commit/galaxy-central: dan: Remove unused parameters from TopHat and Cufflinks tool tests.
by Bitbucket
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/25a02a5c286f/
changeset: r5146:25a02a5c286f
user: dan
date: 2011-02-28 21:17:35
summary: Remove unused parameters from TopHat and Cufflinks tool tests.
affected #: 2 files (171 bytes)
--- a/tools/ngs_rna/cufflinks_wrapper.xml Mon Feb 28 15:03:45 2011 -0500
+++ b/tools/ngs_rna/cufflinks_wrapper.xml Mon Feb 28 15:17:35 2011 -0500
@@ -105,7 +105,6 @@
<test><param name="sPaired" value="No"/><param name="input" value="cufflinks_in.sam"/>
- <param name="mean_inner_distance" value="20"/><param name="max_intron_len" value="300000"/><param name="min_isoform_fraction" value="0.05"/><param name="pre_mrna_fraction" value="0.05"/>
--- a/tools/ngs_rna/tophat_wrapper.xml Mon Feb 28 15:03:45 2011 -0500
+++ b/tools/ngs_rna/tophat_wrapper.xml Mon Feb 28 15:17:35 2011 -0500
@@ -448,7 +448,6 @@
<param name="splice_mismatches" value="0"/><param name="min_intron_length" value="70"/><param name="max_intron_length" value="500000"/>
- <param name="quals_scale" value="default"/><param name="junction_filter" value="0.15"/><param name="max_multihits" value="40"/><param name="min_segment_intron" value="50" />
@@ -494,7 +493,6 @@
<param name="splice_mismatches" value="0"/><param name="min_intron_length" value="70"/><param name="max_intron_length" value="500000"/>
- <param name="quals_scale" value="default"/><param name="junction_filter" value="0.15"/><param name="max_multihits" value="40"/><param name="min_segment_intron" value="50" />
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: dannon: mosaik: Test case uses sim_size instead of diff now, to get around the changing RG tag.
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/05b089557d0d/
changeset: r5144:05b089557d0d
user: dannon
date: 2011-02-28 20:32:36
summary: mosaik: Test case uses sim_size instead of diff now, to get around the changing RG tag.
affected #: 1 file (18 bytes)
--- a/tools/sr_mapping/mosaik.xml Mon Feb 28 14:04:53 2011 -0500
+++ b/tools/sr_mapping/mosaik.xml Mon Feb 28 14:32:36 2011 -0500
@@ -13,8 +13,7 @@
#end if
MosaikBuild -fr
#if $genomeSource.refGenomeSource == 'indexed':
- ##$genomeSource.indexReference
- ${ filter( lambda x: str( x[0] ) == str( $genomeSource.indexReference ), $__app__.tool_data_tables[ 'mosaik_indexes' ].get_fields() )[0][-1] }
+ ${ filter( lambda x: str( x[0] ) == str( $genomeSource.indexReference ), $__app__.tool_data_tables[ 'mosaik_indexes' ].get_fields() )[0][-1] }
#else:
$genomeSource.historyReference
#end if
@@ -95,7 +94,7 @@
<param name="act" value="35"/><param name="bw" value="19"/><param name="mhp" value="100"/>
- <output name="output" ftype="sam" file="mosaik_test_out.sam" sort="True"/>
+ <output name="output" ftype="sam" file="mosaik_test_out.sam" compare="sim_size" delta="0"/></test></tests><help>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: guru: Fixed functional test for 'compute q values' tool - q-value is rounded to 6 significant digits, which shouldn't differ between different runs of the tool.
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/3dce98e473f1/
changeset: r5143:3dce98e473f1
user: guru
date: 2011-02-28 20:04:53
summary: Fixed functional test for 'compute q values' tool - q-value is rounded to 6 significant digits, which shouldn't differ between different runs of the tool.
