Mercurial > repos > rliterman > csp2

comparison csp2_screen.xml @ 4:1f407d5f5899

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload"
author rliterman
date Mon, 02 Dec 2024 16:44:52 -0500
parents 757b7dcd0ee6
children ec2d1d77d44c
comparison
equal deleted inserted replaced
3:757b7dcd0ee6 4:1f407d5f5899
1 <tool id="csp2-screen" name="CSP2 (Screening Mode)" version="0.9.7"> 1 <tool id="csp2-screen" name="CSP2 (Screening Mode)" version="0.9.7">
2 <description>Screen query assemblies against reference assemblies</description> 2 <description>Screen query assemblies against reference assemblies</description>
3 <requirements> 3 <requirements>
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 export CSP2_DIR=\$PWD;
10 mkdir -p \$CSP2_DIR/queries \$CSP2_DIR/references; 10 mkdir -p \$CSP2_DIR/queries \$CSP2_DIR/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 ${query} \$CSP2_DIR/queries/${query.element_identifier}; 14 ln -sf ${query} \$CSP2_DIR/queries/${query.element_identifier};
15 #end for 15 #end for
16 export QUERY_FASTA_ARG="--fasta \$CSP2_DIR/queries"; 16 export QUERY_FASTA_ARG="--fasta \$CSP2_DIR/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 --cores 8 --out \$CSP2_DIR/CSP2_Screen_Output; 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 --cores 8 --out \$CSP2_DIR/CSP2_Screen_Output -log \$CSP2_DIR/CSP2_Screen_Output\.nextflow.log;
61 ]]> 61 ]]>
62 </command> 62 </command>
63 <inputs> 63 <inputs>
64 <param name="query_fasta" type="data" format="fasta" value="" label="Query assemblies" multiple="true" optional="true" /> 64 <param name="query_fasta" type="data" format="fasta" value="" label="Query assemblies" multiple="true" optional="true" />
65 <param name="ref_fasta" type="data" format="fasta" value="" label="Reference assemblies" multiple="true" optional="true" /> 65 <param name="ref_fasta" type="data" format="fasta" value="" label="Reference assemblies" multiple="true" optional="true" />
66 <param name="query_reads" type="data" format="fastq,fastq.gz" value="" label="Query reads" multiple="true" optional="true" /> 66 <param name="query_reads" type="data" format="fastq,fastq.gz" value="" label="Query reads" multiple="true" optional="true" />
67 <param name="ref_reads" type="data" format="fastq,fastq.gz" value="" label="Reference reads" multiple="true" optional="true" /> 67 <param name="ref_reads" type="data" format="fastq,fastq.gz" value="" label="Reference reads" multiple="true" optional="true" />
68 <param name="min_cov" type="float" value="85" label="Minimum reference genome coverage to proceed with distance estimation" optional="true" /> 68 <param name="min_cov" type="float" value="85" label="Minimum reference genome coverage to proceed with distance estimation" optional="true" />
69 <param name="min_iden" type="float" value="99" label="Minimum alignment percent identity to detect SNPs" optional="true" /> 69 <param name="min_iden" type="float" value="99" label="Minimum alignment percent identity to detect SNPs" optional="true" />
70 <param name="min_len" type="integer" value="500" label="Minimum alignment length to detect SNPs" optional="true" /> 70 <param name="min_len" type="integer" value="500" label="Minimum alignment length to detect SNPs" optional="true" />
71 <param name="ref_edge" type="integer" value="150" label="Prune SNPs within this many bases of reference contig edge" optional="true" /> 71 <param name="ref_edge" type="integer" value="150" label="Prune SNPs within this many bases of reference contig edge" optional="true" />
