Mercurial > repos > fubar > blasttools_search_test

comparison blasttoolssearch/blasttoolssearch.xml @ 2:e213ae40f480 draft

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retry with echo -n so no newline
author fubar
date Wed, 19 Jul 2023 05:54:34 +0000
parents 5687b8f1ad69
children a6593725b728
comparison
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1:5687b8f1ad69 2:e213ae40f480
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[bash 13 <command><![CDATA[bash
14 $runme 14 $runme
15 $blastn_search_outputs 15 $blastn_search_outputs
16 $__tool_directory__/BlastTools.jar 16 $__tool_directory__/BlastTools.jar
17 $summary_viruses_viroids 17 $summary_viruses_viroids
18 ]]></command> 18 ]]></command>
19 <configfiles> 19 <configfiles>
20 <configfile name="runme"><![CDATA[#raw 20 <configfile name="runme"><![CDATA[#raw
72 done 72 done
73 73
74 #print the header of the inital summary_blastn file 74 #print the header of the inital summary_blastn file
75 cat summary_${var}.txt | head -1 > header 75 cat summary_${var}.txt | head -1 > header
76 #report 1 76 #report 1
77 echo "#" > $3 77 echo -n "#" > $3
78 cat header ${var}_filtered.txt >> $3 78 cat header ${var}_filtered.txt >> $3
79 79
80 #end raw]]></configfile> 80 #end raw]]></configfile>
81 </configfiles> 81 </configfiles>
82 <inputs> 82 <inputs>
83 <param name="blastn_search_outputs" type="data" optional="false" label="blastn_search_outputs" help="" format="tabular" multiple="false"/> 83 <param name="blastn_search_outputs" type="data" optional="false" label="blastn_search_outputs" help="" format="tabular" multiple="false"/>
95 95
96 **What it Does** 96 **What it Does**
97 97
98 Wraps https://github.com/schmidda/blast-tools/tree/master as a Galaxy tool as a demonstration for Roberto Barrero 98 Wraps https://github.com/schmidda/blast-tools/tree/master as a Galaxy tool as a demonstration for Roberto Barrero
99 99
100 100
101 101
102 ------ 102 ------
103 103
104 104
105 Script:: 105 Script::