From 3531212ff6dd2606d8a9830cebc5dd0693b7ad13 Mon Sep 17 00:00:00 2001 From: Kanwei Li Date: Sun, 27 Sep 2009 23:11:43 -0400 Subject: [PATCH] typo fixes for tools in folders A-M --- templates/base_panels.mako | 2 +- tools/annotation_profiler/annotation_profiler.xml | 12 ++++++------ .../encode_import_all_latest_datasets.xml | 4 ++-- tools/data_source/upload.xml | 4 ++-- tools/extract/extract_genomic_dna.xml | 2 +- tools/fastx_toolkit/fasta_formatter.xml | 2 +- tools/fastx_toolkit/fastq_quality_converter.xml | 2 +- tools/fastx_toolkit/fastx_barcode_splitter.xml | 2 +- tools/fastx_toolkit/fastx_clipper.xml | 4 ++-- tools/fastx_toolkit/fastx_collapser.xml | 2 +- tools/fastx_toolkit/fastx_quality_statistics.xml | 2 +- tools/fastx_toolkit/fastx_renamer.xml | 2 +- tools/filters/axt_to_concat_fasta.xml | 4 ++-- tools/filters/axt_to_fasta.xml | 4 ++-- tools/filters/axt_to_lav.xml | 4 ++-- tools/filters/compare.xml | 2 +- tools/filters/cutWrapper.xml | 2 +- tools/filters/grep.xml | 8 ++++---- tools/filters/joiner.xml | 4 ++-- tools/filters/lav_to_bed.xml | 6 +++--- tools/filters/pasteWrapper.xml | 2 +- tools/filters/remove_beginning.xml | 2 +- tools/hyphy/hyphy_dnds_wrapper.xml | 2 +- tools/hyphy/hyphy_nj_tree_wrapper.xml | 2 +- tools/maf/genebed_maf_to_fasta.xml | 8 ++++---- tools/maf/interval_maf_to_merged_fasta.xml | 10 +++++----- tools/maf/maf_to_bed.xml | 4 ++-- tools/maf/maf_to_fasta.xml | 2 +- tools/maf/maf_to_interval.xml | 2 +- tools/metag_tools/blat_wrapper.xml | 10 +++++----- tools/metag_tools/convert_SOLiD_color2nuc.xml | 4 ++-- tools/metag_tools/mapping_to_ucsc.xml | 2 +- tools/metag_tools/megablast_xml_parser.xml | 4 ++-- .../short_reads_figure_high_quality_length.xml | 4 ++-- tools/metag_tools/short_reads_figure_score.xml | 4 ++-- tools/metag_tools/short_reads_trim_seq.xml | 2 +- tools/metag_tools/shrimp_color_wrapper.xml | 6 +++--- tools/metag_tools/shrimp_wrapper.xml | 6 +++--- 38 files changed, 75 insertions(+), 75 deletions(-) diff --git a/templates/base_panels.mako b/templates/base_panels.mako index 4bdad69c992..97eccfd4360 100644 --- a/templates/base_panels.mako +++ b/templates/base_panels.mako @@ -283,7 +283,7 @@ -
+
## Background displays first
## Layer iframes over backgrounds diff --git a/tools/annotation_profiler/annotation_profiler.xml b/tools/annotation_profiler/annotation_profiler.xml index 2b958cdf175..1d5fbc3a58c 100644 --- a/tools/annotation_profiler/annotation_profiler.xml +++ b/tools/annotation_profiler/annotation_profiler.xml @@ -43,9 +43,9 @@ Takes an input set of intervals and for each interval determines the base coverage of the interval by a set of features (tables) available from UCSC. -By default, this tool will check the coverage of your intervals against all available features; you may, however, choose to select only those tables that you want to include. Selecting a section heading will effectively cause all of it's children to be selected. +By default, this tool will check the coverage of your intervals against all available features; you may, however, choose to select only those tables that you want to include. Selecting a section heading will effectively cause all of its children to be selected. -You may alternatively choose to recieve a summary across all of the intervals that you provide. +You may alternatively choose to receive a summary across all of the intervals that you provide. ----- @@ -118,14 +118,14 @@ Where:: allIntervalCount is the number of provided intervals allIntervalSize is the sum of the lengths of the provided interval file allCoverage is the sum of the coverage for each provided interval - allTableRegionsOverlaped is the sum of the number of regions of the table (non-unique) that were overlaped for each interval - allIntervalsOverlapingTable is the number of provided intervals which overlap the table + allTableRegionsOverlapped is the sum of the number of regions of the table (non-unique) that were overlapped for each interval + allIntervalsOverlappingTable is the number of provided intervals which overlap the table nrIntervalCount is the number of non-redundant intervals nrIntervalSize is the sum of the lengths of non-redundant intervals nrCoverage is the sum of the coverage of non-redundant intervals - nrTableRegionsOverlaped is the number of regions of the table (unique) that were overlaped by the