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annotate csp2_snp.xml @ 66:90e29c1ddeca

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"planemo upload"
author rliterman
date Thu, 19 Dec 2024 15:55:32 -0500
parents c2a886313008
children 0e9998148a16
rev   line source
rliterman@29 1 <tool id="csp2-snp" name="CSP2 (SNP Pipeline Mode)" version="0.9.7_Dev21">
rliterman@29 2 <description>Run SNP Pipeline analysis on isolates using one or more references.</description>
rliterman@29 3 <requirements>
rliterman@29 4 <requirement type="package" version="24.10.1">nextflow</requirement>
rliterman@29 5 <requirement type="package" version="1.5.8">micromamba</requirement>
rliterman@29 6 </requirements>
rliterman@29 7 <version_command>nextflow -version</version_command>
rliterman@29 8 <command detect_errors="aggressive"><![CDATA[
rliterman@51 9 mkdir ./queries ./references;
rliterman@29 10
rliterman@63 11 #if (str($query_fasta.query_fasta_select) == "none"):
rliterman@55 12 export QUERY_FASTA_ARG="";
rliterman@63 13 #elif (str($query_fasta.query_fasta_select) == "collection"):
rliterman@63 14 #for _, $query_assembly in enumerate($query_fasta.coll):
rliterman@63 15 ln -sf ${query_assembly} ./queries/${query_assembly.element_identifier};
rliterman@55 16 #end for
rliterman@55 17 export QUERY_FASTA_ARG="--fasta ./queries";
rliterman@63 18 #else
rliterman@63 19 #for _, $query_assembly in enumerate($query_fasta.list):
rliterman@63 20 ln -sf ${query_assembly} ./queries/${query_assembly.element_identifier};
rliterman@63 21 #end for
rliterman@63 22 export QUERY_FASTA_ARG="--fasta ./queries";
rliterman@63 23 #end if
rliterman@29 24
rliterman@63 25 #if (str($ref_fasta.ref_fasta_select) == "none"):
rliterman@55 26 export REF_FASTA_ARG="";
rliterman@63 27 #elif (str($ref_fasta.ref_fasta_select) == "collection"):
rliterman@63 28 #for _, $ref_assembly in enumerate($ref_fasta.coll):
rliterman@63 29 ln -sf ${ref_assembly} ./references/${ref_assembly.element_identifier};
rliterman@63 30 #end for
rliterman@65 31 export REF_FASTA_ARG="--fasta ./references";
rliterman@65 32 #else
rliterman@63 33 #for _, $ref_assembly in enumerate($ref_fasta.list):
rliterman@63 34 ln -sf ${ref_assembly} ./references/${ref_assembly.element_identifier};
rliterman@55 35 #end for
rliterman@58 36 export REF_FASTA_ARG="--fasta ./references";
rliterman@63 37 #end if
rliterman@29 38
rliterman@63 39 #if (str($query_reads.query_reads_select) == "none"):
rliterman@55 40 export QUERY_READS_ARG="";
rliterman@63 41 #elif (str($query_reads.query_reads_select) == "collection"):
rliterman@63 42 #for _, $pair in enumerate($query_reads.coll):
rliterman@66 43 ln -sf ${pair.forward} ./queries/${pair.forward.name};
rliterman@66 44 ln -sf ${pair.reverse} ./queries/${pair.reverse.name};
rliterman@55 45 #end for
rliterman@55 46 export QUERY_READS_ARG="--reads ./queries";
rliterman@65 47 #else
rliterman@63 48 #for _, $read_file in enumerate($query_reads.list):
rliterman@63 49 ln -sf ${read_file} ./queries/${read_file.element_identifier};
rliterman@63 50 #end for
rliterman@64 51 export QUERY_READS_ARG="--reads ./queries";
rliterman@63 52 #end if
rliterman@29 53
rliterman@63 54 #if (str($ref_reads.ref_reads_select) == "none"):
rliterman@63 55 export REF_READS_ARG="";
rliterman@63 56 #elif (str($ref_reads.ref_reads_select) == "collection"):
rliterman@63 57 #for _, $pair in enumerate($ref_reads.coll):
rliterman@66 58 ln -sf ${pair.forward} ./references/${pair.forward.name};
rliterman@66 59 ln -sf ${pair.reverse} ./references/${pair.reverse.name};
rliterman@63 60 #end for
rliterman@63 61 export REF_READS_ARG="--ref_reads ./references";
rliterman@65 62 #else