72 <param name="query_edge" type="integer" value="150" label="Prune SNPs within this many bases of query contig edge" optional="true" /> 72 <param name="query_edge" type="integer" value="150" label="Prune SNPs within this many bases of query contig edge" optional="true" />
73 <param name="dwin" type="text" value="1000,125,15" label="Comma-separated set of window sizes for SNP density filtration (Set to 0 to disable density filtration)" optional="true" /> 73 <param name="dwin" type="text" value="1000,125,15" label="Comma-separated set of window sizes for SNP density filtration (Set to 0 to disable density filtration)" optional="true" />
74 <param name="wsnps" type="text" value="3,2,1" label="Comma-separated list of maximum SNP counts per density window" optional="true" /> 74 <param name="wsnps" type="text" value="3,2,1" label="Comma-separated list of maximum SNP counts per density window" optional="true" />
75 <param name="readext" type="text" value="fastq.gz" label="Read extension format (e.g., fastq.gz)" optional="true" /> 75 <param name="readext" type="text" value="fastq.gz" label="Read extension format (e.g., fastq.gz)" optional="true" />
76 <param name="forward" type="text" value="_1.fastq.gz" label="Forward read suffix (e.g. _1.fastq.gz)" optional="true" /> 76 <param name="forward" type="text" value="_1.fastq.gz" label="Forward read suffix (e.g. _1.fastq.gz)" optional="true" />
77 <param name="reverse" type="text" value="_2.fastq.gz" label="Forward read suffix (e.g. _2.fastq.gz)" optional="true" /> 77 <param name="reverse" type="text" value="_2.fastq.gz" label="Forward read suffix (e.g. _2.fastq.gz)" optional="true" />
78 <param name="trim_name" type="text" value="" label="Text to remove from all file names (e.g., _contigs_skesa)" optional="true" /> 78 <param name="trim_name" type="text" value="" label="Text to remove from all file names (e.g., _contigs_skesa)" optional="true" />
79 <param name="ref_id" type="text" value="" label="Comma-separated list of desired Reference IDs (e.g., Sample_A,Sample_B)" optional="true" /> 79 <param name="ref_id" type="text" value="" label="Comma-separated list of desired Reference IDs (e.g., Sample_A,Sample_B)" optional="true" />
80 </inputs> 80 </inputs>
81 <outputs> 81 <outputs>
82 <data name="screening_results" format="tabular" label="Screening Results" from_work_dir="CSP2_Screen_Output/Screening_Results.tsv" /> 82 <data name="screening_results" format="tabular" label="Screening Results" from_work_dir="CSP2_Screen_Output/Screening_Results.tsv" />
83 <data name="isolate_data" format="tabular" label="Isolate Data" from_work_dir="CSP2_Screen_Output/Isolate_Data.tsv" /> 83 <data name="isolate_data" format="tabular" label="Isolate Data" from_work_dir="CSP2_Screen_Output/Isolate_Data.tsv" />
84 <data name="nextflow_log" format="text" label="Nextflow Log" from_work_dir="CSP2_Screen_Output/.nextflow.log" />
84 </outputs> 85 </outputs>
85 <tests> 86 <tests>
86 <test> 87 <test>
87 <param name="query_fasta"> 88 <param name="query_fasta">
88 <collection type="list"> 89 <collection type="list">
89 <element name="Sample_A" value="assemblies/Sample_A.fasta" /> 90 <element name="Sample_A" value="assemblies/Sample_A.fasta" />
90 <element name="Sample_B" value="assemblies/Sample_B.fasta" /> 91 <element name="Sample_B" value="assemblies/Sample_B.fasta" />
91 <element name="Sample_C" value="assemblies/Sample_C.fasta" /> 92 <element name="Sample_C" value="assemblies/Sample_C.fasta" />
92 <element name="Sample_D" value="assemblies/Sample_D.fasta" /> 93 <element name="Sample_D" value="assemblies/Sample_D.fasta" />
93 <element name="Sample_E" value="assemblies/Sample_E.fasta" /> 94 <element name="Sample_E" value="assemblies/Sample_E.fasta" />
94 <element name="Sample_F" value="assemblies/Sample_F.fasta" /> 95 <element name="Sample_F" value="assemblies/Sample_F.fasta" />