Also, fixed a bug in microsatellite birth/death tool - cases where microsatellite boundaries aren't defined are skipped.
affected #: 4 files (317 bytes)
--- a/test-data/q_values.tabular Mon Feb 28 12:16:28 2011 -0500
+++ b/test-data/q_values.tabular Mon Feb 28 14:04:53 2011 -0500
@@ -1,4 +1,4 @@
-pi0: 0.243863648325601
+pi0: 0.243864
FDR level: 0.05
--- a/tools/regVariation/compute_q_values.pl Mon Feb 28 12:16:28 2011 -0500
+++ b/tools/regVariation/compute_q_values.pl Mon Feb 28 14:04:53 2011 -0500
@@ -11,6 +11,8 @@
use strict;
use warnings;
use IO::Handle;
+use File::Temp qw/ tempfile tempdir /;
+my $tdir = tempdir( CLEANUP => 0 );
# check to make sure having correct input and output files
my $usage = "usage: compute_q_values.pl [TABULAR.in] [lambda] [pi0_method] [fdr_level] [robust] [TABULAR.out] [PDF.out] \n";
@@ -44,7 +46,8 @@
my $r_script;
# R script to implement the calcualtion of q-values based on multiple simultaneous tests p-values
-# construct an R script file and save it in the same directory where the perl file is located
+# construct an R script file and save it in a temp directory
+chdir $tdir;
$r_script = "q_values_computation.r";
open(Rcmd,">", $r_script) or die "Cannot open $r_script \n\n";
@@ -76,6 +79,7 @@
dev.off();
#save the q-values in the output file $q_valuesOutputFile
+ qobj\$pi0 <- signif(qobj\$pi0,digits=6)
qwrite(qobj, filename=\"$q_valuesOutputFile\");
#options(show.error.messages = TRUE);
--- a/tools/regVariation/compute_q_values.xml Mon Feb 28 12:16:28 2011 -0500
+++ b/tools/regVariation/compute_q_values.xml Mon Feb 28 14:04:53 2011 -0500
@@ -1,4 +1,4 @@
-<tool id="compute_q_values" name="Compute q-values" version="1.0.0">
+<tool id="compute_q_values" name="Compute q-values" version="1.0.1"><description>based on multiple simultaneous tests p-values</description><command interpreter="perl">
--- a/tools/regVariation/microsatellite_birthdeath.pl Mon Feb 28 12:16:28 2011 -0500
+++ b/tools/regVariation/microsatellite_birthdeath.pl Mon Feb 28 14:04:53 2011 -0500
@@ -643,7 +643,11 @@
my %microsatstarts=(); #1 WITHIN EACH ALIGNMENT, IF THERE EXISTS A MICROSATELLITE
#2 THIS HASH CONTAINS THE START SITE OF THE MICROSATELLITE
#3 WIHIN THE ALIGNMENT
-
+ next if !defined $extreme_start;
+ next if !defined $extreme_end;
+ next if $extreme_start > length($sequences{$tags[0]});
+ next if $extreme_start < 0;
+ next if $extreme_end > length($sequences{$tags[0]});
for my $i (0 ... $#tags){ #1 NOW THAT WE HAVE GATHERED INFORMATION REGARDING
#2 SEQUENCE ALIGNMENT AND MICROSATELLITE COORDINATES
@@ -3977,3 +3981,4 @@
foreach my $line (@_) {print "$line\n";}
print "::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::<\n";
}
+
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: dan: Better determination in tests if a provided input is a DataToolParameter to better handle .gz and .zip uploads and allowing uploads from a sub-directory of test-data/.
by Bitbucket
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/4d2d7c952d87/
changeset: r5142:4d2d7c952d87
user: dan
date: 2011-02-28 18:16:28
summary: Better determination in tests if a provided input is a DataToolParameter to better handle .gz and .zip uploads and allowing uploads from a sub-directory of test-data/.
