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annotate csp2_snp.xml @ 58:c8676ac8c6b7

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"planemo upload"
author rliterman
date Thu, 19 Dec 2024 12:19:14 -0500
parents c8dfcb29d91b
children d322910e773c
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@57 11
rliterman@58 12 #set query_fasta_input=""
rliterman@58 13 #if $query_fasta.query_fasta_select == 'collection'
rliterman@58 14 #set query_fasta_input=$query_fasta.coll.elements
rliterman@58 15 #elseif $query_fasta.query_fasta_select == 'history'
rliterman@58 16 #set query_fasta_input=$query_fasta.list
rliterman@58 17 #end if
rliterman@58 18
rliterman@58 19 if [[ "$query_fasta.query_fasta_select" == "none" ]]; then
rliterman@55 20 export QUERY_FASTA_ARG="";
rliterman@29 21 else
rliterman@58 22 #for query in $query_fasta_input:
rliterman@55 23 ln -sf ${query} ./queries/${query.element_identifier};
rliterman@55 24 #end for
rliterman@55 25 export QUERY_FASTA_ARG="--fasta ./queries";
rliterman@29 26 fi;
rliterman@29 27
rliterman@58 28 #set ref_fasta_input=""
rliterman@58 29 #if $ref_fasta.ref_fasta_select == 'collection'
rliterman@58 30 #set ref_fasta_input=$ref_fasta.coll.elements
rliterman@58 31 #elseif $ref_fasta.ref_fasta_select == 'history'
rliterman@58 32 #set ref_fasta_input=$ref_fasta.list
rliterman@58 33 #end if
rliterman@58 34
rliterman@58 35 if [[ "$ref_fasta.ref_fasta_select" == "none" ]]; then
rliterman@55 36 export REF_FASTA_ARG="";
rliterman@58 37 else
rliterman@58 38 #for ref in $ref_fasta_input:
rliterman@55 39 ln -sf ${ref} ./references/${ref.element_identifier};
rliterman@55 40 #end for
rliterman@58 41 export REF_FASTA_ARG="--fasta ./references";
rliterman@29 42 fi;
rliterman@29 43
rliterman@58 44 #set query_reads_forward=""
rliterman@58 45 #set query_reads_reverse=""
rliterman@58 46 #if $query_reads.query_reads_select == 'collection'
rliterman@58 47 #set query_reads_forward=$query_reads.coll.forward
rliterman@58 48 #set query_reads_reverse=$query_reads.coll.revese
rliterman@58 49 #elseif $query_reads.query_reads_select == 'history'
rliterman@58 50 #set query_reads_forward=$query_reads.list
rliterman@58 51 #set query_reads_reverse=""
rliterman@58 52 #end if
rliterman@58 53
rliterman@58 54 if [[ "$query_reads.query_reads_select" == "none" ]]; then
rliterman@55 55 export QUERY_READS_ARG="";
rliterman@29 56 else
rliterman@58 57 #for query in $query_reads_forward $query_reads_reverse:
rliterman@55 58 ln -sf ${query} ./queries/${query.element_identifier};
rliterman@55 59 #end for
rliterman@55 60 export QUERY_READS_ARG="--reads ./queries";
rliterman@29 61 fi;
rliterman@29 62
rliterman@58 63 #set ref_reads_forward=""
rliterman@58 64 #set ref_reads_reverse=""
rliterman@58 65 #if $ref_reads.ref_reads_select == 'collection'
rliterman@58 66 #set ref_reads_forward=$ref_reads.coll.forward
rliterman@58 67 #set ref_reads_reverse=$ref_reads.coll.revese
rliterman@58 68 #elseif $ref_reads.ref_reads_select == 'history'
rliterman@58 69 #set ref_reads_forward=$ref_reads.list
rliterman@58 70 #set ref_reads_reverse=""
rliterman@58 71 #end if
rliterman@58 72
rliterman@58 73 if [[ "$ref_reads.ref_reads_select" == "none" ]]; then
rliterman@58 74 export QUERY_READS_ARG="";
rliterman@58 75 else
rliterman@58 76 #for ref in $ref_reads_forward $ref_reads_reverse:
rliterman@55 77 ln -sf ${ref} ./references/${ref.element_identifier};
rliterman@55 78 #end for
rliterman@58 79 export QUERY_READS_ARG="--reads ./queries";
rliterman@29 80 fi;
rliterman@29 81