rliterman@63 63 #for _, $read_file in enumerate($ref_reads.list):
rliterman@63 64 ln -sf ${read_file} ./references/${read_file.element_identifier};
rliterman@55 65 #end for
rliterman@64 66 export REF_READS_ARG="--ref_reads ./references";
rliterman@63 67 #end if
rliterman@29 68
rliterman@59 69 if [ -n "$trim_name" ] && [ "$trim_name" != "None" ]; then
rliterman@29 70 export TRIM_ARG="--trim_name $trim_name";
rliterman@29 71 else
rliterman@29 72 export TRIM_ARG="";
rliterman@29 73 fi;
rliterman@29 74
rliterman@29 75 if [[ "$rescue" == "true" ]]; then
rliterman@29 76 export RESCUE_ARG="--rescue";
rliterman@29 77 else
rliterman@29 78 export RESCUE_ARG="";
rliterman@29 79 fi;
rliterman@29 80
rliterman@52 81 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 &&
rliterman@51 82 mkdir CSP2_Output &&
rliterman@51 83 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 &&
rliterman@51 84 ls -la CSP2_Output;
rliterman@33 85
rliterman@34 86 ]]>
rliterman@29 87 </command>
rliterman@29 88 <inputs>
rliterman@55 89 <conditional name="query_fasta">
rliterman@55 90 <param name="query_fasta_select" type="select" label="Get query assemblies from a collection or your history">
rliterman@55 91 <option value="none" selected="true">Do not provide query assemblies</option>
rliterman@55 92 <option value="collection">Query assemblies from a collection_type</option>
rliterman@55 93 <option value="history">Query assemblies from your history</option>
rliterman@55 94 </param>
rliterman@55 95 <when value="none">
rliterman@55 96 </when>
rliterman@55 97 <when value="collection">
rliterman@55 98 <param label="Query Assembly Collection" name="coll" type="data_collection" format="fasta" collection_type="list" />
rliterman@55 99 </when>
rliterman@55 100 <when value="history">
rliterman@55 101 <param label="Query Assembly List" type="data" name="list" format="fasta" multiple="true" />
rliterman@55 102 </when>
rliterman@55 103 </conditional>
rliterman@55 104
rliterman@55 105 <conditional name="ref_fasta">
rliterman@55 106 <param name="ref_fasta_select" type="select" label="Get reference assemblies from a collection or your history">
rliterman@55 107 <option value="none" selected="true">Do not provide reference assemblies</option>
rliterman@55 108 <option value="collection">Reference assemblies from a collection_type</option>
rliterman@55 109 <option value="history">Reference assemblies from your history</option>
rliterman@55 110 </param>
rliterman@55 111 <when value="none">
rliterman@55 112 </when>
rliterman@55 113 <when value="collection">
rliterman@55 114 <param label="Reference Assembly Collection" name="coll" type="data_collection" format="fasta" collection_type="list" />
rliterman@55 115 </when>
rliterman@55 116 <when value="history">
rliterman@55 117 <param label="Reference Assembly List" type="data" name="list" format="fasta" multiple="true" />
rliterman@55 118 </when>
rliterman@55 119 </conditional>
rliterman@55 120 <conditional name="query_reads">
rliterman@55 121 <param name="query_reads_select" type="select" label="Get query reads from a paired-end collection or your history">
rliterman@55 122 <option value="none" selected="true">Do not provide query reads</option>
rliterman@55 123 <option value="collection">Query reads from a collection_type</option>
rliterman@55 124 <option value="history">Query reads from your history</option>
rliterman@55 125 </param>
rliterman@55 126 <when value="none">
rliterman@55 127 </when>
rliterman@55 128 <when value="collection">
rliterman@63 129 <param label="Query Reads Collection" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="list:paired" />
rliterman@55 130 </when>
rliterman@55 131 <when value="history">
