Mercurial > repos > rliterman > csp2
changeset 29:b6ec322b1f05
"planemo upload"
| author | rliterman |
|---|---|
| date | Wed, 04 Dec 2024 16:02:07 -0500 |
| parents | 893a6993efe3 |
| children | 1fe21a8717d4 |
| files | CSP2/subworkflows/fetchData/main.nf csp2_screen.xml csp2_snp.xml csp_screen.xml |
| diffstat | 4 files changed, 292 insertions(+), 141 deletions(-) [+] |
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--- a/CSP2/subworkflows/fetchData/main.nf Wed Dec 04 13:48:13 2024 -0500 +++ b/CSP2/subworkflows/fetchData/main.nf Wed Dec 04 16:02:07 2024 -0500 @@ -20,8 +20,7 @@ userSNPDiffs = file("${projectDir}/bin/userSNPDiffs.py") // Set SKESA cores to 4 or fewer -//skesa_cpus = (params.cores as Integer) >= 4 ? 4 : params.cores as Integer -skesa_cpus = 1 +skesa_cpus = (params.cores as Integer) >= 4 ? 4 : params.cores as Integer workflow { main:
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/csp2_screen.xml Wed Dec 04 16:02:07 2024 -0500 @@ -0,0 +1,134 @@ +<tool id="csp2-screen" name="CSP2 (Screening Mode)" version="0.9.7_Dev21"> + <description>Screen query assemblies against reference assemblies</description> + <requirements> + <requirement type="package" version="24.10.1">nextflow</requirement> + <requirement type="package" version="1.5.8">micromamba</requirement> + </requirements> + <version_command>nextflow -version</version_command> + <command detect_errors="aggressive"><![CDATA[ +export CSP2_DIR=\$PWD; +mkdir -p \$CSP2_DIR/queries \$CSP2_DIR/references; + +if [ -n "$query_fasta" ] && [ "$query_fasta" != "None" ]; then + #for query in $query_fasta: + ln -sf ${query} \$CSP2_DIR/queries/${query.element_identifier}; + #end for + export QUERY_FASTA_ARG="--fasta \$CSP2_DIR/queries"; +else + export QUERY_FASTA_ARG=""; +fi; + +if [ -n "$query_reads" ] && [ "$query_reads" != "None" ]; then + #for query in $query_reads: + ln -sf ${query} \$CSP2_DIR/queries/${query.element_identifier}; + #end for + export QUERY_READS_ARG="--reads \$CSP2_DIR/queries"; +else + export QUERY_READS_ARG=""; +fi; + +if [ -n "$ref_fasta" ] && [ "$ref_fasta" != "None" ]; then + #for ref in $ref_fasta: + ln -sf ${ref} \$CSP2_DIR/references/${ref.element_identifier}; + #end for + export REF_FASTA_ARG="--ref_fasta \$CSP2_DIR/references"; +else + export REF_FASTA_ARG=""; +fi; + +if [ -n "$ref_reads" ] && [ "$ref_reads" != "None" ]; then + #for ref in $ref_reads: + ln -sf ${ref} \$CSP2_DIR/references/${ref.element_identifier}; + #end for + export REF_READS_ARG="--ref_reads \$CSP2_DIR/references"; +else + export REF_READS_ARG=""; +fi; + +if [ -n "$trim_name" ] && [ "$trim_name" != "None" ]; then + export TRIM_ARG="--trim_name $trim_name"; +else + export TRIM_ARG=""; +fi; + +if [ -n "$ref_id" ] && [ "$ref_id" != "None" ]; then + export REF_ID_ARG="--ref_id $ref_id"; +else + export REF_ID_ARG=""; +fi; + +nextflow run ${__tool_directory__}/CSP2/CSP2.nf -profile csp2_galaxy --cores 1 --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_DIR/CSP2_Screen_Output > Nextflow_Log.txt 2>&1; +sleep 1; + ]]> + </command> + <inputs> + <param name="query_fasta" type="data" format="fasta" value="" label="Query assemblies" multiple="true" optional="true" /> + <param name="ref_fasta" type="data" format="fasta" value="" label="Reference assemblies" multiple="true" optional="true" /> + <param name="query_reads" type="data" format="fastq,fastq.gz" value="" label="Query reads" multiple="true" optional="true" /> + <param name="ref_reads" type="data" format="fastq,fastq.gz" value="" label="Reference reads" multiple="true" optional="true" /> + <param name="min_cov" type="float" value="85" label="Minimum reference genome coverage to proceed with distance estimation" optional="true" /> + <param name="min_iden" type="float" value="99" label="Minimum