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1 <tool name="blasttoolssearch" id="blasttoolssearch" version="3.0">
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2 <!--Source in git at: https://github.com/fubar2/galaxy-->
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3 <!--Created by toolfactory@galaxy.org at 19/07/2023 12:39:19 using the Galaxy Tool Factory.-->
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4 <description>Runs a legacy Java jar called blasttools from https://github.com/schmidda/blast-tools/tree/master</description>
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5 <requirements>
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6 <requirement type="package">csvtk</requirement>
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7 <requirement type="package">openjdk</requirement>
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8 </requirements>
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9 <stdio>
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10 <exit_code range="1:" level="fatal"/>
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11 </stdio>
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12 <version_command><![CDATA[echo "3.0"]]></version_command>
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13 <command><![CDATA[bash
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14 $runme
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15 $blastn_search_outputs
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16 $__tool_directory__/BlastTools.jar
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17 $summary_viruses_viroids
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18 ]]></command>
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19 <configfiles>
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20 <configfile name="runme"><![CDATA[#raw
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21
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22
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23 ## eResearch Office, QUT
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24 ## Created: 31 March 2021
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25 ## Last modified: 28 September 2022
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26 ## Script: Processes Galaxy Australia generated blastN outputs to summarise and report hits to REGULATED and ENDEMIC viruses/viroids.
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27 ## Usage: ./run_VirReport_Summary.sh
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28 ## changed to accept a single input file name passed as $1
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29 ## Ross Lazarus for a ToolFactory wrapper for Robert Barrero
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30 ## July 18 2023
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31
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32 dataPath=${PWD}
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33
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34 # Requirement: One or more GA-VSD .tabular outputs need to be in the folder where the command above (Usage)is executed.
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35 # The script will Look for all files with the suffix *.tabular
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36
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37 #Processing tabular files
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38 file=$1
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39
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40 var=$(basename $file)
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41
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42 #STEP0: fetch Top 1 Hits
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43 cat $file | awk '{print $1}' | sort | uniq > ${var}.top1.ids
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44 for i in `cat ${var}.top1.ids`
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45 do
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46 echo "fetching top hits..." $i;
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47 grep $i $file | head -1 >> ${var}.top1Hits.txt;
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48 done
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49
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50 #STEP1: modify the columns of Galaxy Australia (GA) blast output to the expected format by the BlastTools.jar tool
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51 ###### namely: qseqid sgi sacc length pident mismatch gapopen qstart qend qlen sstart send slen sstrand evalue bitscore qcovhsp stitle staxids qseq sseq sseqid qcovs qframe sframe
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52 cat ${var}.top1Hits.txt |csvtk cut -H -t -f 1,19,20,4,3,5,6,7,8,17,9,10,18,22,11,12,24,21,25,15,16,2,23,13,14 | sed 's/ /_/g' > ${var}.txt
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53
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54 #STEP2: summarise the GA blastN files
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55 java -jar $2 -t blastn ${var}.txt
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56 #filter virus/viroid/endo
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57 cat summary_${var}.txt | grep "virus\|viroid\|endo" > summary_${var}_filtered.txt
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58
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59 #STEP3: fetch unique names from Blast summary reports
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60 cat summary_${var}_filtered.txt | awk '{print $7}' | awk -F "|" '{print $2}'| sort | uniq | sed 's/Species://' > ${var}_uniq.ids
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61
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62 #STEP4: retrieve the best hit for each virus/viroid
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63 echo "processing top hits ..."
