details: http://www.bx.psu.edu/hg/galaxy/rev/d669408018a1 changeset: 2789:d669408018a1 user: Kanwei Li kanwei@gmail.com date: Sun Sep 27 23:11:43 2009 -0400 description: typo fixes for tools in folders A-M
38 file(s) affected in this change:
templates/base_panels.mako tools/annotation_profiler/annotation_profiler.xml tools/data_source/encode_import_all_latest_datasets.xml tools/data_source/upload.xml tools/extract/extract_genomic_dna.xml tools/fastx_toolkit/fasta_formatter.xml tools/fastx_toolkit/fastq_quality_converter.xml tools/fastx_toolkit/fastx_barcode_splitter.xml tools/fastx_toolkit/fastx_clipper.xml tools/fastx_toolkit/fastx_collapser.xml tools/fastx_toolkit/fastx_quality_statistics.xml tools/fastx_toolkit/fastx_renamer.xml tools/filters/axt_to_concat_fasta.xml tools/filters/axt_to_fasta.xml tools/filters/axt_to_lav.xml tools/filters/compare.xml tools/filters/cutWrapper.xml tools/filters/grep.xml tools/filters/joiner.xml tools/filters/lav_to_bed.xml tools/filters/pasteWrapper.xml tools/filters/remove_beginning.xml tools/hyphy/hyphy_dnds_wrapper.xml tools/hyphy/hyphy_nj_tree_wrapper.xml tools/maf/genebed_maf_to_fasta.xml tools/maf/interval_maf_to_merged_fasta.xml tools/maf/maf_to_bed.xml tools/maf/maf_to_fasta.xml tools/maf/maf_to_interval.xml tools/metag_tools/blat_wrapper.xml tools/metag_tools/convert_SOLiD_color2nuc.xml tools/metag_tools/mapping_to_ucsc.xml tools/metag_tools/megablast_xml_parser.xml tools/metag_tools/short_reads_figure_high_quality_length.xml tools/metag_tools/short_reads_figure_score.xml tools/metag_tools/short_reads_trim_seq.xml tools/metag_tools/shrimp_color_wrapper.xml tools/metag_tools/shrimp_wrapper.xml
diffs (698 lines):
diff -r f7459ad62be9 -r d669408018a1 templates/base_panels.mako --- a/templates/base_panels.mako Sat Sep 26 18:05:36 2009 -0400 +++ b/templates/base_panels.mako Sun Sep 27 23:11:43 2009 -0400 @@ -283,7 +283,7 @@ </head>
<body scroll="no" class="${self.body_class}"> - <div id="everything" style="position: absolute; top: 0; left: 0; width: 100%; height: 100%; min-width: 960px;"> + <div id="everything" style="position: absolute; top: 0; left: 0; width: 100%; height: 100%; min-width: 600px;"> ## Background displays first <div id="background"></div> ## Layer iframes over backgrounds diff -r f7459ad62be9 -r d669408018a1 tools/annotation_profiler/annotation_profiler.xml --- a/tools/annotation_profiler/annotation_profiler.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/annotation_profiler/annotation_profiler.xml Sun Sep 27 23:11:43 2009 -0400 @@ -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.
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@@ -118,14 +118,14 @@ 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 -r f7459ad62be9 -r d669408018a1 tools/data_source/encode_import_all_latest_datasets.xml --- a/tools/data_source/encode_import_all_latest_datasets.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/data_source/encode_import_all_latest_datasets.xml Sun Sep 27 23:11:43 2009 -0400 @@ -46,7 +46,7 @@
*[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 @@
</help> -</tool> +</tool> diff -r f7459ad62be9 -r d669408018a1 tools/data_source/upload.xml --- a/tools/data_source/upload.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/data_source/upload.xml Sun Sep 27 23:11:43 2009 -0400 @@ -94,7 +94,7 @@
