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changeset 2:a9c746142152 draft

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planemo upload commit 0b701b90047a2c860f9289c498cd7e68d3c51561
author oinizan
date Thu, 05 Apr 2018 09:41:15 -0400
parents e12bc43dcb47
children 2d996e4ddbcb
files demultiplex.xml normalisation.xml tool-data/frogs_db.loc upload_tar.xml
diffstat 4 files changed, 69 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/demultiplex.xml	Thu Apr 05 09:14:09 2018 -0400
+++ b/demultiplex.xml	Thu Apr 05 09:41:15 2018 -0400
@@ -184,4 +184,7 @@
 
 Depending on the help provided you can cite us in acknowledgements, references or both.
 	</help>
+	<citations>
+		<citation type="doi">10.7287/peerj.preprints.386v1</citation>
+	</citations>
 </tool>
--- a/normalisation.xml	Thu Apr 05 09:14:09 2018 -0400
+++ b/normalisation.xml	Thu Apr 05 09:41:15 2018 -0400
@@ -99,5 +99,8 @@
 Please cite the FROGS Publication: *Escudie F., Auer L., Bernard M., Cauquil L., Vidal K., Maman S., Mariadassou M., Combes S., Hernandez-Raquet G., Pascal G., 2016. FROGS: Find Rapidly OTU with Galaxy Solution. In: ISME-2016 Montreal, CANADA ,* http://bioinfo.genotoul.fr/wp-content/uploads/FROGS_ISME2016_poster.pdf
 
 Depending on the help provided you can cite us in acknowledgements, references or both.
-	</help> 
+	</help>
+	<citations>
+		<citation type="doi">10.7287/peerj.preprints.386v1</citation>
+	</citations> 
 </tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/frogs_db.loc	Thu Apr 05 09:41:15 2018 -0400
@@ -0,0 +1,51 @@
+# Copyright (C) 2014 INRA
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+#
+#This is a sample file that enables tools FROGS_affiliations_OTU to use taxonomy database for
+#taxonomy affiliation. You will need to create or download Blast+ index and train your database
+#for RDP classifier these data files.
+#download link : http://genoweb.toulouse.inra.fr/frogs_databanks/assignation
+#Finally you will need to create frogs_db.loc file similar to this one in your galaxy
+#tool-data directory.The frogs_db.loc file has this format (longer white space characters are
+#TAB characters):
+#
+#<unique_database_name>   <file_path>
+#
+#First column will be the visible name in galaxy.
+#So, for example, if you had 16S silva 128 indexed stored in
+#/galaxy_databanks/16S/silva_128/ 
+#then the frogs_db.loc entry would look like this:
+#
+#silva 128 16S  /galaxy_databanks/16S/silva_128/silva_128_16S.fasta
+#
+#and your /galaxy_databanks/16S/silva_128/ directory
+#would contain index files:
+#
+#-rw-r--r-- 1 mbernard FROGS    8097966  5 déc.  16:56 bergeyTrainingTree.xml
+#-rw-r--r-- 1 mbernard FROGS 1572981589  5 déc.  16:56 genus_wordConditionalProbList.txt
+#-rw-r--r-- 1 mbernard FROGS       1654  5 déc.  16:56 LICENCE.txt
+#-rw-r--r-- 1 mbernard FROGS    1072228  5 déc.  16:56 logWordPrior.txt
+#-rw-r--r-- 1 mbernard FROGS  940834335  5 déc.  16:56 silva_128_16S.fasta
+#-rw-r--r-- 1 mbernard FROGS  152606489  5 déc.  16:56 silva_128_16S.fasta.nhr
+#-rw-r--r-- 1 mbernard FROGS    6918588  5 déc.  16:56 silva_128_16S.fasta.nin
+#-rw-r--r-- 1 mbernard FROGS  205320030  5 déc.  16:56 silva_128_16S.fasta.nsq
+#-rw-r--r-- 1 mbernard FROGS        281  5 déc.  16:56 silva_128_16S.fasta.properties
+#-rw-r--r-- 1 mbernard FROGS    3420464  5 déc.  16:56 silva_128_16S.tax
+#-rw-r--r-- 1 mbernard FROGS     964048  5 déc.  16:57 wordConditionalProbIndexArr.txt
+#
+#db.fasta	db.fasta	db.fasta	${__HERE__}/test-data/db.fasta
+#db.fasta	db.fasta	db.fasta	/root/mydisk/FROGS-wrappers/test-data/db.fasta
+db.fasta	A sample databank	/root/mydisk/FROGS-wrappers/test-data/db.fasta
--- a/upload_tar.xml	Thu Apr 05 09:14:09 2018 -0400
+++ b/upload_tar.xml	Thu Apr 05 09:41:15 2018 -0400
@@ -18,7 +18,14 @@
 <tool id="FROGS_upload_tar" name="FROGS Upload archive" version="1.1.0" workflow_compatible="false">
 	<description>from your computer</description>
 	<action module="galaxy.tools.actions.upload" class="UploadToolAction"/>
-	<command interpreter="python">
+	<requirements>
+		<requirement type="package" version="2.0.1">frogs</requirement>
+	</requirements>
+	<stdio>
+		<exit_code range="1:" />
+		<exit_code range=":-1" />
+	</stdio>
+	<command>
 		upload_tar.py --param-file $paramfile
 	#set $outnum = 0
 	#while $varExists('output%i' % $outnum):
@@ -78,4 +85,7 @@
 
 Depending on the help provided you can cite us in acknowledgements, references or both.
 	</help>
+	<citations>
+		<citation type="doi">10.7287/peerj.preprints.386v1</citation>
+	</citations>
 </tool>