Mercurial > repos > fubar > blasttools_search_test

annotate blast_tools_search/blasttoolssearch.xml @ 8:186734f1d63c draft default tip

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Replace plotly_blast_tool content with blasttools_search. :(
author fubar
date Fri, 04 Aug 2023 01:57:51 +0000
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8
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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_tf_overlay-->
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3 <!--Created by toolfactory@galaxy.org at 04/08/2023 10:36:33 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 version="0.26.0" type="package">csvtk</requirement>
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7 <requirement version="11.0.13" 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 $runme "$blastn_search_outputs" "$__tool_directory__/BlastTools.jar" "$summary_viruses_viroids" "$all_blasttools_output"]]></command>
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14 <configfiles>
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15 <configfile name="runme"><![CDATA[#raw
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16
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17 ## eResearch Office, QUT
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18 ## Created: 31 March 2021
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19 ## Last modified: 28 September 2022
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20 ## Script: Processes Galaxy Australia generated blastN outputs to summarise and report hits to REGULATED and ENDEMIC viruses/viroids.
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21 ## Usage: ./run_VirReport_Summary.sh
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22 ## changed to accept a single input file name passed as $1
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23 ## Ross Lazarus for a ToolFactory wrapper for Robert Barrero
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24 ## July 18 2023
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25
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26
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27 # 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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28 # The script will Look for all files with the suffix *.tabular
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29
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30 #Processing tabular files
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31 file=$1
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32 var=$(basename $file)
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33
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34 #STEP1: modify the columns of Galaxy Australia (GA) blast output to the expected format by the BlastTools.jar tool
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35 ###### 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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36 cat $file |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}_all.txt
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37 java -jar $2 -t blastn ${var}_all.txt
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38 cat summary_${var}_all.txt | grep "virus\|viroid\|endo" > $4
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39
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40
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41 #STEP0: fetch Top 1 Hits
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42 cat $file | awk '{print $1}' | sort | uniq > ${var}.top1.ids
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43 for i in `cat ${var}.top1.ids`
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44 do
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45 echo "fetching top hits..." $i 1>&2 ;
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46 grep $i $file | head -1 >> ${var}.top1Hits.txt;
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47 done
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48
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49 #STEP1: modify the columns of Galaxy Australia (GA) blast output to the expected format by the BlastTools.jar tool
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50 ###### 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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51 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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52
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53 #STEP2: summarise the GA blastN files
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54 java -jar $2 -t blastn ${var}.txt
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55 #filter virus/viroid/endo
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56 cat summary_${var}.txt | grep "virus\|viroid\|endo" > summary_${var}_filtered.txt
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57
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58 #STEP3: fetch unique names from Blast summary reports
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59 cat summary_${var}_filtered.txt | awk '{print $7}' | awk -F "|" '{print $2}'| sort | uniq | sed 's/Species://' > ${var}_uniq.ids
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60
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61 #STEP4: retrieve the best hit for each virus/viroid
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62 echo "processing top hits ..." 1>&2
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63 touch ${var}_filtered.txt
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64 for id in `cat ${var}_uniq.ids`
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65 do
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66 #print on the screen the name of the virus/viroids to search
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67 #echo "fetching species matches ..." $id 1>&2
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68
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69 #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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70 grep $id summary_${var}.txt | sort -k3,3nr -k5,5nr | head -1 >> ${var}_filtered.txt
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71 done
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72
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73 #print the header of the inital summary_blastn file
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74 cat summary_${var}.txt | head -1 > header
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75 #report 1
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76 cat header ${var}_filtered.txt > $3
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77
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78
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79
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80
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81
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82 #end raw]]></configfile>
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83 </configfiles>
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84 <inputs>
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85 <param name="blastn_search_outputs" type="data" optional="false" label="blastn_search_outputs" help="Nucleotide blast search output from a Galaxy blast search" format="tabular" multiple="false"/>
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86 </inputs>