rliterman@55 132 <param label="Query Reads List" type="data" name="list" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" multiple="true" />
rliterman@55 133 </when>
rliterman@55 134 </conditional>
rliterman@55 135
rliterman@55 136 <conditional name="ref_reads">
rliterman@55 137 <param name="ref_reads_select" type="select" label="Get reference reads from a paired-end collection or your history">
rliterman@55 138 <option value="none" selected="true">Do not provide reference reads</option>
rliterman@55 139 <option value="collection">Refrence reads from a collection_type</option>
rliterman@55 140 <option value="history">Refrence reads from your history</option>
rliterman@55 141 </param>
rliterman@55 142 <when value="none">
rliterman@55 143 </when>
rliterman@55 144 <when value="collection">
rliterman@63 145 <param label="Refrence Reads Collection" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="list:paired" />
rliterman@55 146 </when>
rliterman@55 147 <when value="history">
rliterman@55 148 <param label="Refrence Reads List" type="data" name="list" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" multiple="true" />
rliterman@55 149 </when>
rliterman@55 150 </conditional>
rliterman@55 151
rliterman@29 152 <param name="min_cov" type="float" value="85" label="Minimum reference genome coverage to proceed with distance estimation" optional="true" />
rliterman@29 153 <param name="min_iden" type="float" value="99" label="Minimum alignment percent identity to detect SNPs" optional="true" />
rliterman@29 154 <param name="min_len" type="integer" value="500" label="Minimum alignment length to detect SNPs" optional="true" />
rliterman@29 155 <param name="ref_edge" type="integer" value="150" label="Prune SNPs within this many bases of reference contig edge" optional="true" />
rliterman@29 156 <param name="query_edge" type="integer" value="150" label="Prune SNPs within this many bases of query contig edge" optional="true" />
rliterman@29 157 <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" />
rliterman@29 158 <param name="wsnps" type="text" value="3,2,1" label="Comma-separated list of maximum SNP counts per density window" optional="true" />
rliterman@63 159 <param name="readext" type="text" value="fq.gz" label="Read extension format (e.g., fastq.gz)" optional="true" />
rliterman@63 160 <param name="forward" type="text" value="_1.fq.gz" label="Forward read suffix (e.g. _1.fastq.gz)" optional="true" />
rliterman@63 161 <param name="reverse" type="text" value="_2.fq.gz" label="Forward read suffix (e.g. _2.fastq.gz)" optional="true" />
rliterman@59 162 <param name="trim_name" type="text" value="" label="Text to remove from all file names (e.g., _contigs_skesa)" optional="true" />
rliterman@29 163 <param name="rescue" type="boolean" value="false" label="Enable SNP edge rescue mode" optional="true" />
rliterman@29 164 <param name="max_missing" type="float" value="50" label="Maximum percent of isolates allowed to have missing data to retain a SNP" optional="true" />
rliterman@66 165 <param name="n_ref" type="integer" value="1" label="Number of reference genomes to select" optional="true" />
rliterman@52 166
rliterman@29 167 </inputs>
rliterman@29 168 <outputs>
rliterman@34 169 <data name="isolate_data" format="tabular" label="Isolate Data" from_work_dir="CSP2_SNP_Output/Isolate_Data.tsv" />
rliterman@29 170 <data name="raw_mummer" format="tabular" label="Raw MUMmer Output" from_work_dir="CSP2_SNP_Output/Raw_MUMmer_Summary.tsv" />
rliterman@51 171
rliterman@51 172 <collection name="csp2_logs" type='list' label="CSP2 Log">
rliterman@51 173 <discover_datasets pattern="(?P&lt;designation&gt;.+)_CSP2_SNP_Pipeline\.log" directory="CSP2_Output" format='txt'/>