95 <element name="Sample_G" value="assemblies/Sample_G.fasta" /> 96 <element name="Sample_G" value="assemblies/Sample_G.fasta" />
96 <element name="Sample_H" value="assemblies/Sample_H.fasta" /> 97 <element name="Sample_H" value="assemblies/Sample_H.fasta" />
97 <element name="Sample_I" value="assemblies/Sample_I.fasta" /> 98 <element name="Sample_I" value="assemblies/Sample_I.fasta" />
98 <element name="Sample_J" value="assemblies/Sample_J.fasta" /> 99 <element name="Sample_J" value="assemblies/Sample_J.fasta" />
99 <element name="Sample_K" value="assemblies/Sample_K.fasta" /> 100 <element name="Sample_K" value="assemblies/Sample_K.fasta" />
100 <element name="Sample_L" value="assemblies/Sample_L.fasta" /> 101 <element name="Sample_L" value="assemblies/Sample_L.fasta" />
101 <element name="Sample_M" value="assemblies/Sample_M.fasta" /> 102 <element name="Sample_M" value="assemblies/Sample_M.fasta" />
102 <element name="Sample_N" value="assemblies/Sample_N.fasta" /> 103 <element name="Sample_N" value="assemblies/Sample_N.fasta" />
103 <element name="Sample_O" value="assemblies/Sample_O.fasta" /> 104 <element name="Sample_O" value="assemblies/Sample_O.fasta" />
104 </collection> 105 </collection>
105 </param> 106 </param>
106 <param name="query_reads"> 107 <param name="query_reads">
107 <collection type="list"> 108 <collection type="list">
108 <element name="Forward" value="reads/Week_42_Reads_1.fq.gz" /> 109 <element name="Forward" value="reads/Week_42_Reads_1.fq.gz" />
109 <element name="Reverse" value="reads/Week_42_Reads_2.fq.gz" /> 110 <element name="Reverse" value="reads/Week_42_Reads_2.fq.gz" />
110 </collection> 111 </collection>
111 </param> 112 </param>
112 113
113 <param name="ref_id" value="Sample_A,Sample_B" /> 114 <param name="ref_id" value="Sample_A,Sample_B" />
114 <param name="readext" value="fq.gz" /> 115 <param name="readext" value="fq.gz" />
115 <param name="forward" value="_1.fq.gz" /> 116 <param name="forward" value="_1.fq.gz" />
116 <param name="reverse" value="_2.fq.gz" /> 117 <param name="reverse" value="_2.fq.gz" />
117 118
118 <output name="screening_results" value="Screening_Results.tsv" /> 119 <output name="screening_results" value="Screening_Results.tsv" />
119 <output name="isolate_data" value="Isolate_Data.tsv" /> 120 <output name="isolate_data" value="Isolate_Data.tsv" />
120 </test> 121 </test>
121 </tests> 122 </tests>
122 <help> 123 <help>
123 This tool takes query assemblies and reference assemblies and calculates the pairwise distance between each query/reference combination. If no reference is provided, all queries are compared to all other queries. 124 This tool takes query assemblies and reference assemblies and calculates the pairwise distance between each query/reference combination. If no reference is provided, all queries are compared to all other queries.
124 </help> 125 </help>
125 <citations> 126 <citations>
126 <citation type="doi">10.XXXX/placeholder.doi</citation> 127 <citation type="doi">10.XXXX/placeholder.doi</citation>
127 <citation type="bibtex">@article{example2024,title={CFSAN SNP Pipeline 2 (CSP2): a pipeline for fast and accurate SNP distance estimation from bacterial genome assemblies.},author={Doe, John and Smith, Jane},journal={Submitted},year={2024}} 128 <citation type="bibtex">@article{example2024,title={CFSAN SNP Pipeline 2 (CSP2): a pipeline for fast and accurate SNP distance estimation from bacterial genome assemblies.},author={Doe, John and Smith, Jane},journal={Submitted},year={2024}}
128 </citation> 129 </citation>
129 </citations> 130 </citations>
130 </tool> 131 </tool>
132