comparison blasttoolssearch/blasttoolssearch.xml @ 5:3a499f3ed69c draft

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4:2051ee2bedc4

<tool name="blasttoolssearch" id="blasttoolssearch" version="3.0">
  <!--Source in git at: https://github.com/fubar2/galaxy-->
  <!--Created by [e-mail] at 19/07/2023 12:39:19 using the Galaxy Tool Factory.-->
  <description>Runs a legacy Java jar called blasttools from https://github.com/schmidda/blast-tools/tree/master</description>
  <requirements>
    <requirement type="package">csvtk</requirement>

  </requirements>
  <stdio>
    <exit_code range="1:" level="fatal"/>
  </stdio>
  <version_command><![CDATA[echo "3.0"]]></version_command>
  <command><![CDATA[bash
$runme
$blastn_search_outputs
$__tool_directory__/BlastTools.jar
$summary_viruses_viroids
]]></command>
  <configfiles>
    <configfile name="runme"><![CDATA[#raw

# Requirement: One or more GA-VSD .tabular outputs need to be in the folder where the command above (Usage)is executed.
# The script will Look for all files with the suffix *.tabular

#Processing tabular files
file=$1

    var=$(basename $file)

    #STEP0: fetch Top 1 Hits
    cat $file | awk '{print $1}' | sort | uniq > ${var}.top1.ids
    for i in `cat ${var}.top1.ids`

    #print the header of the inital summary_blastn file
    cat summary_${var}.txt | head -1 > header
    #report 1
    cat header ${var}_filtered.txt > $3

#end raw]]></configfile>
  </configfiles>
  <inputs>
    <param name="blastn_search_outputs" type="data" optional="false" label="blastn_search_outputs" help="" format="tabular" multiple="false"/>
  </inputs>
  <outputs>
    <data name="summary_viruses_viroids" format="tabular" label="summary_viruses_viroids" hidden="false"/>
  </outputs>
  <tests>

5:3a499f3ed69c

<tool name="blasttoolssearch" id="blasttoolssearch" version="3.1">
  <!--Source in git at: https://github.com/fubar2/galaxy-->
  <!--Created by [e-mail] at 19/07/2023 12:39:19 using the Galaxy Tool Factory.-->
  <description>Runs a legacy Java jar called blasttools from https://github.com/schmidda/blast-tools/tree/master</description>
  <requirements>
    <requirement type="package">csvtk</requirement>

  </requirements>
  <stdio>
    <exit_code range="1:" level="fatal"/>
  </stdio>
  <version_command><![CDATA[echo "3.0"]]></version_command>
  <command><![CDATA[
mkdir -p files &&
#for afile in $blastn_search_outputs:
ln -sf '$afile' files/\$(basename '$afile') &&
#end for
bash $runme ./files $__tool_directory__/BlastTools.jar $summary_viruses_viroids
]]></command>
  <configfiles>
    <configfile name="runme"><![CDATA[#raw

# Requirement: One or more GA-VSD .tabular outputs need to be in the folder where the command above (Usage)is executed.
# The script will Look for all files with the suffix *.tabular

#Processing tabular files
for file in files/*.*
  do
    var=$(basename $file)

    #STEP0: fetch Top 1 Hits
    cat $file | awk '{print $1}' | sort | uniq > ${var}.top1.ids
    for i in `cat ${var}.top1.ids`

    #print the header of the inital summary_blastn file
    cat summary_${var}.txt | head -1 > header
    #report 1
    cat header ${var}_filtered.txt > $3
done
#end raw]]></configfile>
  </configfiles>
  <inputs>
    <param name="blastn_search_outputs" type="data" optional="false" label="blastn_search_outputs" help="" format="tabular" multiple="true"/>
  </inputs>
  <outputs>
    <data name="summary_viruses_viroids" format="tabular" label="summary_viruses_viroids" hidden="false"/>
  </outputs>
  <tests>