rliterman@55 82 if [[ "$trim_name" != "DUMMYCSP2TRIM" ]]; then
rliterman@29 83 export TRIM_ARG="--trim_name $trim_name";
rliterman@29 84 else
rliterman@29 85 export TRIM_ARG="";
rliterman@29 86 fi;
rliterman@29 87
rliterman@29 88 if [[ "$rescue" == "true" ]]; then
rliterman@29 89 export RESCUE_ARG="--rescue";
rliterman@29 90 else
rliterman@29 91 export RESCUE_ARG="";
rliterman@29 92 fi;
rliterman@29 93
rliterman@52 94 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 95 mkdir CSP2_Output &&
rliterman@51 96 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 97 ls -la CSP2_Output;
rliterman@33 98
rliterman@34 99 ]]>
rliterman@29 100 </command>
rliterman@29 101 <inputs>
rliterman@55 102 <conditional name="query_fasta">
rliterman@55 103 <param name="query_fasta_select" type="select" label="Get query assemblies from a collection or your history">
rliterman@55 104 <option value="none" selected="true">Do not provide query assemblies</option>
rliterman@55 105 <option value="collection">Query assemblies from a collection_type</option>
rliterman@55 106 <option value="history">Query assemblies from your history</option>
rliterman@55 107 </param>
rliterman@55 108 <when value="none">
rliterman@55 109 </when>
rliterman@55 110 <when value="collection">
rliterman@55 111 <param label="Query Assembly Collection" name="coll" type="data_collection" format="fasta" collection_type="list" />
rliterman@55 112 </when>
rliterman@55 113 <when value="history">
rliterman@55 114 <param label="Query Assembly List" type="data" name="list" format="fasta" multiple="true" />
rliterman@55 115 </when>
rliterman@55 116 </conditional>
rliterman@55 117
rliterman@55 118 <conditional name="ref_fasta">
rliterman@55 119 <param name="ref_fasta_select" type="select" label="Get reference assemblies from a collection or your history">
rliterman@55 120 <option value="none" selected="true">Do not provide reference assemblies</option>
rliterman@55 121 <option value="collection">Reference assemblies from a collection_type</option>
rliterman@55 122 <option value="history">Reference assemblies from your history</option>
rliterman@55 123 </param>
rliterman@55 124 <when value="none">
rliterman@55 125 </when>
rliterman@55 126 <when value="collection">
rliterman@55 127 <param label="Reference Assembly Collection" name="coll" type="data_collection" format="fasta" collection_type="list" />
rliterman@55 128 </when>
rliterman@55 129 <when value="history">
rliterman@55 130 <param label="Reference Assembly List" type="data" name="list" format="fasta" multiple="true" />
rliterman@55 131 </when>
rliterman@55 132 </conditional>
rliterman@55 133 <conditional name="query_reads">
rliterman@55 134 <param name="query_reads_select" type="select" label="Get query reads from a paired-end collection or your history">
rliterman@55 135 <option value="none" selected="true">Do not provide query reads</option>
rliterman@55 136 <option value="collection">Query reads from a collection_type</option>
rliterman@55 137 <option value="history">Query reads from your history</option>
rliterman@55 138 </param>
rliterman@55 139 <when value="none">
rliterman@55 140 </when>
rliterman@55 141 <when value="collection">
rliterman@55 142 <param label="Query Reads Collection" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="paired" />
rliterman@55 143 </when>
rliterman@55 144 <when value="history">
rliterman@55 145 <param label="Query Reads List" type="data" name="list" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" multiple="true" />