alignment percent identity to detect SNPs" optional="true" /> + <param name="min_len" type="integer" value="500" label="Minimum alignment length to detect SNPs" optional="true" /> + <param name="ref_edge" type="integer" value="150" label="Prune SNPs within this many bases of reference contig edge" optional="true" /> + <param name="query_edge" type="integer" value="150" label="Prune SNPs within this many bases of query contig edge" optional="true" /> + <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" /> + <param name="wsnps" type="text" value="3,2,1" label="Comma-separated list of maximum SNP counts per density window" optional="true" /> + <param name="readext" type="text" value="fastq.gz" label="Read extension format (e.g., fastq.gz)" optional="true" /> + <param name="forward" type="text" value="_1.fastq.gz" label="Forward read suffix (e.g. _1.fastq.gz)" optional="true" /> + <param name="reverse" type="text" value="_2.fastq.gz" label="Forward read suffix (e.g. _2.fastq.gz)" optional="true" /> + <param name="trim_name" type="text" value="" label="Text to remove from all file names (e.g., _contigs_skesa)" optional="true" /> + <param name="ref_id" type="text" value="" label="Comma-separated list of desired Reference IDs (e.g., Sample_A,Sample_B)" optional="true" /> + </inputs> + <outputs> + <data name="screening_results" format="tabular" label="Screening Results" from_work_dir="CSP2_Screen_Output/Screening_Results.tsv" /> + <data name="raw_mummer" format="tabular" label="Raw MUMmer Output" from_work_dir="CSP2_Screen_Output/Raw_MUMmer_Summary.tsv" /> + <data name="isolate_data" format="tabular" label="Isolate Data" from_work_dir="CSP2_Screen_Output/Isolate_Data.tsv" /> + <data name="nextflow_log" format="txt" label="Nextflow Log" from_work_dir="Nextflow_Log.txt" /> + </outputs> + <tests> + <test> + <param name="query_fasta"> + <collection type="list"> + <element name="Sample_A" value="assemblies/Sample_A.fasta" /> + <element name="Sample_B" value="assemblies/Sample_B.fasta" /> + <element name="Sample_C" value="assemblies/Sample_C.fasta" /> + <element name="Sample_D" value="assemblies/Sample_D.fasta" /> + <element name="Sample_E" value="assemblies/Sample_E.fasta" /> + <element name="Sample_F" value="assemblies/Sample_F.fasta" /> + <element name="Sample_G" value="assemblies/Sample_G.fasta" /> + <element name="Sample_H" value="assemblies/Sample_H.fasta" /> + <element name="Sample_I" value="assemblies/Sample_I.fasta" /> + <element name="Sample_J" value="assemblies/Sample_J.fasta" /> + <element name="Sample_K" value="assemblies/Sample_K.fasta" /> + <element name="Sample_L" value="assemblies/Sample_L.fasta" /> + <element name="Sample_M" value="assemblies/Sample_M.fasta" /> + <element name="Sample_N" value="assemblies/Sample_N.fasta" /> + <element name="Sample_O" value="assemblies/Sample_O.fasta" /> + </collection> + </param> + <param name="query_reads"> + <collection type="list"> + <element name="Forward" value="reads/Week_42_Reads_1.fq.gz" /> + <element name="Reverse" value="reads/Week_42_Reads_2.fq.gz" /> + </collection> + </param> + + <param name="ref_id" value="Sample_A,Sample_B" /> + <param name="readext" value="fq.gz" /> + <param name="forward" value="_1.fq.gz" /> + <param name="reverse" value="_2.fq.gz" /> + + <output name="screening_results" value="Screening_Results.tsv" /> + <output name="isolate_data" value="Isolate_Data.tsv" /> + </test> + </tests> + <help> + 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. + </help> + <citations> + <citation type="doi">10.XXXX/placeholder.doi</citation> + <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}} + </citation> + </citations> +</tool> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/csp2_snp.xml Wed Dec 04 16:02:07 2024 -0500 @@ -0,0 +1,157 @@ +<tool id="csp2-snp" name="CSP2 (SNP Pipeline Mode)" version="0.9.7_Dev21"> + <description>Run SNP Pipeline analysis on isolates using one or more references.