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87 <outputs>
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88 <data name="summary_viruses_viroids" format="tabular" label="summary_viruses_viroids" hidden="false"/>
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89 <data name="all_blasttools_output" format="tabular" label="all_blasttools_output" hidden="false"/>
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90 </outputs>
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91 <tests>
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92 <test>
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93 <output name="summary_viruses_viroids" value="summary_viruses_viroids_sample" compare="diff" lines_diff="0"/>
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94 <output name="all_blasttools_output" value="all_blasttools_output_sample" compare="diff" lines_diff="0"/>
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95 <param name="blastn_search_outputs" value="blastn_search_outputs_sample"/>
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96 </test>
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97 </tests>
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98 <help><![CDATA[
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99
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100 **What it Does**
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101
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102 Wraps https://github.com/schmidda/blast-tools/tree/master as a Galaxy tool as a demonstration for Roberto Barrero
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103
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104
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105
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106 ------
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107
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108
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109 Script::
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110
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111 ## eResearch Office, QUT
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112 ## Created: 31 March 2021
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113 ## Last modified: 28 September 2022
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114 ## Script: Processes Galaxy Australia generated blastN outputs to summarise and report hits to REGULATED and ENDEMIC viruses/viroids.
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115 ## Usage: ./run_VirReport_Summary.sh
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116 ## changed to accept a single input file name passed as $1
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117 ## Ross Lazarus for a ToolFactory wrapper for Robert Barrero
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118 ## July 18 2023
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119 # 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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120 # The script will Look for all files with the suffix *.tabular
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121 #Processing tabular files
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122 file=$1
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123 var=$(basename $file)
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124 #STEP1: modify the columns of Galaxy Australia (GA) blast output to the expected format by the BlastTools.jar tool
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125 ###### 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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126 cat $file |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}_all.txt
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127 java -jar $2 -t blastn $ {var}_all.txt
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128 cat summary_$ {var}_all.txt | grep "virus\|viroid\|endo" > $4
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129 #STEP0: fetch Top 1 Hits
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130 cat $file | awk '{print $1}' | sort | uniq > $ {var}.top1.ids
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131 for i in `cat $ {var}.top1.ids`
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132 do
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133 echo "fetching top hits..." $i 1>&2 ;
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134 grep $i $file | head -1 >> $ {var}.top1Hits.txt;
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135 done
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136 #STEP1: modify the columns of Galaxy Australia (GA) blast output to the expected format by the BlastTools.jar tool
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137 ###### 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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138 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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139 #STEP2: summarise the GA blastN files
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140 java -jar $2 -t blastn $ {var}.txt
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141 #filter virus/viroid/endo
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142 cat summary_$ {var}.txt | grep "virus\|viroid\|endo" > summary_$ {var}_filtered.txt
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143 #STEP3: fetch unique names from Blast summary reports
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144 cat summary_$ {var}_filtered.txt | awk '{print $7}' | awk -F "|" '{print $2}'| sort | uniq | sed 's/Species://' > $ {var}_uniq.ids
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145 #STEP4: retrieve the best hit for each virus/viroid
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146 echo "processing top hits ..." 1>&2
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147 touch $ {var}_filtered.txt
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148 for id in `cat $ {var}_uniq.ids`
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149 do
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150 #print on the screen the name of the virus/viroids to search
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151 #echo "fetching species matches ..." $id 1>&2
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152 #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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153 grep $id summary_$ {var}.txt | sort -k3,3nr -k5,5nr | head -1 >> $ {var}_filtered.txt
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154 done
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155 #print the header of the inital summary_blastn file
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156 cat summary_$ {var}.txt | head -1 > header
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157 #report 1
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158 cat header $ {var}_filtered.txt > $3
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159
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160 ]]></help>
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161 <citations>
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162 <citation type="doi">10.1093/bioinformatics/bts573</citation>
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163 </citations>
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164 </tool>
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165