non-redundant intervals - nrIntervalsOverlapingTable is the number of non-redundant intervals which overlap the table + nrTableRegionsOverlapped is the number of regions of the table (unique) that were overlapped by the non-redundant intervals + nrIntervalsOverlappingTable is the number of non-redundant intervals which overlap the table .. class:: infomark diff --git a/tools/data_source/encode_import_all_latest_datasets.xml b/tools/data_source/encode_import_all_latest_datasets.xml index e7a3409f153..61f9cd33e5c 100644 --- a/tools/data_source/encode_import_all_latest_datasets.xml +++ b/tools/data_source/encode_import_all_latest_datasets.xml @@ -46,7 +46,7 @@ For detailed information about data deposition and partitioning, click here_. *[gencode_partitioned]* means that the dataset was partitioned according to the protocol below: -A partition scheme has been defined that is similar to what has previously been done with TARs/TRANSFRAGs such that any feature can be cla ssified as falling into one of the following 6 categories: +A partition scheme has been defined that is similar to what has previously been done with TARs/TRANSFRAGs such that any feature can be classified as falling into one of the following 6 categories: 1. **Coding** -- coding exons defined from the GENCODE experimentally verified coding set (coding in any transcript) 2. **5UTR** -- 5' UTR exons defined from the GENCODE experimentally verified coding set (5' UTR in some transcript but never coding in any other) 3. **3UTR** -- 3' UTR exons defined from the GENCODE experimentally verified coding set (3' UTR in some transcript but never coding in any other) @@ -63,4 +63,4 @@ A partition scheme has been defined that is similar to what has previously been - + diff --git a/tools/data_source/upload.xml b/tools/data_source/upload.xml index b7346b4a102..81756f52f88 100644 --- a/tools/data_source/upload.xml +++ b/tools/data_source/upload.xml @@ -94,7 +94,7 @@ A zipped archive consisting of binary sequence files in either 'ab1' or 'scf' fo **Fasta** -A sequence in FASTA format consists of a single-line description, followed by lines of sequence data. The first character of the description line is a greater-than (">") symbol in the first column. All lines should be shorter than 80 charcters:: +A sequence in FASTA format consists of a single-line description, followed by lines of sequence data. The first character of the description line is a greater-than (">") symbol in the first column. All lines should be shorter than 80 characters:: >sequence1 atgcgtttgcgtgc @@ -195,7 +195,7 @@ A zipped archive consisting of flat text sequence files. All files in this arch **Wig** -The wiggle format is line-oriented. Wiggle data is preceeded by a track definition line, which adds a number of options for controlling the default display of this track. +The wiggle format is line-oriented. Wiggle data is preceded by a track definition line, which adds a number of options for controlling the default display of this track. ----- diff --git a/tools/extract/extract_genomic_dna.xml b/tools/extract/extract_genomic_dna.xml index 83d91959818..4714fa438b9 100644 --- a/tools/extract/extract_genomic_dna.xml +++ b/tools/extract/extract_genomic_dna.xml @@ -55,7 +55,7 @@ All of the following will cause a line from the input dataset to be skipped and .. class:: infomark - **Extract genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes** previously were achieved by two seperate tools. + **Extract genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes** previously were achieved by two separate tools. ----- diff --git a/tools/fastx_toolkit/fasta_formatter.xml b/tools/fastx_toolkit/fasta_formatter.xml index e57a60dea82..ca916682635 100644 --- a/tools/fastx_toolkit/fasta_formatter.xml +++ b/tools/fastx_toolkit/fasta_formatter.xml @@ -13,7 +13,7 @@ - + diff --git a/tools/fastx_toolkit/fastq_quality_converter.xml b/tools/fastx_toolkit/fastq_quality_converter.xml index 7c7d6637eeb..514814fd9fd 100644 --- a/tools/fastx_toolkit/fastq_quality_converter.xml +++ b/tools/fastx_toolkit/fastq_quality_converter.xml @@ -53,7 +53,7 @@ **What it does** -Converts a solexa FASTQ file to/from numeric or ASCII quality format. +Converts a Solexa FASTQ file to/from numeric or ASCII quality format. .. class:: warningmark diff --git