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comparison csp2_snp.xml @ 51:2a36d0ebb408

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"planemo upload"
author rliterman
date Fri, 13 Dec 2024 08:49:33 -0500
parents f62b9bcf7cf3
children 44cbdce84814
comparison
equal deleted inserted replaced
50:16b103443761 51:2a36d0ebb408
4 <requirement type="package" version="24.10.1">nextflow</requirement> 4 <requirement type="package" version="24.10.1">nextflow</requirement>
5 <requirement type="package" version="1.5.8">micromamba</requirement> 5 <requirement type="package" version="1.5.8">micromamba</requirement>
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 export CSP2_DIR=\$PWD; 9 mkdir ./queries ./references;
10 mkdir -p \$CSP2_DIR/queries \$CSP2_DIR/references;
11 10
12 if [ -n "$query_fasta" ] && [ "$query_fasta" != "None" ]; then 11 if [ -n "$query_fasta" ] && [ "$query_fasta" != "None" ]; then
13 #for query in $query_fasta: 12 #for query in $query_fasta:
14 ln -sf ${query} \$CSP2_DIR/queries/${query.element_identifier}; 13 ln -sf ${query} ./queries/${query.element_identifier};
15 #end for 14 #end for
16 export QUERY_FASTA_ARG="--fasta \$CSP2_DIR/queries"; 15 export QUERY_FASTA_ARG="--fasta ./queries";
17 else 16 else
18 export QUERY_FASTA_ARG=""; 17 export QUERY_FASTA_ARG="";
19 fi; 18 fi;
20 19
21 if [ -n "$query_reads" ] && [ "$query_reads" != "None" ]; then 20 if [ -n "$query_reads" ] && [ "$query_reads" != "None" ]; then
22 #for query in $query_reads: 21 #for query in $query_reads:
23 ln -sf ${query} \$CSP2_DIR/queries/${query.element_identifier}; 22 ln -sf ${query} ./queries/${query.element_identifier};
24 #end for 23 #end for
25 export QUERY_READS_ARG="--reads \$CSP2_DIR/queries"; 24 export QUERY_READS_ARG="--reads ./queries";
26 else 25 else
27 export QUERY_READS_ARG=""; 26 export QUERY_READS_ARG="";
28 fi; 27 fi;
29 28
30 if [ -n "$ref_fasta" ] && [ "$ref_fasta" != "None" ]; then 29 if [ -n "$ref_fasta" ] && [ "$ref_fasta" != "None" ]; then
31 #for ref in $ref_fasta: 30 #for ref in $ref_fasta:
32 ln -sf ${ref} \$CSP2_DIR/references/${ref.element_identifier}; 31 ln -sf ${ref} ./references/${ref.element_identifier};
33 #end for 32 #end for
34 export REF_FASTA_ARG="--ref_fasta \$CSP2_DIR/references"; 33 export REF_FASTA_ARG="--ref_fasta ./references";
35 else 34 else
36 export REF_FASTA_ARG=""; 35 export REF_FASTA_ARG="";
37 fi; 36 fi;
38 37
39 if [ -n "$ref_reads" ] && [ "$ref_reads" != "None" ]; then 38 if [ -n "$ref_reads" ] && [ "$ref_reads" != "None" ]; then
40 #for ref in $ref_reads: 39 #for ref in $ref_reads:
41 ln -sf ${ref} \$CSP2_DIR/references/${ref.element_identifier}; 40 ln -sf ${ref} ./references/${ref.element_identifier};
42 #end for 41 #end for
43 export REF_READS_ARG="--ref_reads \$CSP2_DIR/references"; 42 export REF_READS_ARG="--ref_reads ./references";
44 else 43 else
45 export REF_READS_ARG=""; 44 export REF_READS_ARG="";
46 fi; 45 fi;
47 46
48 if [ -n "$trim_name" ] && [ "$trim_name" != "None" ]; then 47 if [ -n "$trim_name" ] && [ "$trim_name" != "None" ]; then
55 export RESCUE_ARG="--rescue"; 54 export RESCUE_ARG="--rescue";
56 else 55 else
57 export RESCUE_ARG=""; 56 export RESCUE_ARG="";
58 fi; 57 fi;
59 58
60 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 --out \$CSP2_DIR/CSP2_SNP_Output > Nextflow_Log.txt 2>&1; 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 --out ./CSP2_SNP_Output > Nextflow_Log.txt 2>&1 &&
60 ls -la CSP2_SNP_Output/SNP_Analysis/* &&
61 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 &&
63 ls -la CSP2_Output;
61 64
62 zip -r CSP2_Output.zip CSP2_SNP_Output;
63 ]]> 65 ]]>
64 </command> 66 </command>
65 <inputs> 67 <inputs>
66 <param name="query_fasta" type="data" format="fasta" value="" label="Query assemblies" multiple="true" optional="true" /> 68 <param name="query_fasta" type="data" format="fasta" value="" label="Query assemblies" multiple="true" optional="true" />
