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1 <tool id="csp2-screen" name="CSP2 (Screening Mode)" version="0.9.7_Dev21">
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2 <description>Screen query assemblies against reference assemblies</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.0.9.7.4</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
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11 #set readext=""
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12 #for $reads in $query.coll
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13 #if $hasattr($reads, "is_of_type") and $reads.is_of_type("fasta")
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14 && ln -sf ${reads} 'queries/${reads.element_identifier}.fasta'
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15 #else if $reads.forward.is_of_type("fastq.gz","fastqsanger.gz")
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16 #set readext="fastq.gz"
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17 && ln -sf '${reads.forward}' 'queries/${reads.forward.element_identifier}_1.fastq.gz'
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18 && ln -sf '${reads.reverse}' 'queries/${reads.reverse.element_identifier}_2.fastq.gz'
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19 #else if $reads.forward.is_of_type("fastq.bz2", "fastqsanger.bz2")
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20 #set readext="fastq.bz2"
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21 && ln -sf '${reads.forward}' 'queries/${reads.forward.element_identifier}_1.fastq.bz2'
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22 && ln -sf '${reads.reverse}' 'queries/${reads.reverse.element_identifier}_2.fastq.bz2'
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23 #else
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24 #set readext="fastq"
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25 && ln -sf '${reads.forward}' 'queries/${reads.forward.element_identifier}_1.fastq'
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26 && ln -sf '${reads.reverse}' 'queries/${reads.reverse.element_identifier}_2.fastq'
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27 #end if
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28 #end for
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29 && echo "*** Files in queries directory: ***"
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30 && ls -lah queries/
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31 && ln -sf '$source.reference' 'references/${source.reference.element_identifier}.fasta'
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32 && nextflow run
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33 ${__tool_directory__}/CSP2/CSP2.nf -profile csp2_galaxy
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34 --runmode screen
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35 #if $query.query_select == 'reads'
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36 --reads queries
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37 --readext $readext
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38 --forward "_1.${readext}"
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39 --reverse "_2.${readext}"
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40 #else
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41 --fasta queries
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42 #end if
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43 --ref_fasta 'references/${source.reference.element_identifier}.fasta'
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44 --min_cov $opt.min_cov
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45 --min_iden $opt.min_iden
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46 --min_len $opt.min_len
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47 --ref_edge $opt.ref_edge
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48 --query_edge $opt.query_edge
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49 --dwin $opt.dwin
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50 --wsnps $opt.wsnps
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51 --out CSP2_Screen_Output
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52 && echo "*** Files in output directory: ***"
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53 && ls -lah CSP2_Screen_Output
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54 && echo "*** Nextflow log follows: ***"
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55 && cat .nextflow.log
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56 ]]>
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57 </command>
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58 <inputs>
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59 <conditional name="source">
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60 <param name="source_select" type="select" label="Use a curated GalaxyTrakr reference or a reference from your history">
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61 <option value="curated">Use a GalaxyTrakr reference</option>
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62 <option value="history">Use a reference from your history</option>
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63 </param>
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64 <when value="curated">
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65 <param name="reference" type="select" label="Select reference fasta">
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66 <options from_data_table="all_fasta">
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67 <filter type="sort_by" column="2"/>
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68 <validator type="no_options" message="No assemblies are available for the selected input dataset"/>
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69 </options>
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70 </param>
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71 </when>
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72 <when value="history">
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73 <param type="data" name="reference" format="fasta" label="Select reference FASTA"/>
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74 </when>
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75 </conditional>
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76 <conditional name="query">
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77 <param name="query_select" type="select" label="Screen a list of paired-end reads or a list of assemblies">
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78 <option value="reads">Screen a list of paired reads</option>
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79 <option value="assemblies">Screen a list of assemblies</option>
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80 </param>
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81 <when value="reads">
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82 <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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83 </when>
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84 <when value="assemblies">
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85 <param label="Assemblies" name="coll" type="data_collection" format="fasta" collection_type="list" />
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86 </when>
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87 </conditional>
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88 <section name="opt" title="Advanced options...">