a/tools/fastx_toolkit/fastx_barcode_splitter.xml b/tools/fastx_toolkit/fastx_barcode_splitter.xml index aaa79178047..aec33946bef 100644 --- a/tools/fastx_toolkit/fastx_barcode_splitter.xml +++ b/tools/fastx_toolkit/fastx_barcode_splitter.xml @@ -36,7 +36,7 @@ **What it does** -This tool splits a solexa library (FASTQ file) or a regular FASTA file to several files, using barcodes as the split criteria. +This tool splits a Solexa library (FASTQ file) or a regular FASTA file into several files, using barcodes as the split criteria. -------- diff --git a/tools/fastx_toolkit/fastx_clipper.xml b/tools/fastx_toolkit/fastx_clipper.xml index cd97ede28ed..11c7001ec0e 100644 --- a/tools/fastx_toolkit/fastx_clipper.xml +++ b/tools/fastx_toolkit/fastx_clipper.xml @@ -42,8 +42,8 @@ - - + + diff --git a/tools/fastx_toolkit/fastx_collapser.xml b/tools/fastx_toolkit/fastx_collapser.xml index 9daa2674fba..e879ad265cd 100644 --- a/tools/fastx_toolkit/fastx_collapser.xml +++ b/tools/fastx_toolkit/fastx_collapser.xml @@ -63,7 +63,7 @@ Example Output file:: Original Sequence Names / Lane descriptions (e.g. "CSHL_2_FC0042AGLLOO_1_1_742_502") are discarded. -The output seqeunce name is composed of two numbers: the first is the sequence's number, the second is the multiplicity value. +The output sequence name is composed of two numbers: the first is the sequence's number, the second is the multiplicity value. The following output:: diff --git a/tools/fastx_toolkit/fastx_quality_statistics.xml b/tools/fastx_toolkit/fastx_quality_statistics.xml index d6f791a949d..713caff0550 100644 --- a/tools/fastx_toolkit/fastx_quality_statistics.xml +++ b/tools/fastx_toolkit/fastx_quality_statistics.xml @@ -36,7 +36,7 @@ Creates quality statistics report for the given Solexa/FASTQ library. **The output file will contain the following fields:** -* column = column number (1 to 36 for a 36-cycles read solexa file) +* column = column number (1 to 36 for a 36-cycles read Solexa file) * count = number of bases found in this column. * min = Lowest quality score value found in this column. * max = Highest quality score value found in this column. diff --git a/tools/fastx_toolkit/fastx_renamer.xml b/tools/fastx_toolkit/fastx_renamer.xml index 50497e663bc..51d1366cbd9 100644 --- a/tools/fastx_toolkit/fastx_renamer.xml +++ b/tools/fastx_toolkit/fastx_renamer.xml @@ -23,7 +23,7 @@ This tool renames the sequence identifiers in a FASTQ/A file. .. class:: infomark -Use this tool at the beginning of your workflow, as a way to keep the original sequence (before trimming,clipping,barcode-removal, etc). +Use this tool at the beginning of your workflow, as a way to keep the original sequence (before trimming, clipping, barcode-removal, etc). -------- diff --git a/tools/filters/axt_to_concat_fasta.xml b/tools/filters/axt_to_concat_fasta.xml index a79515751d9..d9f5f8ca312 100644 --- a/tools/filters/axt_to_concat_fasta.xml +++ b/tools/filters/axt_to_concat_fasta.xml @@ -1,5 +1,5 @@ - Converts an AXT formated file to a concatenated FASTA alignment + Converts an AXT formatted file to a concatenated FASTA alignment axt_to_concat_fasta.py $dbkey_1 $dbkey_2 < $axt_input > $out_file1 @@ -27,7 +27,7 @@ **Syntax** -This tool converts an AXT formated file to the FASTA format, and concatenates the results in the same build. +This tool converts an AXT formatted file to the FASTA format, and concatenates the results in the same build. - **AXT format** The alignments are produced from Blastz, an alignment tool available from Webb Miller's lab at Penn State University. The lav format Blastz output, which does not include the sequence, was converted to AXT format with lavToAxt. Each alignment block in an AXT file contains three lines: a summary line and 2 sequence lines. Blocks are separated from one another by blank lines. diff --git a/tools/filters/axt_to_fasta.xml b/tools/filters/axt_to_fasta.xml index b0b6f63acc8..1c560c060a0 100644 --- a/tools/filters/axt_to_fasta.xml +++ b/tools/filters/axt_to_fasta.xml @@ -1,5 +1,5 @@ - Converts an AXT formated file to FASTA format + Converts an AXT formatted file to FASTA format axt_to_fasta.py $dbkey_1 $dbkey_2 < $axt_input > $out_file1 @@ -28,7 +28,7 @@ **Syntax** -This tool converts an AXT formated file to the FASTA format. +This tool converts an AXT formatted file to the FASTA format. - **AXT format** The alignments