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author jpayne
date Mon, 11 Aug 2025 15:46:24 +0000
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1 <tool id="csp2-snp" name="CSP2 (SNP Pipeline Mode)" version="0.9.7.7">
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2 <description>Run SNP Pipeline analysis on isolates using one or more references.</description>
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3 <requirements>
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4 <!-- <requirement type="package" version="24.10.1">nextflow</requirement>
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5 <requirement type="package" version="1.5.8">micromamba</requirement> -->
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6 <container type="docker">cfsanbiostatistics/csp2:v.0.9.7.7-galaxy</container>
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7 </requirements>
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8 <version_command>nextflow -version</version_command>
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9 <command detect_errors="exit_code"><![CDATA[
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10 mkdir -p queries references .nextflow
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11 #set readext=""
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12 #set renamedref=$source.reference.element_identifier.replace(": ", ".").replace(" ", "_")
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13 #for $reads in $coll
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14 && ln -sf '${reads}' 'queries/${reads.element_identifier.replace(": ", ".").replace(" ", "_")}.fasta'
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15 #end for
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16 && ln -sf '$source.reference' 'references/${renamedref}.fasta'
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17 && echo "*** Files in queries directory: ***"
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18 && ls -lah queries/
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19 && nextflow run
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20 /app/CSP2.nf -c $__tool_directory__/nextflow.config -profile standard
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21 --runmode snp
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22 --fasta queries
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23 --ref_fasta 'references/${renamedref}.fasta'
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24 --min_cov $opt.min_cov
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25 --min_iden $opt.min_iden
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26 --min_len $opt.min_len
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27 --ref_edge $opt.ref_edge
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28 --query_edge $opt.query_edge
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29 --dwin $opt.dwin
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30 --wsnps $opt.wsnps
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31 --out CSP2_SNP_Output
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32 --quiet
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33 && echo "*** Files in output directory: ***"
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34 && ls -lahR CSP2_SNP_Output
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35 && tail -n +2 CSP2_SNP_Output/Isolate_Data.tsv > ${isolate_data}
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36 && tail -n +2 CSP2_SNP_Output/Raw_MUMmer_Summary.tsv > ${raw_mummer}
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37 && tail -n +2 CSP2_SNP_Output/SNP_Analysis/${renamedref}/snp_distance_pairwise_preserved.tsv > ${snp_pairwise}
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38 && cat CSP2_SNP_Output/SNP_Analysis/${renamedref}/snplist_preserved.txt > ${snp_list}
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39 && cat CSP2_SNP_Output/SNP_Analysis/${renamedref}/snpma_preserved.fasta > ${snp_matrix}
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40 && echo "*** Nextflow log follows: ***"
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41 && cat .nextflow.log
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42 ]]>
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43 </command>
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44 <inputs>
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45 <conditional name="source">
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46 <param name="source_select" type="select" label="Use a curated GalaxyTrakr reference or a reference from your history">
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47 <option value="curated">Use a GalaxyTrakr reference</option>
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48 <option value="history">Use a reference from your history</option>
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49 </param>
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50 <when value="curated">
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51 <param name="reference" type="select" label="Select reference fasta">
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52 <options from_data_table="all_fasta">
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53 <filter type="sort_by" column="2"/>
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54 <validator type="no_options" message="No assemblies are available for the selected input dataset"/>
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55 </options>
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56 </param>
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57 </when>
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58 <when value="history">
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59 <param type="data" name="reference" format="fasta" label="Select reference FASTA"/>
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60 </when>
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61 </conditional>
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62 <!-- <conditional name="query">
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63 <param name="query_select" type="select" label="Screen a list of paired-reads or a list of assemblies">
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64 <option value="reads">Screen a list of paired reads</option>
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65 <option value="assemblies">Screen a list of assemblies</option>
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66 </param>
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67 <when value="reads">
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68 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="list:paired" />
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69 </when>
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70 <when value="assemblies"> -->
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71 <param label="Assemblies" name="coll" type="data_collection" format="fasta" collection_type="list" />
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72 <!-- </when> -->
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73 <!-- </conditional> -->
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74 <section name="opt" title="Advanced options...">
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75 <param name="min_cov" type="float" value="85" label="Minimum reference genome coverage to proceed with distance estimation" optional="true" />
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76 <param name="min_iden" type="float" value="99" label="Minimum alignment percent identity to detect SNPs" optional="true" />
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77 <param name="min_len" type="integer" value="500" label="Minimum alignment length to detect SNPs" optional="true" />
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78 <param name="ref_edge" type="integer" value="150" label="Prune SNPs within this many bases of reference contig edge" optional="true" />
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79 <param name="query_edge" type="integer" value="150" label="Prune SNPs within this many bases of query contig edge" optional="true" />
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80 <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" />
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81 <param name="wsnps" type="text" value="3,2,1" label="Comma-separated list of maximum SNP counts per density window" optional="true" />
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82 </section>
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83 </inputs>
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84 <outputs>