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89 <param argument="--min_cov" name="min_cov" type="float" value="85" label="Minimum reference genome coverage to proceed with distance estimation" />
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90 <param argument="--min_eden" name="min_iden" type="float" value="99" label="Minimum alignment percent identity to detect SNPs" />
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91 <param argument="--min_len" name="min_len" type="integer" value="500" label="Minimum alignment length to detect SNPs" />
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92 <param argument="--ref_edge" name="ref_edge" type="integer" value="150" label="Prune SNPs within this many bases of reference contig edge" />
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93 <param argument="--query_edge" name="query_edge" type="integer" value="150" label="Prune SNPs within this many bases of query contig edge" />
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94 <param argument="--dwin" 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)" />
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95 <param argument="--wsnips" name="wsnps" type="text" value="3,2,1" label="Comma-separated list of maximum SNP counts per density window" />
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96 </section>
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97 </inputs>
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98 <outputs>
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99 <data name="raw_mummer" format="tabular" label="Raw MUMmer Output" from_work_dir="CSP2_Screen_Output/Raw_MUMmer_Summary.tsv" />
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100 <data name="isolate_data" format="tabular" label="Isolate Data" from_work_dir="CSP2_Screen_Output/Isolate_Data.tsv" />
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101 <data name="screening_results" format="tabular" label="Screening Results" from_work_dir="CSP2_Screen_Output/Screening_Results.tsv" />
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102 <!-- <data name="nextflow_log" format="txt" label="Nextflow Log" from_work_dir="Nextflow_Log.txt" /> -->
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103 </outputs>
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104 <tests>
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105 <test>
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106 <param name="source_select" value="history" />
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107 <param name="reference" value="assemblies/Sample_A.fasta" ftype="fasta" />
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108 <param name="query_select" value="assemblies" />
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109 <param name="coll">
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110 <collection type="list">
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111 <!-- <element name="Sample_A" value="assemblies/Sample_A.fasta" /> -->
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112 <element name="Sample_B" value="assemblies/Sample_B.fasta" />
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113 <element name="Sample_C" value="assemblies/Sample_C.fasta" />
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114 <element name="Sample_D" value="assemblies/Sample_D.fasta" />
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115 <element name="Sample_E" value="assemblies/Sample_E.fasta" />
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116 <element name="Sample_F" value="assemblies/Sample_F.fasta" />
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117 <element name="Sample_G" value="assemblies/Sample_G.fasta" />
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118 <element name="Sample_H" value="assemblies/Sample_H.fasta" />
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119 <element name="Sample_I" value="assemblies/Sample_I.fasta" />
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120 <element name="Sample_J" value="assemblies/Sample_J.fasta" />
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121 <element name="Sample_K" value="assemblies/Sample_K.fasta" />
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122 <element name="Sample_L" value="assemblies/Sample_L.fasta" />
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123 <element name="Sample_M" value="assemblies/Sample_M.fasta" />
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124 <element name="Sample_N" value="assemblies/Sample_N.fasta" />
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125 <element name="Sample_O" value="assemblies/Sample_O.fasta" />
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126 </collection>
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127 </param>
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128
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129 <output name="screening_results" value="Screening_Results.tsv" />
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130 <output name="isolate_data" value="Isolate_Data.tsv" />
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131 </test>
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132 <test>
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133 <param name="source_select" value="history" />
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134 <param name="reference" value="assemblies/Sample_A.fasta" ftype="fasta" />
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135 <param name="query_select" value="reads" />
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136 <param name="coll">
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137 <collection type="list:paired">
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138 <element name="Sample_A" >
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139 <collection type="paired">
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140 <element name="forward" value="reads/Week_42_Reads_1.fq.gz" ftype="fastqsanger.gz" />
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141 <element name="reverse" value="reads/Week_42_Reads_2.fq.gz" ftype="fastqsanger.gz" />
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142 </collection>
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143 </element>
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144 </collection>
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145 </param>
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146 <output name="screening_results" value="Screening_Results.tsv" />
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147 <output name="isolate_data" value="Isolate_Data.tsv" />
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148 </test>
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149 </tests>
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150 <help>
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151 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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152 </help>
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153 <citations>
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154 <citation type="doi">10.XXXX/placeholder.doi</citation>
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155 <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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156 </citation>
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157 </citations>
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158 </tool>
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