Mercurial > repos > jpayne > csp2
diff csp2-snp.xml @ 0:1c1e01265e0f draft default tip
planemo upload commit 7f3c6fb6db52daedaa0c59d6ca7f39710778f242-dirty
| author | jpayne |
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| date | Mon, 11 Aug 2025 15:46:24 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/csp2-snp.xml Mon Aug 11 15:46:24 2025 +0000 @@ -0,0 +1,166 @@ +<tool id="csp2-snp" name="CSP2 (SNP Pipeline Mode)" version="0.9.7.7"> + <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> --> + <container type="docker">cfsanbiostatistics/csp2:v.0.9.7.7-galaxy</container> + </requirements> + <version_command>nextflow -version</version_command> + <command detect_errors="exit_code"><![CDATA[ +mkdir -p queries references .nextflow +#set readext="" +#set renamedref=$source.reference.element_identifier.replace(": ", ".").replace(" ", "_") +#for $reads in $coll + && ln -sf '${reads}' 'queries/${reads.element_identifier.replace(": ", ".").replace(" ", "_")}.fasta' +#end for + && ln -sf '$source.reference' 'references/${renamedref}.fasta' + && echo "*** Files in queries directory: ***" + && ls -lah queries/ + && nextflow run + /app/CSP2.nf -c $__tool_directory__/nextflow.config -profile standard + --runmode snp + --fasta queries + --ref_fasta 'references/${renamedref}.fasta' + --min_cov $opt.min_cov + --min_iden $opt.min_iden + --min_len $opt.min_len + --ref_edge $opt.ref_edge + --query_edge $opt.query_edge + --dwin $opt.dwin + --wsnps $opt.wsnps + --out CSP2_SNP_Output + --quiet + && echo "*** Files in output directory: ***" + && ls -lahR CSP2_SNP_Output + && tail -n +2 CSP2_SNP_Output/Isolate_Data.tsv > ${isolate_data} + && tail -n +2 CSP2_SNP_Output/Raw_MUMmer_Summary.tsv > ${raw_mummer} + && tail -n +2 CSP2_SNP_Output/SNP_Analysis/${renamedref}/snp_distance_pairwise_preserved.tsv > ${snp_pairwise} + && cat CSP2_SNP_Output/SNP_Analysis/${renamedref}/snplist_preserved.txt > ${snp_list} + && cat CSP2_SNP_Output/SNP_Analysis/${renamedref}/snpma_preserved.fasta > ${snp_matrix} + && echo "*** Nextflow log follows: ***" + && cat .nextflow.log +]]> + </command> + <inputs> + <conditional name="source"> + <param name="source_select" type="select" label="Use a curated GalaxyTrakr reference or a reference from your history"> + <option value="curated">Use a GalaxyTrakr reference</option> + <option value="history">Use a reference from your history</option> + </param> + <when value="curated"> + <param name="reference" type="select" label="Select reference fasta"> + <options from_data_table="all_fasta"> + <filter type="sort_by" column="2"/> + <validator type="no_options" message="No assemblies are available for the selected input dataset"/> + </options> + </param> + </when> + <when value="history"> + <param type="data" name="reference" format="fasta" label="Select reference FASTA"/> + </when> + </conditional> + <!-- <conditional name="query"> + <param name="query_select" type="select" label="Screen a list of paired-reads or a list of assemblies"> + <option value="reads">Screen a list of paired reads</option> + <option value="assemblies">Screen a list of assemblies</option> + </param> + <when value="reads"> + <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="list:paired" /> + </when> + <when value="assemblies"> --> + <param label="Assemblies" name="coll" type="data_collection" format="fasta" collection_type="list" /> + <!-- </when> --> + <!-- </conditional> --> + <section name="opt" title="Advanced options..."> + <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" /> + </section> + </inputs> + <outputs> + <!