rliterman@55 146 </when>
rliterman@55 147 </conditional>
rliterman@55 148
rliterman@55 149 <conditional name="ref_reads">
rliterman@55 150 <param name="ref_reads_select" type="select" label="Get reference reads from a paired-end collection or your history">
rliterman@55 151 <option value="none" selected="true">Do not provide reference reads</option>
rliterman@55 152 <option value="collection">Refrence reads from a collection_type</option>
rliterman@55 153 <option value="history">Refrence reads from your history</option>
rliterman@55 154 </param>
rliterman@55 155 <when value="none">
rliterman@55 156 </when>
rliterman@55 157 <when value="collection">
rliterman@55 158 <param label="Refrence Reads Collection" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="paired" />
rliterman@55 159 </when>
rliterman@55 160 <when value="history">
rliterman@55 161 <param label="Refrence Reads List" type="data" name="list" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" multiple="true" />
rliterman@55 162 </when>
rliterman@55 163 </conditional>
rliterman@55 164
rliterman@29 165 <param name="min_cov" type="float" value="85" label="Minimum reference genome coverage to proceed with distance estimation" optional="true" />
rliterman@29 166 <param name="min_iden" type="float" value="99" label="Minimum alignment percent identity to detect SNPs" optional="true" />
rliterman@29 167 <param name="min_len" type="integer" value="500" label="Minimum alignment length to detect SNPs" optional="true" />
rliterman@29 168 <param name="ref_edge" type="integer" value="150" label="Prune SNPs within this many bases of reference contig edge" optional="true" />
rliterman@29 169 <param name="query_edge" type="integer" value="150" label="Prune SNPs within this many bases of query contig edge" optional="true" />
rliterman@29 170 <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@29 171 <param name="wsnps" type="text" value="3,2,1" label="Comma-separated list of maximum SNP counts per density window" optional="true" />
rliterman@29 172 <param name="readext" type="text" value="fastq.gz" label="Read extension format (e.g., fastq.gz)" optional="true" />
rliterman@29 173 <param name="forward" type="text" value="_1.fastq.gz" label="Forward read suffix (e.g. _1.fastq.gz)" optional="true" />
rliterman@29 174 <param name="reverse" type="text" value="_2.fastq.gz" label="Forward read suffix (e.g. _2.fastq.gz)" optional="true" />
rliterman@55 175 <param name="trim_name" type="text" value="DUMMYCSP2TRIM" label="Text to remove from all file names (e.g., _contigs_skesa)" optional="true" />
rliterman@29 176 <param name="rescue" type="boolean" value="false" label="Enable SNP edge rescue mode" optional="true" />
rliterman@29 177 <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@52 178 <param name="n_ref" type="integer" value="1" label="Number of reference genomes to select" optional="true" />
rliterman@52 179
rliterman@29 180 </inputs>
rliterman@29 181 <outputs>
rliterman@34 182 <data name="isolate_data" format="tabular" label="Isolate Data" from_work_dir="CSP2_SNP_Output/Isolate_Data.tsv" />
rliterman@29 183 <data name="raw_mummer" format="tabular" label="Raw MUMmer Output" from_work_dir="CSP2_SNP_Output/Raw_MUMmer_Summary.tsv" />
rliterman@51 184
rliterman@51 185 <collection name="csp2_logs" type='list' label="CSP2 Log">
rliterman@51 186 <discover_datasets pattern="(?P&lt;designation&gt;.+)_CSP2_SNP_Pipeline\.log" directory="CSP2_Output" format='txt'/>
rliterman@51 187 </collection>