are produced from Blastz, an alignment tool available from Webb Miller's lab at Penn State University. The lav format Blastz output, which does not include the sequence, was converted to AXT format with lavToAxt. Each alignment block in an AXT file contains three lines: a summary line and 2 sequence lines. Blocks are separated from one another by blank lines. diff --git a/tools/filters/axt_to_lav.xml b/tools/filters/axt_to_lav.xml index 39c3b734240..33adb210674 100644 --- a/tools/filters/axt_to_lav.xml +++ b/tools/filters/axt_to_lav.xml @@ -1,5 +1,5 @@ - Converts an AXT formated file to LAV format + Converts an AXT formatted file to LAV format axt_to_lav.py /depot/data2/galaxy/$dbkey_1/seq/%s.nib:$dbkey_1:${GALAXY_DATA_INDEX_DIR}/shared/ucsc/chrom/${dbkey_1}.len /depot/data2/galaxy/$dbkey_2/seq/%s.nib:$dbkey_2:${GALAXY_DATA_INDEX_DIR}/shared/ucsc/chrom/${dbkey_2}.len $align_input $lav_file $seq_file1 $seq_file2 @@ -22,7 +22,7 @@ **Syntax** -This tool converts an AXT formated file to the LAV format. +This tool converts an AXT formatted file to the LAV format. - **AXT format** The alignments are produced from Blastz, an alignment tool available from Webb Miller's lab at Penn State University. The lav format Blastz output, which does not include the sequence, was converted to AXT format with lavToAxt. Each alignment block in an AXT file contains three lines: a summary line and 2 sequence lines. Blocks are separated from one another by blank lines. diff --git a/tools/filters/compare.xml b/tools/filters/compare.xml index 2eca79af15a..3615f423822 100644 --- a/tools/filters/compare.xml +++ b/tools/filters/compare.xml @@ -52,7 +52,7 @@ If this is **First query**:: and this is **Second query**:: - geneA tumor-supressor + geneA tumor-suppressor geneB Foxp2 geneC Gnas1 geneE INK4a diff --git a/tools/filters/cutWrapper.xml b/tools/filters/cutWrapper.xml index 6c08135060e..40877f65e13 100644 --- a/tools/filters/cutWrapper.xml +++ b/tools/filters/cutWrapper.xml @@ -33,7 +33,7 @@ .. class:: infomark -The output of this tool is always in tabular format (e.g., if your original delimeter was comma, it will be replaced with tab). For example: +The output of this tool is always in tabular format (e.g., if your original delimiters are commas, they will be replaced with tabs). For example: Cutting columns 1 and 3 from:: diff --git a/tools/filters/grep.xml b/tools/filters/grep.xml index d6a1814ffb9..7268430eeac 100644 --- a/tools/filters/grep.xml +++ b/tools/filters/grep.xml @@ -30,7 +30,7 @@ **Syntax** -The select tool searches the data for lines containing or not containing a match to the given pattern. Regular Expression is introduced in this tool. A Regular Expression is a pattern descibing a certain amount of text. +The select tool searches the data for lines containing or not containing a match to the given pattern. Regular Expression is introduced in this tool. A Regular Expression is a pattern describing a certain amount of text. - **( ) { } [ ] . * ? + \ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for. - **\\A** matches the beginning of a string(but not an internal line). @@ -46,7 +46,7 @@ The select tool searches the data for lines containing or not containing a match - **{** n or n, or n,m **}** specifies an expected number of repetitions of the preceding pattern. - **{n}** The preceding item is matched exactly n times. - - **{n,}** The preceding item ismatched n or more times. + - **{n,}** The preceding item is matched n or more times. - **{n,m}** The preceding item is matched at least n times but not more than m times. - **[** ... **]** creates a character class. Within the brackets, single characters can be placed. A dash (-) may be used to indicate a range such as **a-z**. @@ -64,9 +64,9 @@ The select tool searches the data for lines containing or not containing a match **Example** -- **^chr([0-9A-Za-z])+** would match lines that begin with chromsomes, such as lines in a BED format file. +- **^chr([0-9A-Za-z])+** would match lines that begin with chromosomes, such as lines in a BED format file. - **(ACGT){1,5}** would match at least 1 "ACGT" and at most 5 "ACGT" consecutively. -- **([^,][0-9]{1,3})(,[0-9]{3})\*** would match a large integer that is properly seperated with commas such as 23,078,651. +- **([^,][0-9]{1,3})(,[0-9]{3})\*** would match a large