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64 touch ${var}_filtered.txt
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65 for id in `cat ${var}_uniq.ids`
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66 do
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67 #print on the screen the name of the virus/viroids to search
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68 #echo "fetching species matches ..." $id
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69
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70 #fetch the virus name on the summary_blastn file by selecting the longest alignment (column 3) and highest genome coverage (column 5)
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71 grep $id summary_${var}.txt | sort -k3,3nr -k5,5nr | head -1 >> ${var}_filtered.txt
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72 done
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73
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74 #print the header of the inital summary_blastn file
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75 cat summary_${var}.txt | head -1 > header
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76 #report 1
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77 cat header ${var}_filtered.txt > $3
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78
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79 #end raw]]></configfile>
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80 </configfiles>
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81 <inputs>
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82 <param name="blastn_search_outputs" type="data" optional="false" label="blastn_search_outputs" help="" format="tabular" multiple="false"/>
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83 </inputs>
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84 <outputs>
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85 <data name="summary_viruses_viroids" format="txt" label="summary_viruses_viroids" hidden="false"/>
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86 </outputs>
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87 <tests>
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88 <test>
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89 <output name="summary_viruses_viroids" value="summary_viruses_viroids_sample" compare="diff" lines_diff="0"/>
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90 <param name="blastn_search_outputs" value="blastn_search_outputs_sample"/>
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91 </test>
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92 </tests>
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93 <help><![CDATA[
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94
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95 **What it Does**
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96
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97 Wraps https://github.com/schmidda/blast-tools/tree/master as a Galaxy tool as a demonstration for Roberto Barrero
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98
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99
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100
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101 ------
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102
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103
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104 Script::
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105
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106 ## eResearch Office, QUT
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107 ## Created: 31 March 2021
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108 ## Last modified: 28 September 2022
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109 ## Script: Processes Galaxy Australia generated blastN outputs to summarise and report hits to REGULATED and ENDEMIC viruses/viroids.
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110 ## Usage: ./run_VirReport_Summary.sh
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111 ## changed to accept a single input file name passed as $1
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112 ## Ross Lazarus for a ToolFactory wrapper for Robert Barrero
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113 ## July 18 2023
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114 dataPath=${PWD}
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115 # Requirement: One or more GA-VSD .tabular outputs need to be in the folder where the command above (Usage)is executed.
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116 # The script will Look for all files with the suffix *.tabular
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117 #Processing tabular files
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118 file=$1
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119 var=$(basename $file)
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120 #STEP0: fetch Top 1 Hits
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121 cat $file | awk '{print $1}' | sort | uniq > ${var}.top1.ids
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122 for i in `cat ${var}.top1.ids`
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123 do
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124 echo "fetching top hits..." $i;
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125 grep $i $file | head -1 >> ${var}.top1Hits.txt;
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126 done
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127 #STEP1: modify the columns of Galaxy Australia (GA) blast output to the expected format by the BlastTools.jar tool
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128 ###### namely: qseqid sgi sacc length pident mismatch gapopen qstart qend qlen sstart send slen sstrand evalue bitscore qcovhsp stitle staxids qseq sseq sseqid qcovs qframe sframe
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129 cat ${var}.top1Hits.txt |csvtk cut -H -t -f 1,19,20,4,3,5,6,7,8,17,9,10,18,22,11,12,24,21,25,15,16,2,23,13,14 | sed 's/ /_/g' > ${var}.txt
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130 #STEP2: summarise the GA blastN files
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131 #java -jar /mnt/c/Users/lelwala/HTS/BlastTools.jar -t blastn ${var}.txt
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132 java -jar $3 -t blastn ${var}.txt
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133 #filter virus/viroid/endo
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134 cat summary_${var}.txt | grep "virus\|viroid\|endo" > summary_${var}_filtered.txt
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135 #STEP3: fetch unique names from Blast summary reports
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136 cat summary_${var}_filtered.txt | awk '{print $7}' | awk -F "|" '{print $2}'| sort | uniq | sed 's/Species://' > ${var}_uniq.ids
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137 #STEP4: retrieve the best hit for each virus/viroid
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138 echo "processing top hits ..."
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139 touch ${var}_filtered.txt
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140 for id in `cat ${var}_uniq.ids`
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141 do
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142 #print on the screen the name of the virus/viroids to search
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143 #echo "fetching species matches ..." $id
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144 #fetch the virus name on the summary_blastn file by selecting the longest alignment (column 3) and highest genome coverage (column 5)
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145 grep $id summary_${var}.txt | sort -k3,3nr -k5,5nr | head -1 >> ${var}_filtered.txt
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146 done
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147 #print the header of the inital summary_blastn file
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148 cat summary_${var}.txt | head -1 > header
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149 #report 1
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150 cat header ${var}_filtered.txt > $2
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151 #removing intermediate files
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152 rm summary_${file}.txt ${file}.txt ${file}.top1.ids ${file}_uniq.ids summary_${file}_filtered.txt header* ${var}_filtered.txt *top1Hits.txt
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153
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154 ]]></help>
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155 <citations>
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156 <citation type="doi">10.1093/bioinformatics/bts573</citation>
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157 </citations>
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158 </tool>
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159
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