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85 <!-- <data name="nextflow_log" format="txt" label="Nextflow Log" from_work_dir="Nextflow_Log.txt" /> -->
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86 <data name="isolate_data" format="tabular" label="Isolate Data">
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87 <actions>
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88 <action name="column_names" type="metadata" default="Isolate_ID,Isolate_Type,Assembly_Path,Contig_Count,Assembly_Bases,N50,N90,L50,L90,SHA256" />
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89 </actions>
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90 </data>
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91 <data name="raw_mummer" format="tabular" label="Raw MUMmer Output">
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92 <actions>
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93 <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" />
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94 </actions>
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95 </data>
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96 <!-- <data name="csp2_zip" format="zip" label="Zipped Output" from_work_dir="CSP2_Output.zip" /> -->
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97 <!-- <discover_datasets pattern="(?P&lt;name&gt;.+)/CSP2_SNP_Pipeline\.log" format="txt" visible="true" directory="./CSP2_SNP_Output/SNP_Analysis" /> -->
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98 <!-- <discover_datasets pattern="(?P&lt;name&gt;.+)/Reference_Screening\.tsv" format="tabular" visible="true" directory="./CSP2_SNP_Output/SNP_Analysis" />
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99 <discover_datasets pattern="(?P&lt;name&gt;.+)/snp_distance_matrix_preserved\.tsv" format="tabular" visible="true" directory="./CSP2_SNP_Output/SNP_Analysis" />
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100 <discover_datasets pattern="(?P&lt;name&gt;.+)/snp_distance_pairwise_preserved\.tsv" format="tabular" visible="true" directory="./CSP2_SNP_Output/SNP_Analysis" />
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101 <discover_datasets pattern="(?P&lt;name&gt;.+)/snpma_preserved\.fasta" format="fasta" visible="true" directory="./CSP2_SNP_Output/SNP_Analysis" /> -->
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102 <data name="snp_pairwise" format="tabular" label="Preserved Pairwise SNP Distances">
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103 <actions>
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104 <action name="column_names" type="metadata" default="Query_1,Query_2,SNP_Distance,SNPs_Cocalled" />
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105 </actions>
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106 </data>
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107 <data name="snp_list" format="txt" label="Preserved SNP List" />
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108 <data name="snp_matrix" format="fasta" label="Preserved SNP Matrix" />
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109 <discover_datasets pattern="(?P&lt;name&gt;.+)/snp_distance_matrix\.tsv" format="tabular" visible="false" directory="./CSP2_SNP_Output/SNP_Analysis" />
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110 <discover_datasets pattern="(?P&lt;name&gt;.+)/snp_distance_pairwise\.tsv" format="tabular" visible="false" directory="./CSP2_SNP_Output/SNP_Analysis" />
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111 <discover_datasets pattern="(?P&lt;name&gt;.+)/snpma\.fasta" format="fasta" visible="false" directory="./CSP2_SNP_Output/SNP_Analysis" />
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112 </outputs>
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113 <tests>
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114 <test>
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115 <param name="source_select" value="history" />
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116 <param name="reference" value="assemblies/Sample_A.fasta" />
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117 <!-- <param name="query_select" value="assemblies" /> -->
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118 <param name="coll">
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119 <collection type="list">
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120 <!-- <element name="Sample_A" value="assemblies/Sample_A.fasta" /> -->
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121 <element name="Sample_B" value="assemblies/Sample_B.fasta" />
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122 <element name="Sample_C" value="assemblies/Sample_C.fasta" />
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123 <element name="Sample_D" value="assemblies/Sample_D.fasta" />
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124 <element name="Sample_E" value="assemblies/Sample_E.fasta" />
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125 <element name="Sample_F" value="assemblies/Sample_F.fasta" />
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126 <element name="Sample_G" value="assemblies/Sample_G.fasta" />
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127 <element name="Sample_H" value="assemblies/Sample_H.fasta" />
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128 <element name="Sample_I" value="assemblies/Sample_I.fasta" />
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129 <element name="Sample_J" value="assemblies/Sample_J.fasta" />
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130 <element name="Sample_K" value="assemblies/Sample_K.fasta" />
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131 <element name="Sample_L" value="assemblies/Sample_L.fasta" />
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132 <element name="Sample_M" value="assemblies/Sample_M.fasta" />
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133 <element name="Sample_N" value="assemblies/Sample_N.fasta" />
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134 <element name="Sample_O" value="assemblies/Sample_O.fasta" />
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135 </collection>
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136 </param>
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137
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138 <output name="isolate_data" value="Isolate_Data.tsv" />
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139 </test>
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140 <!-- <test>
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141 <param name="source_select" value="history" />
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142 <param name="reference" value="assemblies/Sample_A.fasta" ftype="fasta" />
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143 <param name="query_select" value="reads" />
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144 <param name="coll">
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145 <collection type="list:paired">
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146 <element name="Sample_A">
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147 <collection type="paired">
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148 <element name="forward" value="reads/Week_42_Reads_1.fq.gz" ftype="fastqsanger.gz" />
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149 <element name="reverse" value="reads/Week_42_Reads_2.fq.gz" ftype="fastqsanger.gz" />
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150 </collection>
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151 </element>
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152 </collection>
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153 </param>
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154 <output name="screening_results" value="Screening_Results.tsv" />
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155 <output name="isolate_data" value="Isolate_Data.tsv" />
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156 </test> -->
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157 </tests>
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158 <help>
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159 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.
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160 </help>
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161 <citations>
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162 <citation type="doi">10.XXXX/placeholder.doi</citation>
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163 <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}}
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164 </citation>
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165 </citations>
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166 </tool>