Mercurial > repos > cmonjeau > commet
changeset 4:29d66e64918f
fix R packages and remove prepare_commet files
| author | cmonjeau |
|---|---|
| date | Thu, 10 Sep 2015 14:02:02 +0000 |
| parents | d085f995d556 |
| children | 8b2edb8a315e |
| files | commet.xml commet_datatype.py datatypes_conf.xml prepare_commet.py prepare_commet.xml tool_dependencies.xml |
| diffstat | 6 files changed, 2 insertions(+), 143 deletions(-) [+] |
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--- 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
--- 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' -
--- 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>
--- 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__()
--- 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. <https://www.e-biogenouest.org/resources/128>`_ - - </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> -
--- 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>