Mercurial > repos > fubar > blasttools_search_test

comparison blasttoolssearch/blasttoolssearch.xml @ 6:c23d0b047de9 draft

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author fubar
date Wed, 19 Jul 2023 23:39:38 +0000
parents 3a499f3ed69c
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5:3a499f3ed69c 6:c23d0b047de9
10 <exit_code range="1:" level="fatal"/> 10 <exit_code range="1:" level="fatal"/>
11 </stdio> 11 </stdio>
12 <version_command><![CDATA[echo "3.0"]]></version_command> 12 <version_command><![CDATA[echo "3.0"]]></version_command>
13 <command><![CDATA[ 13 <command><![CDATA[
14 mkdir -p files && 14 mkdir -p files &&
15 #for afile in $blastn_search_outputs: 15 ln -sf '$blastn_search_outputs' files/\$(basename '$blastn_search_outputs') &&
16 ln -sf '$afile' files/\$(basename '$afile') &&
17 #end for
18 bash $runme ./files $__tool_directory__/BlastTools.jar $summary_viruses_viroids 16 bash $runme ./files $__tool_directory__/BlastTools.jar $summary_viruses_viroids
19 ]]></command> 17 ]]></command>
20 <configfiles> 18 <configfiles>
21 <configfile name="runme"><![CDATA[#raw 19 <configfile name="runme"><![CDATA[#raw
22 20
78 cat header ${var}_filtered.txt > $3 76 cat header ${var}_filtered.txt > $3
79 done 77 done
80 #end raw]]></configfile> 78 #end raw]]></configfile>
81 </configfiles> 79 </configfiles>
82 <inputs> 80 <inputs>
83 <param name="blastn_search_outputs" type="data" optional="false" label="blastn_search_outputs" help="" format="tabular" multiple="true"/> 81 <param name="blastn_search_outputs" type="data" optional="false" label="blastn_search_outputs" help="" format="tabular" multiple="false"/>
84 </inputs> 82 </inputs>
85 <outputs> 83 <outputs>
86 <data name="summary_viruses_viroids" format="tabular" label="summary_viruses_viroids" hidden="false"/> 84 <data name="summary_viruses_viroids" format="tabular" label="summary_viruses_viroids" hidden="false"/>
87 </outputs> 85 </outputs>
88 <tests> 86 <tests>