rliterman@51 174 </collection>
rliterman@51 175 <collection name="csp2_alignments" type='list' label="CSP2 Alignment">
rliterman@51 176 <discover_datasets pattern="(?P&lt;designation&gt;.+)_snpma_preserved\.fasta" directory="CSP2_Output" format='fasta'/>
rliterman@51 177 </collection>
rliterman@51 178 <collection name="csp2_matrices" type='list' label="CSP2 Matrices">
rliterman@51 179 <discover_datasets pattern="(?P&lt;designation&gt;.+)_snp_distance_matrix_preserved\.tsv" directory="CSP2_Output" format='tabular'/>
rliterman@51 180 </collection>
rliterman@51 181 <collection name="csp2_pairwise" type='list' label="CSP2 Pairwise Distances">
rliterman@51 182 <discover_datasets pattern="(?P&lt;designation&gt;.+)_snp_distance_pairwise_preserved\.tsv" directory="CSP2_Output" format='tabular'/>
rliterman@51 183 </collection>
rliterman@51 184 <collection name="csp2_ref_screening" type='list' label="CSP2 Reference Screening">
rliterman@51 185 <discover_datasets pattern="(?P&lt;designation&gt;.+)_Reference_Screening\.tsv" directory="CSP2_Output" format='tabular'/>
rliterman@37 186 </collection>
rliterman@29 187 </outputs>
rliterman@29 188 <tests>
rliterman@29 189 <test>
rliterman@29 190 <param name="query_fasta">
rliterman@29 191 <collection type="list">
rliterman@29 192 <element name="Sample_A" value="assemblies/Sample_A.fasta" />
rliterman@29 193 <element name="Sample_B" value="assemblies/Sample_B.fasta" />
rliterman@29 194 <element name="Sample_C" value="assemblies/Sample_C.fasta" />
rliterman@29 195 <element name="Sample_D" value="assemblies/Sample_D.fasta" />
rliterman@29 196 <element name="Sample_E" value="assemblies/Sample_E.fasta" />
rliterman@29 197 <element name="Sample_F" value="assemblies/Sample_F.fasta" />
rliterman@29 198 <element name="Sample_G" value="assemblies/Sample_G.fasta" />
rliterman@29 199 <element name="Sample_H" value="assemblies/Sample_H.fasta" />
rliterman@29 200 <element name="Sample_I" value="assemblies/Sample_I.fasta" />
rliterman@29 201 <element name="Sample_J" value="assemblies/Sample_J.fasta" />
rliterman@29 202 <element name="Sample_K" value="assemblies/Sample_K.fasta" />
rliterman@29 203 <element name="Sample_L" value="assemblies/Sample_L.fasta" />
rliterman@29 204 <element name="Sample_M" value="assemblies/Sample_M.fasta" />
rliterman@29 205 <element name="Sample_N" value="assemblies/Sample_N.fasta" />
rliterman@29 206 <element name="Sample_O" value="assemblies/Sample_O.fasta" />
rliterman@29 207 </collection>
rliterman@29 208 </param>
rliterman@29 209 <param name="query_reads">
rliterman@29 210 <collection type="list">
rliterman@29 211 <element name="Forward" value="reads/Week_42_Reads_1.fq.gz" />
rliterman@29 212 <element name="Reverse" value="reads/Week_42_Reads_2.fq.gz" />
rliterman@29 213 </collection>
rliterman@29 214 </param>
rliterman@29 215
rliterman@29 216 <param name="ref_id" value="Sample_A,Sample_B" />
rliterman@29 217 <param name="readext" value="fq.gz" />
rliterman@29 218 <param name="forward" value="_1.fq.gz" />
rliterman@29 219 <param name="reverse" value="_2.fq.gz" />
rliterman@29 220
rliterman@29 221 <output name="isolate_data" value="Isolate_Data.tsv" />
rliterman@29 222 </test>
rliterman@29 223 </tests>
rliterman@29 224 <help>
rliterman@29 225 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.
rliterman@29 226 </help>
rliterman@29 227 <citations>
rliterman@29 228 <citation type="doi">10.XXXX/placeholder.doi</citation>
rliterman@29 229 <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}}
rliterman@29 230 </citation>
rliterman@29 231 </citations>
rliterman@29 232 </tool>
rliterman@29 233