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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 </requirements>
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7 <version_command>nextflow -version</version_command>
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8 <command detect_errors="aggressive"><![CDATA[
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9
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10 mkdir ./queries ./references;
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11
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12 #if (str($query_fasta.query_fasta_select) == "none"):
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13 export QUERY_FASTA_ARG="";
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14 #elif (str($query_fasta.query_fasta_select) == "collection"):
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15 #for _, $query_assembly in enumerate($query_fasta.coll):
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16 ln -sf ${query_assembly} ./queries/${query_assembly.element_identifier};
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17 #end for
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18 export QUERY_FASTA_ARG="--fasta ./queries";
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19 #else
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20 #for _, $query_assembly in enumerate($query_fasta.list):
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21 ln -sf ${query_assembly} ./queries/${query_assembly.element_identifier};
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22 #end for
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23 export QUERY_FASTA_ARG="--fasta ./queries";
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24 #end if
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25
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26 #if (str($ref_fasta.ref_fasta_select) == "none"):
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27 export REF_FASTA_ARG="";
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28 #elif (str($ref_fasta.ref_fasta_select) == "collection"):
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29 #for _, $ref_assembly in enumerate($ref_fasta.coll):
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30 ln -sf ${ref_assembly} ./references/${ref_assembly.element_identifier};
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31 #end for
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32 export REF_FASTA_ARG="--fasta ./references";
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33 #else
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34 #for _, $ref_assembly in enumerate($ref_fasta.list):
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35 ln -sf ${ref_assembly} ./references/${ref_assembly.element_identifier};
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36 #end for
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37 export REF_FASTA_ARG="--fasta ./references";
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38 #end if
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39
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40 #if (str($query_reads.query_reads_select) == "none"):
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41 export QUERY_READS_ARG="";
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42 #elif (str($query_reads.query_reads_select) == "collection"):
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43 #for _, $pair in enumerate($query_reads.coll):
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44 ln -sf ${pair.forward} ./queries/${pair.forward.name};
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45 ln -sf ${pair.reverse} ./queries/${pair.reverse.name};
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46 #end for
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47 export QUERY_READS_ARG="--reads ./queries";
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48 #else
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49 #for _, $read_file in enumerate($query_reads.list):
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50 ln -sf ${read_file} ./queries/${read_file.element_identifier};
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51 #end for
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52 export QUERY_READS_ARG="--reads ./queries";
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53 #end if
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54
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55 #if (str($ref_reads.ref_reads_select) == "none"):
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56 export REF_READS_ARG="";
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57 #elif (str($ref_reads.ref_reads_select) == "collection"):
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58 #for _, $pair in enumerate($ref_reads.coll):
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59 ln -sf ${pair.forward} ./references/${pair.forward.name};
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60 ln -sf ${pair.reverse} ./references/${pair.reverse.name};
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61 #end for
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62 export REF_READS_ARG="--ref_reads ./references";
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63 #else
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64 #for _, $read_file in enumerate($ref_reads.list):
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65 ln -sf ${read_file} ./references/${read_file.element_identifier};
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66 #end for
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67 export REF_READS_ARG="--ref_reads ./references";
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68 #end if
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69
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70 if [ -n "$trim_name" ] && [ "$trim_name" != "None" ]; then
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71 export TRIM_ARG="--trim_name $trim_name";
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72 else
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73 export TRIM_ARG="";
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74 fi;
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75
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76 if [ -n "$ref_id" ] && [ "$ref_id" != "None" ]; then
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77 export REF_ID_ARG="--ref_id $ref_id";
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78 else
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79 export REF_ID_ARG="";
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80 fi;
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81
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82 nextflow run ${__tool_directory__}/CSP2/CSP2.nf -profile csp2_galaxy --runmode screen \$QUERY_FASTA_ARG \$REF_FASTA_ARG \$QUERY_READS_ARG \$REF_READS_ARG \$REF_ID_ARG \$TRIM_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 --out ./CSP2_Screen_Output > Nextflow_Log.txt 2>&1 &&
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83 ls -la CSP2_Screen_Output;
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84 ]]>
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85 </command>
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86 <inputs>
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87 <conditional name="query_fasta">
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88 <param name="query_fasta_select" type="select" label="Get query assemblies from a collection or your history">
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89 <option value="none" selected="true">Do not provide query assemblies</option>
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90 <option value="collection">Query assemblies from a FASTA collection</option>
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91 <option value="history">Query assemblies from your history</option>
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92 </param>
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93 <when value="none">
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94 </when>
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95 <when value="collection">
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96 <param label="Query Assembly Collection" name="coll" type="data_collection" format="fasta" collection_type="list" />
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97 </when>
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98 <when value="history">
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99 <param label="Query Assembly List" type="data" name="list" format="fasta" multiple="true" />
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100 </when>
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101 </conditional>
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102
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103 <conditional name="ref_fasta">
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104 <param name="ref_fasta_select" type="select" label="Get reference assemblies from a collection or your history">
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105 <option value="none" selected="true">Do not provide reference assemblies</option>
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106 <option value="collection">Reference assemblies from a FASTA collection</option>
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107 <option value="history">Reference assemblies from your history</option>
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108 </param>
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109 <when value="none">
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110 </when>
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111 <when value="collection">
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112 <param label="Reference Assembly Collection" name="coll" type="data_collection" format="fasta" collection_type="list" />
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113 </when>
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114 <when value="history">
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115 <param label="Reference Assembly List" type="data" name="list" format="fasta" multiple="true" />