</description> + <requirements> + <requirement type="package" version="24.10.1">nextflow</requirement> + <requirement type="package" version="1.5.8">micromamba</requirement> + </requirements> + <version_command>nextflow -version</version_command> + <command detect_errors="aggressive"><![CDATA[ +export CSP2_DIR=\$PWD; +mkdir -p \$CSP2_DIR/queries \$CSP2_DIR/references; + +if [ -n "$query_fasta" ] && [ "$query_fasta" != "None" ]; then + #for query in $query_fasta: + ln -sf ${query} \$CSP2_DIR/queries/${query.element_identifier}; + #end for + export QUERY_FASTA_ARG="--fasta \$CSP2_DIR/queries"; +else + export QUERY_FASTA_ARG=""; +fi; + +if [ -n "$query_reads" ] && [ "$query_reads" != "None" ]; then + #for query in $query_reads: + ln -sf ${query} \$CSP2_DIR/queries/${query.element_identifier}; + #end for + export QUERY_READS_ARG="--reads \$CSP2_DIR/queries"; +else + export QUERY_READS_ARG=""; +fi; + +if [ -n "$ref_fasta" ] && [ "$ref_fasta" != "None" ]; then + #for ref in $ref_fasta: + ln -sf ${ref} \$CSP2_DIR/references/${ref.element_identifier}; + #end for + export REF_FASTA_ARG="--ref_fasta \$CSP2_DIR/references"; +else + export REF_FASTA_ARG=""; +fi; + +if [ -n "$ref_reads" ] && [ "$ref_reads" != "None" ]; then + #for ref in $ref_reads: + ln -sf ${ref} \$CSP2_DIR/references/${ref.element_identifier}; + #end for + export REF_READS_ARG="--ref_reads \$CSP2_DIR/references"; +else + export REF_READS_ARG=""; +fi; + +if [ -n "$trim_name" ] && [ "$trim_name" != "None" ]; then + export TRIM_ARG="--trim_name $trim_name"; +else + export TRIM_ARG=""; +fi; + +if [ -n "$ref_id" ] && [ "$ref_id" != "None" ]; then + export REF_ID_ARG="--ref_id $ref_id"; +else + export REF_ID_ARG=""; +fi; + +if [[ "$rescue" == "true" ]]; then + export RESCUE_ARG="--rescue"; +else + export RESCUE_ARG=""; +fi; + +nextflow run ${__tool_directory__}/CSP2/CSP2.nf -profile csp2_galaxy --cores 1 --runmode snp \$QUERY_FASTA_ARG \$REF_FASTA_ARG \$QUERY_READS_ARG \$REF_READS_ARG \$REF_ID_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_DIR/CSP2_SNP_Output > Nextflow_Log.txt 2>&1; +sleep 1; + ]]> + </command> + <inputs> + <param name="query_fasta" type="data" format="fasta" value="" label="Query assemblies" multiple="true" optional="true" /> + <param name="ref_fasta" type="data" format="fasta" value="" label="Reference assemblies" multiple="true" optional="true" /> + <param name="query_reads" type="data" format="fastq,fastq.gz" value="" label="Query reads" multiple="true" optional="true" /> + <param name="ref_reads" type="data" format="fastq,fastq.gz" value="" label="Reference reads" multiple="true" optional="true" /> + <param name="min_cov" type="float" value="85" label="Minimum reference genome coverage to proceed with distance estimation" optional="true" /> + <param name="min_iden" type="float" value="99" label="Minimum alignment percent identity to detect SNPs" optional="true" /> + <param name="min_len" type="integer" value="500" label="Minimum alignment length to detect SNPs" optional="true" /> + <param name="ref_edge" type="integer" value="150" label="Prune SNPs within this many bases of reference contig edge" optional="true" /> + <param name="query_edge" type="integer" value="150" label="Prune SNPs within this many bases of query contig edge" optional="true" /> + <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" /> + <param name="wsnps" type="text" value="3,2,1" label="Comma-separated list of maximum SNP counts per density window" optional="true" /> + <param name="readext" type="text" value="fastq.gz" label="Read extension format (e.g., fastq.gz)" optional="true" /> + <param name="forward" type="text" value="_1.fastq.gz" label="Forward read suffix (e.g. _1.fastq.gz)" optional="true" /> + <param name="reverse" type="text" value="_2.fastq.gz" label="Forward read suffix (e.g. _2.fastq.gz)" optional="true" /> + <param name="trim_name" type="text" value="" label="Text to remove from all file names (e.g., _contigs_skesa)" optional="true" /> + <param name="ref_id" type="text" value="" label="Comma-separated list of desired Reference IDs (e.g., Sample_A,Sample_B)" optional="true" /> + <param name="rescue" type="boolean" value="false" label="Enable SNP edge rescue mode" optional="true" /> + <param name="max_missing" type="float" value="50" label="Maximum percent of isolates allowed to have missing data to retain a SNP" optional="true" /> + <param name="n_ref" type="integer" value="1" label="Number of reference isolates for CSP2 to select" optional="true" /> + + </inputs> + <outputs> + <data name="raw_mummer" format="tabular" label="Raw MUMmer Output" from_work_dir="CSP2_SNP_Output/Raw_MUMmer_Summary.tsv" /> + <data name="isolate_data" format="tabular" label="Isolate Data" from_work_dir="CSP2_SNP_Output/Isolate_Data.tsv" /> + <data name="nextflow_log" format="txt" label="Nextflow Log" from_work_dir="Nextflow_Log.txt" /> + + <collection name="snp_analysis_results" type="list:dataset" label="SNP Analysis Results by Reference ID"> + <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/CSP2_SNP_Pipeline.log" format="txt" /> + <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snplist.txt" format="txt" /> + <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snplist_preserved.txt" format="txt" /> + <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/Reference_Screening.tsv" format="tabular" /> + <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/Locus_Categories.tsv" format="tabular" /> + <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/Query_Coverage.tsv" format="tabular" /> + <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snp_distance_matrix_preserved.tsv" format="tabular" /> + <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snp_distance_matrix.tsv" format="tabular" /> + <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snp_distance_pairwise_preserved.tsv" format="tabular" /> + <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snp_distance_pairwise.tsv" format="tabular" /> + <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snpma_preserved.fasta" format="fasta" /> + <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snpma.fasta" format="fasta" /> + </collection> + </outputs> + <tests> + <test> + <param name="query_fasta"> + <collection type="list"> + <element name="Sample_A" value="assemblies/Sample_A.fasta" /> + <element name="Sample_B" value="assemblies/Sample_B.fasta" /> + <element name="Sample_C" value="assemblies/Sample_C.fasta" /> + <element name="Sample_D" value="assemblies/Sample_D.fasta" /> + <element name="Sample_E" value="assemblies/Sample_E.fasta" /> + <element name="Sample_F" value="assemblies/Sample_F.fasta" /> + <element name="Sample_G" value="assemblies/Sample_G.fasta" /> + <element name="Sample_H" value="assemblies/Sample_H.fasta" /> + <element name="Sample_I" value="assemblies/Sample_I.fasta" /> + <element name="Sample_J" value="assemblies/Sample_J.fasta" /> + <element name="Sample_K" value="assemblies/Sample_K.fasta" /> + <element name="Sample_L" value="assemblies/Sample_L.fasta" /> + <element name="Sample_M" value="assemblies/Sample_M.fasta" /> + <element name="Sample_N" value="assemblies/Sample_N.fasta" /> + <element name="Sample_O" value="assemblies/Sample_O.fasta" /> + </collection> + </param> + <param name="query_reads"> + <collection type="list"> + <element