affected #: 16 files (2.5 KB)
--- a/lib/galaxy/tools/test.py Mon Feb 28 09:59:30 2011 -0500
+++ b/lib/galaxy/tools/test.py Mon Feb 28 12:16:28 2011 -0500
@@ -1,4 +1,5 @@
import new, sys
+import os.path
import galaxy.util
import parameters
from parameters import basic
@@ -12,7 +13,7 @@
"""
Encapsulates information about a tool test, and allows creation of a
dynamic TestCase class (the unittest framework is very class oriented,
- doing dynamic tests in this was allows better integration)
+ doing dynamic tests in this way allows better integration)
"""
def __init__( self, tool, name, maxseconds ):
self.tool = tool
@@ -26,19 +27,17 @@
def add_param( self, name, value, extra ):
try:
if name not in self.tool.inputs:
+ found_parameter = False
for input_name, input_value in self.tool.inputs.items():
- if isinstance( input_value, grouping.Conditional ) or isinstance( input_value, grouping.Repeat ):
- self.__expand_grouping_for_data_input(name, value, extra, input_name, input_value)
- elif isinstance( self.tool.inputs[name], parameters.DataToolParameter ) and ( value, extra ) not in self.required_files:
- name_change = [ att for att in extra.get( 'edit_attributes', [] ) if att.get( 'type' ) == 'name' ]
- if name_change:
- name_change = name_change[-1].get( 'value' ) #only the last name change really matters
- if value is None and not name_change:
- assert self.tool.inputs[name].optional, '%s is not optional. You must provide a valid filename.' % name
- else:
- self.required_files.append( ( value, extra ) ) #these files will be uploaded
- if name_change:
- value = name_change #change value for select to renamed uploaded file for e.g. composite dataset
+ if isinstance( input_value, grouping.Group ):
+ found_parameter, new_value = self.__expand_grouping_for_data_input(name, value, extra, input_name, input_value)
+ if found_parameter:
+ value = new_value
+ break
+ if not found_parameter:
+ raise ValueError( "Unable to determine parameter type of test input '%s'. Ensure that the parameter exists and that any container groups are defined first." % name )
+ elif isinstance( self.tool.inputs[name], basic.DataToolParameter ):
+ value = self.__add_uploaded_dataset( name, value, extra, self.tool.inputs[name] )
except Exception, e:
log.debug( "Error in add_param for %s: %s" % ( name, e ) )
self.inputs.append( ( name, value, extra ) )
@@ -47,27 +46,65 @@
def __expand_grouping_for_data_input( self, name, value, extra, grouping_name, grouping_value ):
# Currently handles grouping.Conditional and grouping.Repeat
if isinstance( grouping_value, grouping.Conditional ):
- if name != grouping_value.test_param.name:
- for case in grouping_value.cases:
- for case_input_name, case_input_value in case.inputs.items():
- if case_input_name == name and isinstance( case_input_value, basic.DataToolParameter ) and ( value, extra ) not in self.required_files:
- if value is None:
- assert case_input_value.optional, '%s is not optional. You must provide a valid filename.' % name
- else:
- self.required_files.append( ( value, extra ) )
- return True
- elif isinstance( case_input_value, grouping.Conditional ):
- self.__expand_grouping_for_data_input(name, value, extra, case_input_name, case_input_value)
+ if name == grouping_value.test_param.name:
+ return True, value
+ case_test_param_value = None
+ for input in self.inputs:
+ if input[0] == grouping_value.test_param.name:
+ case_test_param_value = input[1]
+ break
+ if case_test_param_value is None:
+ #case for this group has not been set yet
+ return False, value
+ for case in grouping_value.cases:
+ if case.value == case_test_param_value:
+ break
+ if case.value != case_test_param_value:
+ return False, value
+ #assert case.value == case_test_param_value, "Current case could not be determined for parameter '%s'. Provided value '%s' could not be found in '%s'." % ( grouping_value.name, value, grouping_value.test_param.name )
+ if name in case.inputs:
+ if isinstance( case.inputs[name], basic.DataToolParameter ):
+ return True, self.__add_uploaded_dataset( name, value, extra, case.inputs[name] )
+ else:
+ return True, value
+ else:
+ for input_name, input_parameter in case.inputs.iteritems():
+ if isinstance( input_parameter, grouping.Group ):
+ found_parameter, new_value = self.__expand_grouping_for_data_input( name, value, extra, input_name, input_parameter )
+ if found_parameter:
+ return True, new_value
elif isinstance( grouping_value, grouping.Repeat ):
# FIXME: grouping.Repeat can only handle 1 repeat param element since the param name
# is something like "input2" and the expanded page display is something like "queries_0|input2".
# The problem is that the only param name on the page is "input2", and adding more test input params
- # with the same name ( "input2" ) is not yet supported in our test code ( the lat one added is the only
- # one used ).
- for input_name, input_value in grouping_value.inputs.items():
- if input_name == name and isinstance( input_value, basic.DataToolParameter ) and ( value, extra ) not in self.required_files:
- if value is None:
- assert input_value.optional, '%s is not optional. You must provide a valid filename.' % name
- else:
- self.required_files.append( ( value, extra ) )
- return True
+ # with the same name ( "input2" ) is not yet supported in our test code ( the last one added is the only
+ # one used ).
