# HG changeset patch
# User cmonjeau
# Date 1441893722 0
# Node ID 29d66e64918f0572e0b20e07ac79140ed806f267
# Parent  d085f995d556999b9fead81196cd2bf7b1c42e21
fix R packages and remove prepare_commet files

diff -r d085f995d556 -r 29d66e64918f commet.xml
--- a/commet.xml	Thu Sep 10 13:38:21 2015 +0000
+++ b/commet.xml	Thu Sep 10 14:02:02 2015 +0000
@@ -2,7 +2,7 @@
   <description>COmpare Multiple METagenomes</description>
   <requirements>
     <requirement type="package" version="24.7.14">commet</requirement>
-    <requirement type="package" version="3.0.1">R</requirement>
+    <requirement type="package" version="3.0.1">R_3_0_1</requirement>
   </requirements>
 <command interpreter="python">
 commet.py
diff -r d085f995d556 -r 29d66e64918f commet_datatype.py
--- a/commet_datatype.py	Thu Sep 10 13:38:21 2015 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,42 +0,0 @@
-
-"""
-Commet input file datatype
-"""
-
-
-import logging, os, os.path, sys, time, tempfile, shutil, string, glob, re
-
-from galaxy.datatypes.sniff import *
-from galaxy.datatypes import data
-from galaxy.datatypes.metadata import MetadataElement
-from galaxy.datatypes.xml import GenericXml
-
-log = logging.getLogger(__name__)
-
-
-class Commet( data.Text ):
-    """
-    Resource Description Framework format (http://www.w3.org/RDF/).
-    """
-    file_ext = "commet"
-
-    def sniff( self, filename ):
-        """
-	Returns false and the user must manually set.
-        """
-	with open( filename ) as handle:
-	    first_line = handle.readline()
-	    if first_line.startswith('//commet input file//'):
-		return True
-
-        return False
-
-    def set_peek( self, dataset, is_multi_byte=False ):
-        """Set the peek and blurb text"""
-        if not dataset.dataset.purged:
-            dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
-            dataset.blurb = 'Commet input data'
-        else:
-            dataset.peek = 'file does not exist'
-            dataset.blurb = 'file purged from disk'
-
diff -r d085f995d556 -r 29d66e64918f datatypes_conf.xml
--- a/datatypes_conf.xml	Thu Sep 10 13:38:21 2015 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
-<?xml version="1.0"?>
-<datatypes>
-    <datatype_files>
-        <datatype_file name="commet_datatype.py"/>
-    </datatype_files>
-    <registration>
-    <datatype extension="commet" type="galaxy.datatypes.commet_datatype:Commet" display_in_upload="true"/>
-    </registration>
-  <sniffers>
-    <sniffer type="galaxy.datatypes.commet_datatype:Commet"/>
-  </sniffers>
-</datatypes>
diff -r d085f995d556 -r 29d66e64918f prepare_commet.py
--- a/prepare_commet.py	Thu Sep 10 13:38:21 2015 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,26 +0,0 @@
-import sys, os, re
-
-"""
-
-Created by Cyril Monjeaud
-Cyril.Monjeaud@irisa.fr
-
-"""
-
-def __main__():
-
-	# open the outpt file
-	read_set=open(sys.argv[1], 'w')
-        read_set.write("//commet input file//\n")
-
-	# write the files path
-	i = 2
-	while i < len(sys.argv):
-		read_set.write(sys.argv[i+1]+":")
-                read_set.write(sys.argv[i].replace(",", ";")+"\n") 
-		i = i+2 	
-
-	# close output file
-	read_set.close()
-
-if __name__ == "__main__": __main__()
diff -r d085f995d556 -r 29d66e64918f prepare_commet.xml
--- a/prepare_commet.xml	Thu Sep 10 13:38:21 2015 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,61 +0,0 @@
-<tool id="preparecommet" name="Prepare commet" version="1.0">
-  <description>input sets file</description>
-<command interpreter="python">
-prepare_commet.py
-${read_sets}
-#for $set in $sets
-    ${set.reads}
-    "${set.setname}"
-#end for
-
-</command>
-
-  <inputs>
-	<!-- Input data files -->
-	<repeat name="sets" title="Read sets" min="1">
-	    <param name="reads" type="data" multiple="true" format="fasta, fasta.gz, fastq, fastq.gz" label="Dataset"/>
-	    <param name="setname" type="text" label="Set name" value="set_name"/>
-	</repeat>
-  </inputs>
-
-  <outputs>
-      <data format="commet" name="read_sets" label="read_sets : ${tool.name} on ${on_string}" />
-  </outputs>
-  <help>
-
-**Description**
-
-Prepare a configuration file with sets for commet tool 
-
--------
-
-**Created and integrated by**
-
-Yvan Le Bras and Cyril Monjeaud 
-
-GenOuest Bio-informatics Core Facility
-
-UMR 6074 IRISA INRIA-CNRS-UR1 Rennes (France)
-
-support@genouest.org
-
-If you use this tool in Galaxy, please cite :
-
-`Y. Le Bras, A. Roult, C. Monjeaud, M. Bahin, O. Quenez, C. Heriveau, A. Bretaudeau, O. Sallou, O. Collin, Towards a Life Sciences Virtual Research Environment : an e-Science initiative in Western France. JOBIM 2013. &lt;https://www.e-biogenouest.org/resources/128&gt;`_
-
-  </help>
-
-<citations>
-<citation type="bibtex">@INPROCEEDINGS{JOBIM2013,
-    author = {Le Bras, Y. and ROULT, A. and Monjeaud, C. and Bahin, M. and Quenez, O. and Heriveau, C. and Bretaudeau, A. and Sallou, O. and Collin, O.},
-    title = {Towards a Life Sciences Virtual Research Environment: An e-Science initiative in Western France},
-    booktitle = {JOBIM 2013 Proceedings},
-    year = {2013},
-    url = {https://www.e-biogenouest.org/resources/128},
-    pages = {97-106}
-    }
-</citation>
-</citations>
-
-</tool>
-
diff -r d085f995d556 -r 29d66e64918f tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Sep 10 13:38:21 2015 +0000
+++ b/tool_dependencies.xml	Thu Sep 10 14:02:02 2015 +0000
@@ -3,7 +3,7 @@
   <package name="commet" version="24.7.14">
       <repository changeset_revision="741836b9e2c5" name="package_commet_24_07_14" owner="cmonjeau" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
-  <package name="R" version="3.0.1">
+  <package name="R_3_0_1" version="3.0.1">
       <repository changeset_revision="59b82e6e0801" name="package_r_3_0_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
 </tool_dependency>