name="Forward" value="reads/Week_42_Reads_1.fq.gz" /> + <element name="Reverse" value="reads/Week_42_Reads_2.fq.gz" /> + </collection> + </param> + + <param name="ref_id" value="Sample_A,Sample_B" /> + <param name="readext" value="fq.gz" /> + <param name="forward" value="_1.fq.gz" /> + <param name="reverse" value="_2.fq.gz" /> + + <output name="isolate_data" value="Isolate_Data.tsv" /> + </test> + </tests> + <help> + 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. + </help> + <citations> + <citation type="doi">10.XXXX/placeholder.doi</citation> + <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}} + </citation> + </citations> +</tool> +
--- a/csp_screen.xml Wed Dec 04 13:48:13 2024 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,139 +0,0 @@ -<tool id="csp2-screen" name="CSP2 (Screening Mode)" version="0.9.7_Dev21"> - <description>Screen query assemblies against reference assemblies</description> - <requirements> - <requirement type="package" version="24.10.1">nextflow</requirement> - <requirement type="package" version="1.5.8">micromamba</requirement> - </requirements> - <version_command>nextflow -version</version_command> - <command detect_errors="aggressive"><![CDATA[ -export CSP2_DIR=\$PWD; -mkdir -p \$CSP2_DIR/queries \$CSP2_DIR/references; - -if [ -n "$query_fasta" ] && [ "$query_fasta" != "None" ]; then - #for query in $query_fasta: - ln -sf ${query} \$CSP2_DIR/queries/${query.element_identifier}; - #end for - export QUERY_FASTA_ARG="--fasta \$CSP2_DIR/queries"; -else - export QUERY_FASTA_ARG=""; -fi; - -if [ -n "$query_reads" ] && [ "$query_reads" != "None" ]; then - #for query in $query_reads: - ln -sf ${query} \$CSP2_DIR/queries/${query.element_identifier}; - #end for - export QUERY_READS_ARG="--reads \$CSP2_DIR/queries"; -else - export QUERY_READS_ARG=""; -fi; - -if [ -n "$ref_fasta" ] && [ "$ref_fasta" != "None" ]; then - #for ref in $ref_fasta: - ln -sf ${ref} \$CSP2_DIR/references/${ref.element_identifier}; - #end for - export REF_FASTA_ARG="--ref_fasta \$CSP2_DIR/references"; -else - export REF_FASTA_ARG=""; -fi; - -if [ -n "$ref_reads" ] && [ "$ref_reads" != "None" ]; then - #for ref in $ref_reads: - ln -sf ${ref} \$CSP2_DIR/references/${ref.element_identifier}; - #end for - export REF_READS_ARG="--ref_reads \$CSP2_DIR/references"; -else - export REF_READS_ARG=""; -fi; - -if [ -n "$trim_name" ] && [ "$trim_name" != "None" ]; then - export TRIM_ARG="--trim_name $trim_name"; -else - export TRIM_ARG=""; -fi; - -if [ -n "$ref_id" ] && [ "$ref_id" != "None" ]; then - export REF_ID_ARG="--ref_id $ref_id"; -else - export REF_ID_ARG=""; -fi; - - nextflow run ${__tool_directory__}/CSP2/CSP2.nf -profile csp2_galaxy --cores $cores --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 > Nextflow_Log.txt 2>&1; - sleep 5; - zip -r work.zip work; - zip -r csp2.zip CSP2_Screen_Output; - ]]> - </command> - <inputs> - <param name="query_fasta" type="data" format="fasta" value="" label="Query assemblies" multiple="true" optional="true" /> - <param name="ref_fasta" type="data" format="fasta" value="" label="Reference assemblies" multiple="true" optional="true" /> - <param name="query_reads" type="data" format="fastq,fastq.gz" value="" label="Query reads" multiple="true" optional="true" /> - <param name="ref_reads" type="data" format="fastq,fastq.gz" value="" label="Reference reads" multiple="true" optional="true" /> - <param name="min_cov" type="float" value="85" label="Minimum reference genome coverage to proceed with distance estimation" optional="true" /> - <param name="min_iden" type="float" value="99" label="Minimum alignment percent identity to detect SNPs" optional="true" /> - <param name="min_len" type="integer" value="500" label="Minimum alignment length to detect SNPs" optional="true" /> - <param