-- <data name="nextflow_log" format="txt" label="Nextflow Log" from_work_dir="Nextflow_Log.txt" /> --> + <data name="isolate_data" format="tabular" label="Isolate Data"> + <actions> + <action name="column_names" type="metadata" default="Isolate_ID,Isolate_Type,Assembly_Path,Contig_Count,Assembly_Bases,N50,N90,L50,L90,SHA256" /> + </actions> + </data> + <data name="raw_mummer" format="tabular" label="Raw MUMmer Output"> + <actions> + <action name="column_names" type="metadata" default="SNPDiffs_File,Query_ID,Query_Assembly,Query_Contig_Count,Query_Assembly_Bases,Query_N50,Query_N90,Query_L50,Query_L90,Query_SHA256,Reference_ID,Reference_Assembly,Reference_Contig_Count,Reference_Assembly_Bases,Reference_N50,Reference_N90,Reference_L50,Reference_L90,Reference_SHA256,SNPs,Reference_Percent_Aligned,Query_Percent_Aligned,Median_Percent_Identity,Median_Alignment_Length,Kmer_Similarity,Shared_Kmers,Reference_Unique_Kmers,Query_Unique_Kmers,Reference_Breakpoints,Query_Breakpoints,Reference_Relocations,Query_Relocations,Reference_Translocations,Query_Translocations,Reference_Inversions,Query_Inversions,Reference_Insertions,Query_Insertions,Reference_Tandem,Query_Tandem,Indels,Invalid,gSNPs,gIndels" /> + </actions> + </data> + <!-- <data name="csp2_zip" format="zip" label="Zipped Output" from_work_dir="CSP2_Output.zip" /> --> + <!-- <discover_datasets pattern="(?P<name>.+)/CSP2_SNP_Pipeline\.log" format="txt" visible="true" directory="./CSP2_SNP_Output/SNP_Analysis" /> --> + <!-- <discover_datasets pattern="(?P<name>.+)/Reference_Screening\.tsv" format="tabular" visible="true" directory="./CSP2_SNP_Output/SNP_Analysis" /> + <discover_datasets pattern="(?P<name>.+)/snp_distance_matrix_preserved\.tsv" format="tabular" visible="true" directory="./CSP2_SNP_Output/SNP_Analysis" /> + <discover_datasets pattern="(?P<name>.+)/snp_distance_pairwise_preserved\.tsv" format="tabular" visible="true" directory="./CSP2_SNP_Output/SNP_Analysis" /> + <discover_datasets pattern="(?P<name>.+)/snpma_preserved\.fasta" format="fasta" visible="true" directory="./CSP2_SNP_Output/SNP_Analysis" /> --> + <data name="snp_pairwise" format="tabular" label="Preserved Pairwise SNP Distances"> + <actions> + <action name="column_names" type="metadata" default="Query_1,Query_2,SNP_Distance,SNPs_Cocalled" /> + </actions> + </data> + <data name="snp_list" format="txt" label="Preserved SNP List" /> + <data name="snp_matrix" format="fasta" label="Preserved SNP Matrix" /> + <discover_datasets pattern="(?P<name>.+)/snp_distance_matrix\.tsv" format="tabular" visible="false" directory="./CSP2_SNP_Output/SNP_Analysis" /> + <discover_datasets pattern="(?P<name>.+)/snp_distance_pairwise\.tsv" format="tabular" visible="false" directory="./CSP2_SNP_Output/SNP_Analysis" /> + <discover_datasets pattern="(?P<name>.+)/snpma\.fasta" format="fasta" visible="false" directory="./CSP2_SNP_Output/SNP_Analysis" /> + </outputs> + <tests> + <test> + <param name="source_select" value="history" /> + <param name="reference" value="assemblies/Sample_A.fasta" /> + <!-- <param name="query_select" value="assemblies" /> --> + <param name="coll"> + <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> + + <output name="isolate_data" value="Isolate_Data.tsv" /> + </test> + <!-- <test> + <param name="source_select" value="history" /> + <param name="reference" value="assemblies/Sample_A.fasta" ftype="fasta" /> + <param name="query_select" value="reads" /> + <param name="coll"> + <collection type="list:paired"> + <element name="Sample_A"> + <collection type="paired"> + <element name="forward" value="reads/Week_42_Reads_1.fq.gz" ftype="fastqsanger.gz" /> + <element name="reverse" value="reads/Week_42_Reads_2.fq.gz" ftype="fastqsanger.gz" /> + </collection> + </element> + </collection> + </param> + <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>