+ if name in grouping_value.inputs:
+ if isinstance( grouping_value.inputs[name], basic.DataToolParameter ):
+ return True, self.__add_uploaded_dataset( name, value, extra, grouping_value.inputs[name] )
+ else:
+ return True, value
+ else:
+ for input_name, input_parameter in grouping_value.inputs.iteritems():
+ if isinstance( input_parameter, grouping.Group ):
+ found_parameter, new_value = self.__expand_grouping_for_data_input( name, value, extra, input_name, input_parameter )
+ if found_parameter:
+ return True, new_value
+ return False, value
+ def __add_uploaded_dataset( self, name, value, extra, input_parameter ):
+ if value is None:
+ assert input_parameter.optional, '%s is not optional. You must provide a valid filename.' % name
+ return value
+ if ( value, extra ) not in self.required_files:
+ self.required_files.append( ( value, extra ) ) #these files will be uploaded
+ name_change = [ att for att in extra.get( 'edit_attributes', [] ) if att.get( 'type' ) == 'name' ]
+ if name_change:
+ name_change = name_change[-1].get( 'value' ) #only the last name change really matters
+ value = name_change #change value for select to renamed uploaded file for e.g. composite dataset
+ else:
+ for end in [ '.zip', '.gz' ]:
+ if value.endswith( end ):
+ value = value[ :-len( end ) ]
+ break
+ value = os.path.basename( value ) #if uploading a file in a path other than root of test-data
+ return value
--- a/test/functional/test_toolbox.py Mon Feb 28 09:59:30 2011 -0500
+++ b/test/functional/test_toolbox.py Mon Feb 28 12:16:28 2011 -0500
@@ -1,5 +1,4 @@
import sys, new
-import os.path
from galaxy.tools.parameters import grouping
from galaxy.tools.parameters import basic
from base.twilltestcase import TwillTestCase
@@ -56,12 +55,6 @@
# tool will have uncompressed it on the fly.
all_inputs = {}
for name, value, _ in testdef.inputs:
- if value:
- for end in [ '.zip', '.gz' ]:
- if value.endswith( end ):
- value = value[ :-len( end ) ]
- break
- value = os.path.basename( value ) #if uploading a file in a path other than root of test-data
all_inputs[ name ] = value
# See if we have a grouping.Repeat element
repeat_name = None
--- a/tools/human_genome_variation/ldtools.xml Mon Feb 28 09:59:30 2011 -0500
+++ b/tools/human_genome_variation/ldtools.xml Mon Feb 28 12:16:28 2011 -0500
@@ -24,7 +24,7 @@
<param name="input" value="ldInput1.txt" /><param name="rsquare" value="0.64" /><param name="freq" value="0.00" />
- <param name="output" file="ldOutput1.txt" />
+ <output name="output" file="ldOutput1.txt" /></test></tests>
--- a/tools/maf/maf_to_fasta.xml Mon Feb 28 09:59:30 2011 -0500
+++ b/tools/maf/maf_to_fasta.xml Mon Feb 28 12:16:28 2011 -0500
@@ -38,15 +38,15 @@
<tests><test><param name="input1" value="3.maf" ftype="maf"/>
+ <param name="fasta_type" value="concatenated"/><param name="species" value="canFam1"/>
- <param name="fasta_type" value="concatenated"/><output name="out_file1" file="cf_maf2fasta_concat.dat" ftype="fasta"/></test><test><param name="input1" value="4.maf" ftype="maf"/>
+ <param name="fasta_type" value="multiple"/><param name="species" value="hg17,panTro1,rheMac2,rn3,mm7,canFam2,bosTau2,dasNov1"/><param name="complete_blocks" value="partial_allowed"/>
- <param name="fasta_type" value="multiple"/><output name="out_file1" file="cf_maf2fasta_new.dat" ftype="fasta"/></test></tests>
--- a/tools/new_operations/intersect.xml Mon Feb 28 09:59:30 2011 -0500
+++ b/tools/new_operations/intersect.xml Mon Feb 28 12:16:28 2011 -0500
@@ -38,7 +38,6 @@
<code file="operation_filter.py"/><tests><test>
- <param name="type" value="Interval"/><param name="input1" value="1.bed" /><param name="input2" value="2.bed" /><param name="min" value="1" />