rliterman@51 188 <collection name="csp2_alignments" type='list' label="CSP2 Alignment">
rliterman@51 189 <discover_datasets pattern="(?P&lt;designation&gt;.+)_snpma_preserved\.fasta" directory="CSP2_Output" format='fasta'/>
rliterman@51 190 </collection>
rliterman@51 191 <collection name="csp2_matrices" type='list' label="CSP2 Matrices">
rliterman@51 192 <discover_datasets pattern="(?P&lt;designation&gt;.+)_snp_distance_matrix_preserved\.tsv" directory="CSP2_Output" format='tabular'/>
rliterman@51 193 </collection>
rliterman@51 194 <collection name="csp2_pairwise" type='list' label="CSP2 Pairwise Distances">
rliterman@51 195 <discover_datasets pattern="(?P&lt;designation&gt;.+)_snp_distance_pairwise_preserved\.tsv" directory="CSP2_Output" format='tabular'/>
rliterman@51 196 </collection>
rliterman@51 197 <collection name="csp2_ref_screening" type='list' label="CSP2 Reference Screening">
rliterman@51 198 <discover_datasets pattern="(?P&lt;designation&gt;.+)_Reference_Screening\.tsv" directory="CSP2_Output" format='tabular'/>
rliterman@37 199 </collection>
rliterman@29 200 </outputs>
rliterman@29 201 <tests>
rliterman@29 202 <test>
rliterman@29 203 <param name="query_fasta">
rliterman@29 204 <collection type="list">
rliterman@29 205 <element name="Sample_A" value="assemblies/Sample_A.fasta" />
rliterman@29 206 <element name="Sample_B" value="assemblies/Sample_B.fasta" />
rliterman@29 207 <element name="Sample_C" value="assemblies/Sample_C.fasta" />
rliterman@29 208 <element name="Sample_D" value="assemblies/Sample_D.fasta" />
rliterman@29 209 <element name="Sample_E" value="assemblies/Sample_E.fasta" />
rliterman@29 210 <element name="Sample_F" value="assemblies/Sample_F.fasta" />
rliterman@29 211 <element name="Sample_G" value="assemblies/Sample_G.fasta" />
rliterman@29 212 <element name="Sample_H" value="assemblies/Sample_H.fasta" />
rliterman@29 213 <element name="Sample_I" value="assemblies/Sample_I.fasta" />
rliterman@29 214 <element name="Sample_J" value="assemblies/Sample_J.fasta" />
rliterman@29 215 <element name="Sample_K" value="assemblies/Sample_K.fasta" />
rliterman@29 216 <element name="Sample_L" value="assemblies/Sample_L.fasta" />
rliterman@29 217 <element name="Sample_M" value="assemblies/Sample_M.fasta" />
rliterman@29 218 <element name="Sample_N" value="assemblies/Sample_N.fasta" />
rliterman@29 219 <element name="Sample_O" value="assemblies/Sample_O.fasta" />
rliterman@29 220 </collection>
rliterman@29 221 </param>
rliterman@29 222 <param name="query_reads">
rliterman@29 223 <collection type="list">
rliterman@29 224 <element name="Forward" value="reads/Week_42_Reads_1.fq.gz" />
rliterman@29 225 <element name="Reverse" value="reads/Week_42_Reads_2.fq.gz" />
rliterman@29 226 </collection>
rliterman@29 227 </param>
rliterman@29 228
rliterman@29 229 <param name="ref_id" value="Sample_A,Sample_B" />
rliterman@29 230 <param name="readext" value="fq.gz" />
rliterman@29 231 <param name="forward" value="_1.fq.gz" />
rliterman@29 232 <param name="reverse" value="_2.fq.gz" />
rliterman@29 233
rliterman@29 234 <output name="isolate_data" value="Isolate_Data.tsv" />
rliterman@29 235 </test>
rliterman@29 236 </tests>
rliterman@29 237 <help>
rliterman@29 238 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@29 239 </help>
rliterman@29 240 <citations>
rliterman@29 241 <citation type="doi">10.XXXX/placeholder.doi</citation>
rliterman@29 242 <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@29 243 </citation>
rliterman@29 244 </citations>
rliterman@29 245 </tool>
rliterman@29 246