diff --git a/lib/galaxy/schema/terms.yml b/lib/galaxy/schema/terms.yml index 5662116813f..f284e73b5b9 100644 --- a/lib/galaxy/schema/terms.yml +++ b/lib/galaxy/schema/terms.yml @@ -163,7 +163,7 @@ galaxy: whyHomogenousCollections: | Dataset collections are designed to streamline the analysis of large numbers of datasets by grouping them together into a single, manageable entity. Unlike generic folders on your computer, which can hold - any mix of file types, dataset collections are specifically intended to be homogenous. This homogeneity + any mix of file types, dataset collections are specifically intended to be homogeneous. This homogeneity is crucial for consistency in processing. Homogeneous datasets ensure that each dataset in the collection can be processed uniformly with the same tools and workflows. This eliminates the need for individual adjustments, which can be time-consuming and prone to error. Most tools and workflows in Galaxy are designed diff --git a/run_tests.sh b/run_tests.sh index cca4a79e946..257c9331890 100755 --- a/run_tests.sh +++ b/run_tests.sh @@ -154,7 +154,7 @@ Selenium can also be setup a remote service - to target a service set GALAXY_TEST_SELENIUM_REMOTE to 1. The target service may be configured with GALAXY_TEST_SELENIUM_REMOTE_PORT and GALAXY_TEST_SELENIUM_REMOTE_HOST. By default Galaxy will assume the -remote service being targetted is CHROME - but this can be overridden +remote service being targeted is CHROME - but this can be overridden with GALAXY_TEST_SELENIUM_BROWSER. In this remote mode, please ensure that GALAXY_TEST_HOST is set to a @@ -251,7 +251,7 @@ GALAXY_TEST_VERBOSE_ERRORS Enable more verbose errors during API tests. GALAXY_TEST_UPLOAD_ASYNC Upload tool test inputs asynchronously (may overwhelm sqlite database). GALAXY_TEST_RAW_DIFF Don't slice up tool test diffs to keep output - managable - print all output. (default off) + manageable - print all output. (default off) GALAXY_TEST_DEFAULT_WAIT Max time allowed for a tool test before Galaxy gives up (default 86400) - tools may define a maxseconds attribute to extend this. @@ -297,10 +297,10 @@ GALAXY_TEST_DISABLE_ACCESS_LOG Do not log access messages. GALAXY_TEST_LOG_LEVEL Set Galaxy server log level for tests (default: DEBUG). E.g. WARNING to reduce output. GALAXY_TEST_AXE_SCRIPT_URL URL of aXe script to use for accessibility testing. -GALAXY_TEST_SKIP_AXE Set this to '1' to skip aXe accessibilty testing when +GALAXY_TEST_SKIP_AXE Set this to '1' to skip aXe accessibility testing when running selenium tests. -We're tyring annotate API and Selenium tests with the resources they require +We're trying annotate API and Selenium tests with the resources they require and create to make them more appropriate to run on established Galaxy instances. The following variables can be used to disable certain classes of properly tests. diff --git a/tools/filters/changeCase.pl b/tools/filters/changeCase.pl old mode 100644 new mode 100755 index f3aa1aeb1c1..070628ee6d1 --- a/tools/filters/changeCase.pl +++ b/tools/filters/changeCase.pl @@ -24,7 +24,7 @@ foreach ( split /,/, $ARGV[1] ) { } } -die "No columns specified, columns are not preceeded with 'c', or commas are not used to separate column numbers: $ARGV[1]\n" if keys %$columns == 0; +die "No columns specified, columns are not preceded with 'c', or commas are not used to separate column numbers: $ARGV[1]\n" if keys %$columns == 0; my $column_delimiters_href = { 'TAB' => q{\t}, @@ -35,14 +35,14 @@ my $column_delimiters_href = { 'DOT' => q{\.}, 'SPACE' => q{\s+} }; - + $del = $column_delimiters_href->{$ARGV[2]}; open (OUT, ">$ARGV[4]") or die "Cannot create $ARGV[4]:$!\n"; open (IN, "<$ARGV[0]") or die "Cannot open $ARGV[0]:$!\n"; while () { chop; - @in = split /$del/; + @in = split /$del/; for ( my $i = 0; $i <= $#in; ++$i) { if (exists $columns->{$i}) { push(@out, $ARGV[3] eq 'up' ? uc($in[$i]) : lc($in[$i])); diff --git a/tools/filters/gtf2bedgraph.xml b/tools/filters/gtf2bedgraph.xml index f1123afd58c..18946970a21 100644 --- a/tools/filters/gtf2bedgraph.xml +++ b/tools/filters/gtf2bedgraph.xml @@ -7,7 +7,7 @@ - + @@ -39,7 +39,7 @@ using the attribute name 'FPKM' will be converted to BEDGraph (**note** that 1 i chr22 9999999 10001000 2.75 - chr22 10009999 10010100 2.25 + chr22 10009999 10010100 2.25 ------ @@ -58,10 +58,10 @@ using the attribute name 'FPKM' will be converted to BEDGraph (**note** that 1 i 7. strand - Valid entries include '+', '-', or '.' (for don't know/care). 8. frame - If the feature is a coding exon, frame should be a number between 0-2 that represents the reading frame of the first base. If the feature is not a coding exon, the value should be '.'. 9. group - The group field is a list of attributes. Each attribute consists of a type/value pair. Attributes must end in a semi-colon, and be separated from any following attribute by exactly one space. The attribute list must begin with the two mandatory attributes: (i) gene_id value - A globally unique identifier for the genomic source of the sequence and (ii) transcript_id value - A globally unique identifier for the predicted transcript. - + **BEDGraph format** -The bedGraph format is line-oriented. Bedgraph data are preceeded by a track definition line, which adds a number of options for controlling the default display of this track. +The bedGraph format is line-oriented. Bedgraph data are preceded by a track definition line, which adds a number of options for controlling the default display of this track. For the track definition line, all options are placed in a single line separated by spaces: track type=bedGraph name=track_label description=center_label diff --git a/tools/filters/sff_extract.py b/tools/filters/sff_extract.py old mode 100644 new mode 100755 index 41bf7ef08f2..c9fbe10b5ba --- a/tools/filters/sff_extract.py +++ b/tools/filters/sff_extract.py @@ -1170,7 +1170,7 @@ def read_ssaha_data(ssahadata_fh): if len(ml) != 12: print("\n", line, end=" ") raise RuntimeError( - "Expected 12 elements in the SSAHA2 line with ALIGMENT keyword, but found " + str(len(ml)) + "Expected 12 elements in the SSAHA2 line with ALIGNMENT keyword, but found " + str(len(ml)) ) if ml[2] not in ssahapematches: ssahapematches[ml[2]] = [] diff --git a/tools/filters/trimmer.py b/tools/filters/trimmer.py old mode 100644 new mode 100755 index 9374c0561f0..908bad50cc7 --- a/tools/filters/trimmer.py +++ b/tools/filters/trimmer.py @@ -40,7 +40,7 @@ options (listed below) default to 'None' if omitted parser.add_option("-s", "--start", type="int", default=0, help="Trim from beginning to here (1-based)") - parser.add_option("-e", "--end", type="int", default="0", help="Trim from here to the ned (1-based)") + parser.add_option("-e", "--end", type="int", default="0", help="Trim from here to the end (1-based)") parser.add_option( "-f", "--file", dest="input_txt", default=False, help="Name of file to be chopped. STDIN is default"