@@ -46,7 +45,6 @@
<output name="output" file="gops_intersect_out.bed" /></test><test>
- <param name="type" value="Interval"/><param name="input1" value="1.bed" /><param name="input2" value="2_mod.bed" ftype="interval"/><param name="min" value="1" />
--- a/tools/next_gen_conversion/solid2fastq.xml Mon Feb 28 09:59:30 2011 -0500
+++ b/tools/next_gen_conversion/solid2fastq.xml Mon Feb 28 12:16:28 2011 -0500
@@ -54,9 +54,9 @@
<test><param name="input1" value="fr.csfasta" ftype="csfasta"/><param name="input2" value="fr.qualsolid" ftype="qualsolid" />
+ <param name="paired" value="yes"/><param name="input3" value="rr.csfasta" ftype="csfasta"/><param name="input4" value="rr.qualsolid" ftype="qualsolid" />
- <param name="paired" value="yes"/><param name="qual" value="0" /><param name="trim_first_base" value="No" /><param name="trim_name" value="Yes" />
--- a/tools/peak_calling/macs_wrapper.xml Mon Feb 28 09:59:30 2011 -0500
+++ b/tools/peak_calling/macs_wrapper.xml Mon Feb 28 12:16:28 2011 -0500
@@ -140,10 +140,10 @@
</configfiles><tests><test>
+ <param name="input_type_selector" value="single_end" /><param name="input_chipseq_file1" value="chipseq_enriched.bed.gz" ftype="bed" /><param name="input_control_file1" value="chipseq_input.bed.gz" ftype="bed" /><param name="experiment_name" value="Galaxy Test Run" />
- <param name="input_type_selector" value="single_end" /><param name="tsize" value="36" /><param name="mfold" value="13" /><param name="gsize" value="2.7e+9" />
@@ -166,10 +166,10 @@
</output></test><test>
+ <param name="input_type_selector" value="single_end" /><param name="input_chipseq_file1" value="chipseq_enriched.bed.gz" ftype="bed" /><param name="input_control_file1" value="chipseq_input.bed.gz" ftype="bed" /><param name="experiment_name" value="Galaxy Test Run" />
- <param name="input_type_selector" value="single_end" /><param name="tsize" value="36" /><param name="mfold" value="13" /><param name="gsize" value="2.7e+9" />
@@ -190,10 +190,10 @@
</output></test><!-- <test>
+ <param name="input_type_selector" value="single_end" /><param name="input_chipseq_file1" value="chipseq_enriched.bed.gz" ftype="bed" /><param name="input_control_file1" value="chipseq_input.bed.gz" ftype="bed" /><param name="experiment_name" value="Galaxy Test Run" />
- <param name="input_type_selector" value="single_end" /><param name="tsize" value="36" /><param name="mfold" value="13" /><param name="gsize" value="2.7e+9" />
--- a/tools/regVariation/maf_cpg_filter.xml Mon Feb 28 09:59:30 2011 -0500
+++ b/tools/regVariation/maf_cpg_filter.xml Mon Feb 28 12:16:28 2011 -0500
@@ -56,7 +56,6 @@
<param name="input" value="6.maf"/><param name="mask_char" value="0"/><param name="type" value="nonCpG" />
- <param name="definition" value="NA" /><output name="out_file1" file="6_mask_noncpg.maf"/></test></tests>
--- a/tools/regVariation/microsatellite_birthdeath.xml Mon Feb 28 09:59:30 2011 -0500
+++ b/tools/regVariation/microsatellite_birthdeath.xml Mon Feb 28 12:16:28 2011 -0500
@@ -41,7 +41,6 @@
<param name="alignment" value="chr22_5sp.maf"/><param name="orthfile" value="chr22_5sp.microraw.tabular"/><param name="thresholds" value="9,10,12,12"/>
- <param name="species" value="hg18,panTro2,ponAbe2,rheMac2,calJac1"/><param name="tree_definition" value="((((hg18, panTro2), ponAbe2), rheMac2), calJac1)"/><param name="separation" value="40"/><param name="simthresh" value="80"/>
--- a/tools/regVariation/quality_filter.xml Mon Feb 28 09:59:30 2011 -0500
+++ b/tools/regVariation/quality_filter.xml Mon Feb 28 12:16:28 2011 -0500
@@ -74,7 +74,6 @@
<param name="score" value="50"/><param name="mask_char" value="0"/><param name="region" value="0" />
