";
34 else 49 else
35 export REF_FASTA_ARG=""; 50 export REF_FASTA_ARG="";
36 fi; 51 fi;
37 52
38 if [ -n "$ref_reads" ] && [ "$ref_reads" != "None" ]; then 53 if [ -n "$ref_reads" ] && [ "$ref_reads" != "None" ]; then
39 #for ref in $ref_reads: 54 if [ -n "$ref_reads__collection_type" ]; then
40 ln -sf ${ref} ./references/${ref.element_identifier}; 55 #for ref in $ref_reads_ELEMENTS:
41 #end for 56 ln -sf ${ref} ./references/${ref.element_identifier};
57 #end for
58 else
59 #for ref in $ref_reads:
60 ln -sf ${ref} ./references/${ref.element_identifier};
61 #end for
42 export REF_READS_ARG="--ref_reads ./references"; 62 export REF_READS_ARG="--ref_reads ./references";
43 else 63 else
44 export REF_READS_ARG=""; 64 export REF_READS_ARG="";
45 fi; 65 fi;
66
46 67
47 if [ -n "$trim_name" ] && [ "$trim_name" != "None" ]; then 68 if [ -n "$trim_name" ] && [ "$trim_name" != "None" ]; then
48 export TRIM_ARG="--trim_name $trim_name"; 69 export TRIM_ARG="--trim_name $trim_name";
49 else 70 else
50 export TRIM_ARG=""; 71 export TRIM_ARG="";
55 else 76 else
56 export RESCUE_ARG=""; 77 export RESCUE_ARG="";
57 fi; 78 fi;
58 79
59 nextflow run ${__tool_directory__}/CSP2/CSP2.nf -profile csp2_galaxy --runmode snp \$QUERY_FASTA_ARG \$REF_FASTA_ARG \$QUERY_READS_ARG \$REF_READS_ARG \$TRIM_ARG \$RESCUE_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 --max_missing $max_missing --n_ref $n_ref --out ./CSP2_SNP_Output > Nextflow_Log.txt 2>&1 && 80 nextflow run ${__tool_directory__}/CSP2/CSP2.nf -profile csp2_galaxy --runmode snp \$QUERY_FASTA_ARG \$REF_FASTA_ARG \$QUERY_READS_ARG \$REF_READS_ARG \$TRIM_ARG \$RESCUE_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 --max_missing $max_missing --n_ref $n_ref --out ./CSP2_SNP_Output > Nextflow_Log.txt 2>&1 &&
60 ls -la CSP2_SNP_Output/SNP_Analysis/* &&
61 mkdir CSP2_Output && 81 mkdir CSP2_Output &&
62 cat CSP2_SNP_Output/logs/Reference_IDs.txt | while read line; do cp 'CSP2_SNP_Output/SNP_Analysis/'\$line'/CSP2_SNP_Pipeline.log' 'CSP2_Output/'\$line'_CSP2_SNP_Pipeline.log'; cp 'CSP2_SNP_Output/SNP_Analysis/'\$line'/Reference_Screening.tsv' 'CSP2_Output/'\$line'_Reference_Screening.tsv'; cp 'CSP2_SNP_Output/SNP_Analysis/'\$line'/snp_distance_matrix_preserved.tsv' 'CSP2_Output/'\$line'_snp_distance_matrix_preserved.tsv'; cp 'CSP2_SNP_Output/SNP_Analysis/'\$line'/snp_distance_pairwise_preserved.tsv' 'CSP2_Output/'\$line'_snp_distance_pairwise_preserved.tsv'; cp 'CSP2_SNP_Output/SNP_Analysis/'\$line'/snpma_preserved.fasta' 'CSP2_Output/'\$line'_snpma_preserved.fasta';done && 82 cat CSP2_SNP_Output/logs/Reference_IDs.txt | while read line; do cp 'CSP2_SNP_Output/SNP_Analysis/'\$line'/CSP2_SNP_Pipeline.log' 'CSP2_Output/'\$line'_CSP2_SNP_Pipeline.log'; cp 'CSP2_SNP_Output/SNP_Analysis/'\$line'/Reference_Screening.tsv' 'CSP2_Output/'\$line'_Reference_Screening.tsv'; cp 'CSP2_SNP_Output/SNP_Analysis/'\$line'/snp_distance_matrix_preserved.tsv' 'CSP2_Output/'\$line'_snp_distance_matrix_preserved.tsv'; cp 'CSP2_SNP_Output/SNP_Analysis/'\$line'/snp_distance_pairwise_preserved.tsv' 'CSP2_Output/'\$line'_snp_distance_pairwise_preserved.tsv'; cp 'CSP2_SNP_Output/SNP_Analysis/'\$line'/snpma_preserved.fasta' 'CSP2_Output/'\$line'_snpma_preserved.fasta';done &&
63 ls -la CSP2_Output; 83 ls -la CSP2_Output;
64 84
65 ]]> 85 ]]>