# HG changeset patch
# User fubar
# Date 1689809978 0
# Node ID c23d0b047de99cb49db6dfd673ffd69217b89974
# Parent  3a499f3ed69c517f84b433774ee5d5a859ac0ff5
Uploaded

diff -r 3a499f3ed69c -r c23d0b047de9 blasttoolssearch/.shed.yml
--- a/blasttoolssearch/.shed.yml	Wed Jul 19 10:18:30 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-category: ToolFactory generated Tools
-description: Runs a legacy Java jar called blasttools from https://github.com/schmidda/blast-tools/tree/master
-name: blasttoolssearch
-owner: toolfactory
-synopsis: Runs a legacy Java jar called blasttools from https://github.com/schmidda/blast-tools/tree/master
-type: unrestricted
diff -r 3a499f3ed69c -r c23d0b047de9 blasttoolssearch/LICENSE
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/blasttoolssearch/LICENSE	Wed Jul 19 23:39:38 2023 +0000
@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2023 Ross
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff -r 3a499f3ed69c -r c23d0b047de9 blasttoolssearch/README.md
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/blasttoolssearch/README.md	Wed Jul 19 23:39:38 2023 +0000
@@ -0,0 +1,4 @@
+# blast_tools_search
+ToolFactory wrapper for a legacy java program for Robert Barrero's work with biosecurity. 
+Code from https://github.com/schmidda/blast-tools/tree/master
+Needs the BlastTools.jar file from that repository - copied here permanently.
diff -r 3a499f3ed69c -r c23d0b047de9 blasttoolssearch/blasttoolssearch.xml
--- a/blasttoolssearch/blasttoolssearch.xml	Wed Jul 19 10:18:30 2023 +0000
+++ b/blasttoolssearch/blasttoolssearch.xml	Wed Jul 19 23:39:38 2023 +0000
@@ -12,9 +12,7 @@
   <version_command><![CDATA[echo "3.0"]]></version_command>
   <command><![CDATA[
 mkdir -p files &&
-#for afile in $blastn_search_outputs:
-ln -sf '$afile' files/\$(basename '$afile') &&
-#end for
+ln -sf '$blastn_search_outputs' files/\$(basename '$blastn_search_outputs') &&
 bash $runme ./files $__tool_directory__/BlastTools.jar $summary_viruses_viroids
 ]]></command>
   <configfiles>
@@ -80,7 +78,7 @@
 #end raw]]></configfile>
   </configfiles>
   <inputs>
-    <param name="blastn_search_outputs" type="data" optional="false" label="blastn_search_outputs" help="" format="tabular" multiple="true"/>
+    <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"/>