- <param name="length" value="1" /><output name="out_file1" file="6_quality_filter.maf"/></test></tests>
--- a/tools/rgenetics/rgPedSub.xml Mon Feb 28 09:59:30 2011 -0500
+++ b/tools/rgenetics/rgPedSub.xml Mon Feb 28 12:16:28 2011 -0500
@@ -76,10 +76,10 @@
<edit_attributes type='name' value='tinywga' /></param><param name='title' value='rgPedSubtest1' />
+ <param name="mtype" value="grslist" /><param name="region" value="" /><param name="rslist" value="rs2283802Xrs2267000Xrs16997606Xrs4820537Xrs3788347Xrs756632Xrs4820539Xrs2283804Xrs2267006Xrs4822363X" /><param name="relfilter" value="all" />
- <param name="mtype" value="grslist" /><output name='output1' file='rgtestouts/rgPedSub/rgPedSubtest1.lped' ftype='lped' linesDiff='7'/></test></tests>
--- a/tools/samtools/bam_to_sam.xml Mon Feb 28 09:59:30 2011 -0500
+++ b/tools/samtools/bam_to_sam.xml Mon Feb 28 12:16:28 2011 -0500
@@ -29,7 +29,7 @@
samtools view -o bam_to_sam_out2.sam test-data/1.bam
--><param name="input1" value="3.bam" ftype="bam" />
- <param name="output1" file="bam_to_sam_out2.sam" sorted="True" />
+ <output name="output1" file="bam_to_sam_out2.sam" sorted="True" /></test></tests><help>
--- a/tools/samtools/sam2interval.xml Mon Feb 28 09:59:30 2011 -0500
+++ b/tools/samtools/sam2interval.xml Mon Feb 28 12:16:28 2011 -0500
@@ -15,13 +15,11 @@
<tests><test><param name="input1" value="sam_bioinf_example.sam" ftype="sam"/>
- <param name="flags" value="Read is mapped in a proper pair"/><param name="print_all" value="Yes"/><output name="out_file1" file="sam2interval_printAll.dat" ftype="interval"/></test><test><param name="input1" value="sam_bioinf_example.sam" ftype="sam"/>
- <param name="flags" value="Read is mapped in a proper pair"/><param name="print_all" value="No"/><output name="out_file1" file="sam2interval_noprintAll.dat" ftype="interval"/></test>
--- a/tools/samtools/sam_to_bam.xml Mon Feb 28 09:59:30 2011 -0500
+++ b/tools/samtools/sam_to_bam.xml Mon Feb 28 12:16:28 2011 -0500
@@ -60,7 +60,7 @@
--><param name="index_source" value="cached" /><param name="input1" value="3.sam" ftype="sam" dbkey="equCab2" />
- <param name="output1" file="sam_to_bam_out2.bam" />
+ <output name="output1" file="sam_to_bam_out2.bam" /></test></tests><help>
--- a/tools/samtools/samtools_flagstat.xml Mon Feb 28 09:59:30 2011 -0500
+++ b/tools/samtools/samtools_flagstat.xml Mon Feb 28 12:16:28 2011 -0500
@@ -14,7 +14,7 @@
<tests><test><param name="input1" value="3.bam" ftype="bam" />
- <param name="output1" file="samtools_flagstat_out1.txt" />
+ <output name="output1" file="samtools_flagstat_out1.txt" /></test></tests><help>
--- a/tools/sr_mapping/bfast_wrapper.xml Mon Feb 28 09:59:30 2011 -0500
+++ b/tools/sr_mapping/bfast_wrapper.xml Mon Feb 28 12:16:28 2011 -0500
@@ -368,8 +368,6 @@
<param name="indices" value="phiX_nt_50" /><param name="source_select" value="pre_set" /><param name="suppressHeader" value="False" />
- <param name="indexing_repeatmasker" value="" />
- <param name="indexing_option_selector" value="default" /><output name="output" ftype="sam" file="bfast_out3.sam" lines_diff="2" /><!-- MD:Z:11T38 instead of MD:Z:50 on one line--></test></tests>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: jgoecks: Fix bad value in cufflinks functional test.
by Bitbucket
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/4146f64da13d/
changeset: r5141:4146f64da13d
user: jgoecks
date: 2011-02-28 15:59:30
summary: Fix bad value in cufflinks functional test.
affected #: 1 file (4 bytes)
--- a/tools/ngs_rna/cufflinks_wrapper.xml Mon Feb 28 09:52:17 2011 -0500
+++ b/tools/ngs_rna/cufflinks_wrapper.xml Mon Feb 28 09:59:30 2011 -0500
@@ -103,7 +103,7 @@
Simple test that uses test data included with cufflinks.