integer that is properly separated with commas such as 23,078,651. - **(abc)|(def)** would match either "abc" or "def". - **^\\W+#** would match any line that is a comment. diff --git a/tools/filters/joiner.xml b/tools/filters/joiner.xml index 14365c4b228..1e455e76a7b 100644 --- a/tools/filters/joiner.xml +++ b/tools/filters/joiner.xml @@ -166,12 +166,12 @@ Query2:: Joining the 4th column of Query1 with the 1st column of Query2 will yield:: - chr1 10 20 geneA geneA tumor-supressor + chr1 10 20 geneA geneA tumor-suppressor chr1 50 80 geneB geneB Foxp2 Joining the 4th column of Query1 with the 1st column of Query2, while keeping all lines from Query1, will yield:: - chr1 10 20 geneA geneA tumor-supressor + chr1 10 20 geneA geneA tumor-suppressor chr1 50 80 geneB geneB Foxp2 chr5 10 40 geneL diff --git a/tools/filters/lav_to_bed.xml b/tools/filters/lav_to_bed.xml index 1bbf4283339..d58b1d72df7 100644 --- a/tools/filters/lav_to_bed.xml +++ b/tools/filters/lav_to_bed.xml @@ -1,5 +1,5 @@ - Converts a LAV formated file to BED format + Converts a LAV formatted file to BED format lav_to_bed.py $lav_file $bed_file1 $bed_file2 @@ -19,7 +19,7 @@ **Syntax** -This tool converts a LAV formated file to the BED format. +This tool converts a LAV formatted file to the BED format. - **LAV format** LAV is an alignment format developed by Webb Miller's group at Penn State University. It is the primary output format for BLASTZ. @@ -54,7 +54,7 @@ This tool converts a LAV formated file to the BED format. } #:eof -- To two BED formated files:: +- To two BED formatted files:: chr19 3001011 3001075 hg16_0 0 + chr19 3008278 3008357 hg16_1 0 + diff --git a/tools/filters/pasteWrapper.xml b/tools/filters/pasteWrapper.xml index c2969677940..41252798515 100644 --- a/tools/filters/pasteWrapper.xml +++ b/tools/filters/pasteWrapper.xml @@ -33,7 +33,7 @@ .. class:: infomark -Paste preserves column assignments of the first dataset +Paste preserves column assignments of the first dataset. ----- diff --git a/tools/filters/remove_beginning.xml b/tools/filters/remove_beginning.xml index 6718a9b05a3..2641ae1f774 100644 --- a/tools/filters/remove_beginning.xml +++ b/tools/filters/remove_beginning.xml @@ -19,7 +19,7 @@ **What it does** -This tool removes specified number of lines from the beginning of a dataset +This tool removes a specified number of lines from the beginning of a dataset. ----- diff --git a/tools/hyphy/hyphy_dnds_wrapper.xml b/tools/hyphy/hyphy_dnds_wrapper.xml index 7711133057c..47d1c6ed46d 100644 --- a/tools/hyphy/hyphy_dnds_wrapper.xml +++ b/tools/hyphy/hyphy_dnds_wrapper.xml @@ -47,7 +47,7 @@ Any block/s not containing as many species as mentioned in the tree definition w ----- -For the tree definition, you only need to specify the species build names. For example, you could use the tree *((hg17,panTro1),(mm5,rn3),canFam1)*, if your FASTA file looks like the example below. You may also use **Neighbor Joining Tree Builder** tool to obtain the tree definition:: +For the tree definition, you only need to specify the species build names. For example, you could use the tree *(hg17,panTro1),(mm5,rn3),canFam1)*, if your FASTA file looks like the example below. You may also use **Neighbor Joining Tree Builder** tool to obtain the tree definition:: >hg17.chr7(+):26907301-26907310|hg17_0 GTGGGAGGT diff --git a/tools/hyphy/hyphy_nj_tree_wrapper.xml b/tools/hyphy/hyphy_nj_tree_wrapper.xml index 7ef6edeee4d..cc05d030b6b 100644 --- a/tools/hyphy/hyphy_nj_tree_wrapper.xml +++ b/tools/hyphy/hyphy_nj_tree_wrapper.xml @@ -16,7 +16,7 @@ - + diff --git a/tools/maf/genebed_maf_to_fasta.xml b/tools/maf/genebed_maf_to_fasta.xml index a458ea80c19..ea209878646 100644 --- a/tools/maf/genebed_maf_to_fasta.xml +++ b/tools/maf/genebed_maf_to_fasta.xml @@ -48,10 +48,10 @@ - + - + @@ -61,7 +61,7 @@ in aligning species - + @@ -69,7 +69,7 @@ - + diff --git a/tools/maf/interval_maf_to_merged_fasta.xml b/tools/maf/interval_maf_to_merged_fasta.xml index d4e2d7cebe6..fbb41363b17 100644 --- a/tools/maf/interval_maf_to_merged_fasta.xml +++ b/tools/maf/interval_maf_to_merged_fasta.xml @@ -49,10 +49,10 @@ - + - + @@ -63,7 +63,7 @@ - + @@ -71,7 +71,7 @@ - + @@ -79,7 +79,7 @@ - + diff --git a/tools/maf/maf_to_bed.xml b/tools/maf/maf_to_bed.xml index d3eb35b112d..c10b9ae56d2 100644 --- a/tools/maf/maf_to_bed.xml +++ b/tools/maf/maf_to_bed.xml @@ -36,12 +36,12 @@ The interface for this tool contains two pages (steps): * **Step 2 of 2**. Choose species from the alignment to be included in the output and specify how to deal with alignment blocks that lack one or more species: * **Choose species** - the tool reads the alignment provided during Step 1 and generates a list of species contained within that alignment. Using checkboxes you can specify taxa to be included in the output (only reference genome, shown in **bold**, is selected by default). If you select more than one species, then more than one history item will be created. - * **Choose to include/exclude blocks with missing species** - if an alignment block does not contain any one of the species you selected within **Choose species** menu and this option is set to **exclude blocks with missing species**, then coordiantes of such a block **will not** be included in the output (see **Example 2** below). + * **Choose to include/exclude blocks with missing species** - if an alignment block does not contain any one of the species you selected within **Choose species** menu and this option is set to **exclude blocks with missing species**, then coordinates of such a block **will not** be included in the output (see **Example 2** below). ----- -**Example 1**: **Include only refernce genome** (hg18 in this case) and **include blocks with missing species**: +**Example 1**: **Include only reference genome** (hg18 in this case) and **include blocks with missing species**: For the following alignment:: diff --git a/tools/maf/maf_to_fasta.xml b/tools/maf/maf_to_fasta.xml index 3f6ef2138ff..056c4afb710 100644 --- a/tools/maf/maf_to_fasta.xml +++ b/tools/maf/maf_to_fasta.xml @@ -71,7 +71,7 @@ The interface for this tool contains two pages (steps): Multiple Block output has additional options: * **Choose species** - the tool reads the alignment provided during Step 1 and generates a list of species contained within that alignment. Using checkboxes you can specify taxa to be included in the output (all species are selected by default). - * **Choose to include/exclude blocks with missing species** - if an alignment block does not contain any one of the species you selected within **Choose species** menu and this option is set to **exclude blocks with missing species**, then such a block **will not** be included in the output (see **Example 2** below). For example, if you want to extact human, mouse, and rat from a series of alignments and one of the blocks does not contain mouse sequence, then this block will not be converted to FASTA and will not be returned. + * **Choose to include/exclude blocks with missing species** - if an alignment block does not contain any one of the species you selected within **Choose species** menu and this option is set to **exclude blocks with missing species**, then such a block **will not** be included in the output (see **Example 2** below). For example, if you want to extract human, mouse, and rat from a series of alignments and one of the blocks does not contain mouse sequence, then this block will not be converted to FASTA and will not be returned. ----- diff --git a/tools/maf/maf_to_interval.xml b/tools/maf/maf_to_interval.xml index 8704481c04e..d3a641a637d 100644 --- a/tools/maf/maf_to_interval.xml +++ b/tools/maf/maf_to_interval.xml @@ -1,5 +1,5 @@ - Converts a MAF formated file to the Interval format + Converts a MAF formatted file to the Interval format maf_to_interval.py $input1 $out_file1 $out_file1.id $__new_file_path__ $input1.dbkey $species $input1.metadata.species $complete_blocks $remove_gaps diff --git a/tools/metag_tools/blat_wrapper.xml b/tools/metag_tools/blat_wrapper.xml index 7d0451659c6..2da6827ab03 100644 --- a/tools/metag_tools/blat_wrapper.xml +++ b/tools/metag_tools/blat_wrapper.xml @@ -45,17 +45,17 @@ .. class:: warningmark - Use a smaller word size (*Minimal Size of Exact Match*) will increase the computational time. +Using a smaller word size (*Minimal Size of Exact Match*) will increase the computational time. .. class:: warningmark -Use a larger mismatch number (*Number of Mismatch in the Word*) will increase the computational time. +Using a larger mismatch number (*Number of Mismatch in the Word*) will increase the computational time. ----- **What it does** -This tool currently