Mercurial > repos > fubar > blasttools_search_test
changeset 6:c23d0b047de9 draft
Uploaded
| author | fubar |
|---|---|
| date | Wed, 19 Jul 2023 23:39:38 +0000 |
| parents | 3a499f3ed69c |
| children | bb99f2c0e358 |
| files | blasttoolssearch/.shed.yml blasttoolssearch/LICENSE blasttoolssearch/README.md blasttoolssearch/blasttoolssearch.xml |
| diffstat | 4 files changed, 27 insertions(+), 10 deletions(-) [+] |
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--- 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
--- /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.
--- /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.
--- 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"/>