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116 </when>
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117 </conditional>
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118 <conditional name="query_reads">
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119 <param name="query_reads_select" type="select" label="Get query reads from a paired-end collection or your history">
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120 <option value="none" selected="true">Do not provide query reads</option>
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121 <option value="collection">Paired-end query reads from a collection</option>
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122 <option value="history">Query reads from your history</option>
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123 </param>
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124 <when value="none">
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125 </when>
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126 <when value="collection">
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127 <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" />
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128 </when>
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129 <when value="history">
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130 <param label="Query Reads List" type="data" name="list" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" multiple="true" />
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131 </when>
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132 </conditional>
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133
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134 <conditional name="ref_reads">
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135 <param name="ref_reads_select" type="select" label="Get reference reads from a paired-end collection or your history">
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136 <option value="none" selected="true">Do not provide reference reads</option>
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137 <option value="collection">Paired-end reference reads from a collection_type</option>
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138 <option value="history">Reference reads from your history</option>
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139 </param>
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140 <when value="none">
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141 </when>
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142 <when value="collection">
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143 <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" />
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144 </when>
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145 <when value="history">
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146 <param label="Refrence Reads List" type="data" name="list" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" multiple="true" />
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147 </when>
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148 </conditional>
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149 <param name="min_cov" type="float" value="85" label="Minimum reference genome coverage to proceed with distance estimation" optional="true" />
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150 <param name="min_iden" type="float" value="99" label="Minimum alignment percent identity to detect SNPs" optional="true" />
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151 <param name="min_len" type="integer" value="500" label="Minimum alignment length to detect SNPs" optional="true" />
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152 <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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153 <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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154 <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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155 <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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156 <param name="readext" type="text" value="fastq.gz" label="Read extension format (e.g., fastq.gz)" optional="true" />
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157 <param name="forward" type="text" value="_1.fastq.gz" label="Forward read suffix (e.g. _1.fastq.gz)" optional="true" />
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158 <param name="reverse" type="text" value="_2.fastq.gz" label="Forward read suffix (e.g. _2.fastq.gz)" optional="true" />
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159 <param name="trim_name" type="text" value="" label="Text to remove from all file names (e.g., _contigs_skesa)" optional="true" />
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160 <param name="ref_id" type="text" value="" label="Comma-separated list of desired Reference IDs (e.g., Sample_A,Sample_B)" optional="true" />
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161 </inputs>
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162 <outputs>
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163 <data name="raw_mummer" format="tabular" label="Raw MUMmer Output" from_work_dir="CSP2_Screen_Output/Raw_MUMmer_Summary.tsv" />
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164 <data name="isolate_data" format="tabular" label="Isolate Data" from_work_dir="CSP2_Screen_Output/Isolate_Data.tsv" />
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165 <data name="screening_results" format="tabular" label="Screening Results" from_work_dir="CSP2_Screen_Output/Screening_Results.tsv" />
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166 </outputs>
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167 <tests>
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168 <test>
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169 <param name="query_fasta">
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170 <collection type="list">
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171 <element name="Sample_A" value="assemblies/Sample_A.fasta" />
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172 <element name="Sample_B" value="assemblies/Sample_B.fasta" />
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173 <element name="Sample_C" value="assemblies/Sample_C.fasta" />
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174 <element name="Sample_D" value="assemblies/Sample_D.fasta" />
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175 <element name="Sample_E" value="assemblies/Sample_E.fasta" />
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176 <element name="Sample_F" value="assemblies/Sample_F.fasta" />
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177 <element name="Sample_G" value="assemblies/Sample_G.fasta" />
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178 <element name="Sample_H" value="assemblies/Sample_H.fasta" />
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179 <element name="Sample_I" value="assemblies/Sample_I.fasta" />
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180 <element name="Sample_J" value="assemblies/Sample_J.fasta" />
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181 <element name="Sample_K" value="assemblies/Sample_K.fasta" />
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182 <element name="Sample_L" value="assemblies/Sample_L.fasta" />
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183 <element name="Sample_M" value="assemblies/Sample_M.fasta" />
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184 <element name="Sample_N" value="assemblies/Sample_N.fasta" />
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185 <element name="Sample_O" value="assemblies/Sample_O.fasta" />
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186 </collection>
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187 </param>
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188 <param name="query_reads">
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189 <collection type="list">
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190 <element name="Forward" value="reads/Week_42_Reads_1.fq.gz" />
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191 <element name="Reverse" value="reads/Week_42_Reads_2.fq.gz" />
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192 </collection>
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193 </param>
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194
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195 <param name="ref_id" value="Sample_A,Sample_B" />
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196 <param name="readext" value="fq.gz" />
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197 <param name="forward" value="_1.fq.gz" />
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198 <param name="reverse" value="_2.fq.gz" />
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199
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200 <output name="screening_results" value="Screening_Results.tsv" />
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201 <output name="isolate_data" value="Isolate_Data.tsv" />
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202 </test>
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203 </tests>
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204 <help>
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205 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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206 </help>
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207 <citations>
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208 <citation type="doi">10.XXXX/placeholder.doi</citation>
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209 <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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210 </citation>
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211 </citations>
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212 </tool>
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213
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