uses alignment program **BLAT**. Your short reads file is searched against a genome build or another uploaded file. +This tool currently uses the **BLAT** alignment program. Your short reads file is searched against a genome build or another uploaded file. ----- @@ -66,13 +66,13 @@ This tool currently uses alignment program **BLAT**. Your short reads file is se >seq1 TGGTAATGGTGGTTTTTTTTTTTTTTTTTTATTTTT -- Use default settings: +- Use the default settings: - alignment identity must be higher than or equal to 90%. - minimal size of exact match to trigger an alignment is 11. - - allow 0 mismatch in the above exact match size. + - allow 0 mismatches in the above exact match size. - Search against ce2 (C. elegans March 2004), partial result:: diff --git a/tools/metag_tools/convert_SOLiD_color2nuc.xml b/tools/metag_tools/convert_SOLiD_color2nuc.xml index 112dff64af8..d6963bac368 100644 --- a/tools/metag_tools/convert_SOLiD_color2nuc.xml +++ b/tools/metag_tools/convert_SOLiD_color2nuc.xml @@ -25,13 +25,13 @@ .. class:: warningmark - The tool was designed for color space files generated from ABI SOLiD sequencer. The file format must be fasta-like: the title starts with a ">" sign, and each color space sequence starts with a leading nucleotide. +The tool was designed for color space files generated from an ABI SOLiD sequencer. The file format must be fasta-like: the title starts with a ">" character, and each color space sequence starts with a leading nucleotide. ----- **What it does** - This tool convert a color space sequence to nucleotides. The leading character must be one of the nucleotides: A, C, G, T. +This tool converts a color space sequence to nucleotides. The leading character must be a nucleotide: A, C, G, or T. ----- diff --git a/tools/metag_tools/mapping_to_ucsc.xml b/tools/metag_tools/mapping_to_ucsc.xml index dde8353a9c5..ddfd88134c1 100644 --- a/tools/metag_tools/mapping_to_ucsc.xml +++ b/tools/metag_tools/mapping_to_ucsc.xml @@ -145,7 +145,7 @@ **What it does** -This tool formats mapping data generated by short read mappers, as a custom track that can be displayed at UCSC genome browser. +This tool turns mapping data generated by short read mappers into a format that can be displayed in the UCSC genome browser as a custom track. ----- diff --git a/tools/metag_tools/megablast_xml_parser.xml b/tools/metag_tools/megablast_xml_parser.xml index eca32b754d8..01355429aec 100644 --- a/tools/metag_tools/megablast_xml_parser.xml +++ b/tools/metag_tools/megablast_xml_parser.xml @@ -26,13 +26,13 @@ Blast XML output **must** be uploaded to Galaxy in zipped form. **What it does** -This tool will process XML output of any NCBI blast tool (if you run your own blast jobs, the XML output can be generated with **-m 7** option). +This tool processes the XML output of any NCBI blast tool (if you run your own blast jobs, the XML output can be generated with **-m 7** option). ----- **Output fields** -This tools returns tab-delimted output with the following fields:: +This tools returns tab-delimited output with the following fields:: Description Example ----------------------------------------- ----------------- diff --git a/tools/metag_tools/short_reads_figure_high_quality_length.xml b/tools/metag_tools/short_reads_figure_high_quality_length.xml index d35dfb6588e..1db3fe14c55 100644 --- a/tools/metag_tools/short_reads_figure_high_quality_length.xml +++ b/tools/metag_tools/short_reads_figure_high_quality_length.xml @@ -32,7 +32,7 @@ .. class:: warningmark - To use this tool your dataset needs to be in *Quality Score* format. Click pencil icon next to your dataset to set datatype to *Quality Score* (see below for examples of quality scores). +To use this tool, your dataset needs to be in the *Quality Score* format. Click the pencil icon next to your dataset to set the datatype to *Quality Score* (see below for examples). ----- @@ -62,7 +62,7 @@ Illumina (Solexa) data:: >seq1 23 33 34 25 28 28 28 32 23 34 27 4 28 28 31 21 28 -- If the threshold was set to 20: +- If the threshold is set to 20: - a low quality score 4 in the middle separated two segments of lengths 11 and 5. diff --git a/tools/metag_tools/short_reads_figure_score.xml b/tools/metag_tools/short_reads_figure_score.xml index c7a5baa24e6..7eb57db0276 100644 --- a/tools/metag_tools/short_reads_figure_score.xml +++ b/tools/metag_tools/short_reads_figure_score.xml @@ -29,7 +29,7 @@ .. class:: warningmark - To use this tool your dataset needs to be in *Quality Score* format. Click pencil icon next to your dataset to set datatype to *Quality Score* (see below for examples of quality scores). +To use this tool, your dataset needs to be in the *Quality Score* format. Click the pencil icon next to your dataset to set the datatype to *Quality Score* (see below for examples). ----- @@ -58,7 +58,7 @@ Quality scores are summarized as boxplot (Roche 454 FLX data): .. image:: ../static/images/short_reads_boxplot.png -where the **X-axis** is coordiante along the read and the **Y-axis** is quality score adjusted to comply with the Phred score metric. Units on the X-axis depend on whether your data comes from Roche (454) or Illumina (Solexa) and ABI SOLiD machines: +where the **X-axis** is coordinate along the read and the **Y-axis** is quality score adjusted to comply with the Phred score metric. Units on the X-axis depend on whether your data comes from Roche (454) or Illumina (Solexa) and ABI SOLiD machines: - For Roche (454) X-axis (shown above) indicates **relative** position (in %) within reads as this technology produces reads of different lengths; - For Illumina (Solexa) and ABI SOLiD X-axis shows **absolute** position in nucleotides within reads. diff --git a/tools/metag_tools/short_reads_trim_seq.xml b/tools/metag_tools/short_reads_trim_seq.xml index b28337e447c..ce326ba442c 100644 --- a/tools/metag_tools/short_reads_trim_seq.xml +++ b/tools/metag_tools/short_reads_trim_seq.xml @@ -57,7 +57,7 @@ .. class:: warningmark - To use this tool your quality score dataset needs to be in *Quality Score* format. Click pencil icon next to your dataset to set datatype to *Quality Score*. +To use this tool, your dataset needs to be in the *Quality Score* format. Click the pencil icon next to your dataset to set the datatype to *Quality Score* (see below for examples). ----- diff --git a/tools/metag_tools/shrimp_color_wrapper.xml b/tools/metag_tools/shrimp_color_wrapper.xml index de2db722e48..a564ece2a02 100644 --- a/tools/metag_tools/shrimp_color_wrapper.xml +++ b/tools/metag_tools/shrimp_color_wrapper.xml @@ -55,7 +55,7 @@ .. class:: warningmark -To use this tool your dataset needs to be in *csfasta* (as ABI SOLiD color-space sequences) format. Click pencil icon next to your dataset to set datatype to *csfasta*. +To use this tool your dataset needs to be in the *csfasta* (as ABI SOLiD color-space sequences) format. Click pencil icon next to your dataset to set the datatype to *csfasta*. ----- @@ -166,8 +166,8 @@ The commonly used parameters with default value setting:: -h S-W Full Hit Threshold (default: 68.00%) In letter-space, this parameter determines the threshold score for both vectored and full Smith-Waterman alignments. - Any values less than this quanitity will be thrown away. - *Note* This option differs slightly in meaning between letter-space and colour-space. + Any values less than this quantity will be thrown away. + *Note* This option differs slightly in meaning between letter-space and color-space. -v diff --git a/tools/metag_tools/shrimp_wrapper.xml b/tools/metag_tools/shrimp_wrapper.xml index f1eb9cd6dd3..0d400315fec 100644 --- a/tools/metag_tools/shrimp_wrapper.xml +++ b/tools/metag_tools/shrimp_wrapper.xml @@ -219,7 +219,7 @@ The commonly used parameters with default value setting:: running time. Higher values will have the opposite effect. -t Seed Hit Taboo Length (default: 4) The seed taboo length specifies how many target genome bases - or colours must exist prior to a previous seed match in order + or colors must exist prior to a previous seed match in order to count another seed match as a hit. -9 Seed Generation Taboo Length (default: 0) @@ -265,8 +265,8 @@ The commonly used parameters with default value setting:: -h S-W Hit Threshold (default: 68.00%) In letter-space, this parameter determines the threshold score for both vectored and full Smith-Waterman alignments. - Any values less than this quanitity will be thrown away. - *Note* This option differs slightly in meaning between letter-space and colour-space. + Any values less than this quantity will be thrown away. + *Note* This option differs slightly in meaning between letter-space and color-space. -----