67 <param name="ref_fasta" type="data" format="fasta" value="" label="Reference assemblies" multiple="true" optional="true" /> 69 <param name="ref_fasta" type="data" format="fasta" value="" label="Reference assemblies" multiple="true" optional="true" />
80 <param name="trim_name" type="text" value="" label="Text to remove from all file names (e.g., _contigs_skesa)" optional="true" /> 82 <param name="trim_name" type="text" value="" label="Text to remove from all file names (e.g., _contigs_skesa)" optional="true" />
81 <param name="rescue" type="boolean" value="false" label="Enable SNP edge rescue mode" optional="true" /> 83 <param name="rescue" type="boolean" value="false" label="Enable SNP edge rescue mode" optional="true" />
82 <param name="max_missing" type="float" value="50" label="Maximum percent of isolates allowed to have missing data to retain a SNP" optional="true" /> 84 <param name="max_missing" type="float" value="50" label="Maximum percent of isolates allowed to have missing data to retain a SNP" optional="true" />
83 </inputs> 85 </inputs>
84 <outputs> 86 <outputs>
85 <data name="nextflow_log" format="txt" label="Nextflow Log" from_work_dir="Nextflow_Log.txt" />
86 <data name="isolate_data" format="tabular" label="Isolate Data" from_work_dir="CSP2_SNP_Output/Isolate_Data.tsv" /> 87 <data name="isolate_data" format="tabular" label="Isolate Data" from_work_dir="CSP2_SNP_Output/Isolate_Data.tsv" />
87 <data name="raw_mummer" format="tabular" label="Raw MUMmer Output" from_work_dir="CSP2_SNP_Output/Raw_MUMmer_Summary.tsv" /> 88 <data name="raw_mummer" format="tabular" label="Raw MUMmer Output" from_work_dir="CSP2_SNP_Output/Raw_MUMmer_Summary.tsv" />
88 <data name="csp2_zip" format="zip" label="Zipped Output" from_work_dir="CSP2_Output.zip" /> 89
89 <collection name="reference_results" type="list:list"> 90 <collection name="csp2_logs" type='list' label="CSP2 Log">
90 <discover_datasets pattern="*/CSP2_SNP_Pipeline.log" format="txt" visible="true" directory="./CSP2_SNP_Output/SNP_Analysis" /> 91 <discover_datasets pattern="(?P&lt;designation&gt;.+)_CSP2_SNP_Pipeline\.log" directory="CSP2_Output" format='txt'/>
91 <discover_datasets pattern="*/Reference_Screening.tsv" format="tabular" visible="true" directory="./CSP2_SNP_Output/SNP_Analysis" /> 92 </collection>
92 <discover_datasets pattern="*/snp_distance_matrix_preserved.tsv" format="tabular" visible="true" directory="./CSP2_SNP_Output/SNP_Analysis" /> 93 <collection name="csp2_alignments" type='list' label="CSP2 Alignment">
93 <discover_datasets pattern="*/snp_distance_pairwise_preserved.tsv" format="tabular" visible="true" directory="./CSP2_SNP_Output/SNP_Analysis" /> 94 <discover_datasets pattern="(?P&lt;designation&gt;.+)_snpma_preserved\.fasta" directory="CSP2_Output" format='fasta'/>
94 <discover_datasets pattern="*/snpma_preserved.fasta" format="fasta" visible="true" directory="./CSP2_SNP_Output/SNP_Analysis" /> 95 </collection>
96 <collection name="csp2_matrices" type='list' label="CSP2 Matrices">
97 <discover_datasets pattern="(?P&lt;designation&gt;.+)_snp_distance_matrix_preserved\.tsv" directory="CSP2_Output" format='tabular'/>
98 </collection>
99 <collection name="csp2_pairwise" type='list' label="CSP2 Pairwise Distances">
100 <discover_datasets pattern="(?P&lt;designation&gt;.+)_snp_distance_pairwise_preserved\.tsv" directory="CSP2_Output" format='tabular'/>
101 </collection>
102 <collection name="csp2_ref_screening" type='list' label="CSP2 Reference Screening">
103 <discover_datasets pattern="(?P&lt;designation&gt;.+)_Reference_Screening\.tsv" directory="CSP2_Output" format='tabular'/>
95 </collection> 104 </collection>
96 </outputs> 105 </outputs>
97 <tests> 106 <tests>
98 <test> 107 <test>
99 <param name="query_fasta"> 108 <param name="query_fasta">