name="ref_edge" type="integer" value="150" label="Prune SNPs within this many bases of reference contig edge" optional="true" /> - <param name="query_edge" type="integer" value="150" label="Prune SNPs within this many bases of query contig edge" optional="true" /> - <param name="cores" type="integer" value="2" label="Available cores per node" optional="true" /> - <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" /> - <param name="wsnps" type="text" value="3,2,1" label="Comma-separated list of maximum SNP counts per density window" optional="true" /> - <param name="readext" type="text" value="fastq.gz" label="Read extension format (e.g., fastq.gz)" optional="true" /> - <param name="forward" type="text" value="_1.fastq.gz" label="Forward read suffix (e.g. _1.fastq.gz)" optional="true" /> - <param name="reverse" type="text" value="_2.fastq.gz" label="Forward read suffix (e.g. _2.fastq.gz)" optional="true" /> - <param name="trim_name" type="text" value="" label="Text to remove from all file names (e.g., _contigs_skesa)" optional="true" /> - <param name="ref_id" type="text" value="" label="Comma-separated list of desired Reference IDs (e.g., Sample_A,Sample_B)" optional="true" /> - </inputs> - <outputs> - <data name="screening_results" format="tabular" label="Screening Results" from_work_dir="CSP2_Screen_Output/Screening_Results.tsv" /> - <data name="raw_mummer" format="tabular" label="Raw MUMmer Output" from_work_dir="CSP2_Screen_Output/Raw_MUMmer_Summary.tsv" /> - <data name="isolate_data" format="tabular" label="Isolate Data" from_work_dir="CSP2_Screen_Output/Isolate_Data.tsv" /> - <data name="nextflow_log" format="txt" label="Nextflow Log" from_work_dir="Nextflow_Log.txt" /> - <data name="out_dir" format="zip" label="CSP2 Directory" from_work_dir="csp2.zip" /> - <data name="work_dir" format="zip" label="Nextflow Work Directory" from_work_dir="work.zip" /> - </outputs> - <tests> - <test> - <param name="query_fasta"> - <collection type="list"> - <element name="Sample_A" value="assemblies/Sample_A.fasta" /> - <element name="Sample_B" value="assemblies/Sample_B.fasta" /> - <element name="Sample_C" value="assemblies/Sample_C.fasta" /> - <element name="Sample_D" value="assemblies/Sample_D.fasta" /> - <element name="Sample_E" value="assemblies/Sample_E.fasta" /> - <element name="Sample_F" value="assemblies/Sample_F.fasta" /> - <element name="Sample_G" value="assemblies/Sample_G.fasta" /> - <element name="Sample_H" value="assemblies/Sample_H.fasta" /> - <element name="Sample_I" value="assemblies/Sample_I.fasta" /> - <element name="Sample_J" value="assemblies/Sample_J.fasta" /> - <element name="Sample_K" value="assemblies/Sample_K.fasta" /> - <element name="Sample_L" value="assemblies/Sample_L.fasta" /> - <element name="Sample_M" value="assemblies/Sample_M.fasta" /> - <element name="Sample_N" value="assemblies/Sample_N.fasta" /> - <element name="Sample_O" value="assemblies/Sample_O.fasta" /> - </collection> - </param> - <param name="query_reads"> - <collection type="list"> - <element name="Forward" value="reads/Week_42_Reads_1.fq.gz" /> - <element name="Reverse" value="reads/Week_42_Reads_2.fq.gz" /> - </collection> - </param> - - <param name="ref_id" value="Sample_A,Sample_B" /> - <param name="readext" value="fq.gz" /> - <param name="forward" value="_1.fq.gz" /> - <param name="reverse" value="_2.fq.gz" /> - - <output name="screening_results" value="Screening_Results.tsv" /> - <output name="isolate_data" value="Isolate_Data.tsv" /> - </test> - </tests> - <help> - 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. - </help> - <citations> - <citation type="doi">10.XXXX/placeholder.doi</citation> - <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}} - </citation> - </citations> -</tool> -