--><test>
- <param name="sPaired" value="single"/>
+ <param name="sPaired" value="No"/><param name="input" value="cufflinks_in.sam"/><param name="mean_inner_distance" value="20"/><param name="max_intron_len" value="300000"/>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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11 years, 11 months
commit/galaxy-central: natefoo: Bugfix for the last commit when running functional tests with sqlite.
by Bitbucket
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/2e88578ef7e1/
changeset: r5140:2e88578ef7e1
user: natefoo
date: 2011-02-28 15:52:17
summary: Bugfix for the last commit when running functional tests with sqlite.
affected #: 1 file (49 bytes)
--- a/scripts/functional_tests.py Mon Feb 28 09:35:36 2011 -0500
+++ b/scripts/functional_tests.py Mon Feb 28 09:52:17 2011 -0500
@@ -139,13 +139,15 @@
if psu_production:
global_conf = None
+ if not database_connection.startswith( 'sqlite://' ):
+ kwargs['database_engine_option_max_overflow'] = '20'
+
# Build the Universe Application
app = UniverseApplication( job_queue_workers = 5,
id_secret = 'changethisinproductiontoo',
template_path = "templates",
database_connection = database_connection,
database_engine_option_pool_size = '10',
- database_engine_option_max_overflow = '20',
file_path = file_path,
new_file_path = new_file_path,
tool_path = tool_path,
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: natefoo: Require ctypes egg before pysam on Python 2.4
by Bitbucket
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/b9b772f2e4eb/
changeset: r5139:b9b772f2e4eb
user: natefoo
date: 2011-02-28 15:35:36
summary: Require ctypes egg before pysam on Python 2.4
affected #: 2 files (157 bytes)
--- a/lib/galaxy/datatypes/converters/bam_to_summary_tree_converter.py Mon Feb 28 08:33:48 2011 -0500
+++ b/lib/galaxy/datatypes/converters/bam_to_summary_tree_converter.py Mon Feb 28 09:35:36 2011 -0500
@@ -4,7 +4,11 @@
import sys
from galaxy import eggs
-import pkg_resources; pkg_resources.require( "pysam" )
+import pkg_resources
+
+if sys.version_info[:2] == (2, 4):
+ pkg_resources.require( "ctypes" )
+pkg_resources.require( "pysam" )
from pysam import csamtools
from galaxy.visualization.tracks.summary import *
@@ -24,4 +28,4 @@
st.write(out_fname)
if __name__ == "__main__":
- main()
\ No newline at end of file
+ main()
--- a/lib/galaxy/visualization/tracks/data_providers.py Mon Feb 28 08:33:48 2011 -0500
+++ b/lib/galaxy/visualization/tracks/data_providers.py Mon Feb 28 09:35:36 2011 -0500
@@ -2,9 +2,14 @@
Data providers for tracks visualizations.
"""
+import sys
from math import floor, ceil, log, pow
import pkg_resources
-pkg_resources.require( "bx-python" ); pkg_resources.require( "pysam" ); pkg_resources.require( "numpy" )
+pkg_resources.require( "bx-python" )
+if sys.version_info[:2] == (2, 4):
+ pkg_resources.require( "ctypes" )
+pkg_resources.require( "pysam" )
+pkg_resources.require( "numpy" )
from galaxy.datatypes.util.gff_util import *
from bx.interval_index_file import Indexes
from bx.arrays.array_tree import FileArrayTreeDict
@@ -671,4 +676,4 @@
blocks = zip( block_sizes, block_starts )
payload.append( [ ( feature.start + block[1], feature.start + block[1] + block[0] ) for block in blocks ] )
- return payload
\ No newline at end of file
+ return payload
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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11 years, 11 months
commit/galaxy-central: natefoo: Increase the SQLAlchemy SuquePool limits for functional tests.
by Bitbucket
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/5bced201f40a/
changeset: r5137:5bced201f40a
user: natefoo
date: 2011-02-28 13:58:52
summary: Increase the SQLAlchemy SuquePool limits for functional tests.
affected #: 1 file (155 bytes)
--- a/scripts/functional_tests.py Sun Feb 27 14:48:23 2011 -0500
+++ b/scripts/functional_tests.py Mon Feb 28 07:58:52 2011 -0500
@@ -144,6 +144,8 @@
id_secret = 'changethisinproductiontoo',
template_path = "templates",
database_connection = database_connection,
+ database_engine_option_pool_size = '10',
+ database_engine_option_max_overflow = '20',
file_path = file_path,
new_file_path = new_file_path,
tool_path = tool_path,
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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