**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 @@
**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.
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diff -r f7459ad62be9 -r d669408018a1 tools/extract/extract_genomic_dna.xml --- a/tools/extract/extract_genomic_dna.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/extract/extract_genomic_dna.xml Sun Sep 27 23:11:43 2009 -0400 @@ -55,7 +55,7 @@
.. 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 -r f7459ad62be9 -r d669408018a1 tools/fastx_toolkit/fasta_formatter.xml --- a/tools/fastx_toolkit/fasta_formatter.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/fastx_toolkit/fasta_formatter.xml Sun Sep 27 23:11:43 2009 -0400 @@ -13,7 +13,7 @@ <inputs> <param format="fasta" name="input" type="data" label="Library to re-format" />
- <param name="width" type="integer" value="0" label="New width for nucleotides strings" help="Use 0 for single line outout." /> + <param name="width" type="integer" value="0" label="New width for nucleotides strings" help="Use 0 for single line out." /> </inputs>
<tests> diff -r f7459ad62be9 -r d669408018a1 tools/fastx_toolkit/fastq_quality_converter.xml --- a/tools/fastx_toolkit/fastq_quality_converter.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/fastx_toolkit/fastq_quality_converter.xml Sun Sep 27 23:11:43 2009 -0400 @@ -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 -r f7459ad62be9 -r d669408018a1 tools/fastx_toolkit/fastx_barcode_splitter.xml --- a/tools/fastx_toolkit/fastx_barcode_splitter.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/fastx_toolkit/fastx_barcode_splitter.xml Sun Sep 27 23:11:43 2009 -0400 @@ -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 -r f7459ad62be9 -r d669408018a1 tools/fastx_toolkit/fastx_clipper.xml --- a/tools/fastx_toolkit/fastx_clipper.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/fastx_toolkit/fastx_clipper.xml Sun Sep 27 23:11:43 2009 -0400 @@ -42,8 +42,8 @@ </param>
<param name="DISCARD_OPTIONS" type="select" label="Output options"> - <option value="-c">Output only clipped seqeunces (i.e. sequences which contained the adapter)</option> - <option value="-C">Output only non-clipped seqeunces (i.e. sequences which did not contained the adapter)</option> + <option value="-c">Output only clipped sequences (i.e. sequences which contained the adapter)</option> + <option value="-C">Output only non-clipped sequences (i.e. sequences which did not contained the adapter)</option> <option value="">Output both clipped and non-clipped sequences</option> </param>
diff -r f7459ad62be9 -r d669408018a1 tools/fastx_toolkit/fastx_collapser.xml --- a/tools/fastx_toolkit/fastx_collapser.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/fastx_toolkit/fastx_collapser.xml Sun Sep 27 23:11:43 2009 -0400 @@ -63,7 +63,7 @@
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 -r f7459ad62be9 -r d669408018a1 tools/fastx_toolkit/fastx_quality_statistics.xml --- a/tools/fastx_toolkit/fastx_quality_statistics.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/fastx_toolkit/fastx_quality_statistics.xml Sun Sep 27 23:11:43 2009 -0400 @@ -36,7 +36,7 @@
**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 -r f7459ad62be9 -r d669408018a1 tools/fastx_toolkit/fastx_renamer.xml --- a/tools/fastx_toolkit/fastx_renamer.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/fastx_toolkit/fastx_renamer.xml Sun Sep 27 23:11:43 2009 -0400 @@ -23,7 +23,7 @@
.. 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 -r f7459ad62be9 -r d669408018a1 tools/filters/axt_to_concat_fasta.xml --- a/tools/filters/axt_to_concat_fasta.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/filters/axt_to_concat_fasta.xml Sun Sep 27 23:11:43 2009 -0400 @@ -1,5 +1,5 @@ <tool id="axt_to_concat_fasta" name="AXT to concatenated FASTA"> - <description>Converts an AXT formated file to a concatenated FASTA alignment</description> + <description>Converts an AXT formatted file to a concatenated FASTA alignment</description> <command interpreter="python">axt_to_concat_fasta.py $dbkey_1 $dbkey_2 < $axt_input > $out_file1</command> <inputs> <param format="axt" name="axt_input" type="data" label="AXT file"/> @@ -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 -r f7459ad62be9 -r d669408018a1 tools/filters/axt_to_fasta.xml --- a/tools/filters/axt_to_fasta.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/filters/axt_to_fasta.xml Sun Sep 27 23:11:43 2009 -0400 @@ -1,5 +1,5 @@ <tool id="axt_to_fasta" name="AXT to FASTA"> - <description>Converts an AXT formated file to FASTA format</description> + <description>Converts an AXT formatted file to FASTA format</description> <command interpreter="python">axt_to_fasta.py $dbkey_1 $dbkey_2 < $axt_input > $out_file1</command> <inputs> <param format="axt" name="axt_input" type="data" label="AXT file"/> @@ -28,7 +28,7 @@
**Syntax**
-This tool converts an AXT formated file to the FASTA format. +This tool converts an AXT formatted file to the FASTA format.
- **AXT format** The alignments are produced from Blastz, an alignment tool available from Webb Miller's lab at Penn State University. The lav format Blastz output, which does not include the sequence, was converted to AXT format with lavToAxt. Each alignment block in an AXT file contains three lines: a summary line and 2 sequence lines. Blocks are separated from one another by blank lines.
diff -r f7459ad62be9 -r d669408018a1 tools/filters/axt_to_lav.xml --- a/tools/filters/axt_to_lav.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/filters/axt_to_lav.xml Sun Sep 27 23:11:43 2009 -0400 @@ -1,5 +1,5 @@ <tool id="axt_to_lav_1" name="AXT to LAV"> - <description>Converts an AXT formated file to LAV format</description> + <description>Converts an AXT formatted file to LAV format</description> <command interpreter="python">axt_to_lav.py /depot/data2/galaxy/$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</command> <inputs> <param name="align_input" type="data" format="axt" label="Alignment File" optional="False"/> @@ -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 -r f7459ad62be9 -r d669408018a1 tools/filters/compare.xml --- a/tools/filters/compare.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/filters/compare.xml Sun Sep 27 23:11:43 2009 -0400 @@ -52,7 +52,7 @@
and this is **Second query**::
- geneA tumor-supressor + geneA tumor-suppressor geneB Foxp2 geneC Gnas1 geneE INK4a diff -r f7459ad62be9 -r d669408018a1 tools/filters/cutWrapper.xml --- a/tools/filters/cutWrapper.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/filters/cutWrapper.xml Sun Sep 27 23:11:43 2009 -0400 @@ -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 -r f7459ad62be9 -r d669408018a1 tools/filters/grep.xml --- a/tools/filters/grep.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/filters/grep.xml Sun Sep 27 23:11:43 2009 -0400 @@ -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 @@ - **{** 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 @@
**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. </help> diff -r f7459ad62be9 -r d669408018a1 tools/filters/joiner.xml --- a/tools/filters/joiner.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/filters/joiner.xml Sun Sep 27 23:11:43 2009 -0400 @@ -166,12 +166,12 @@
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 -r f7459ad62be9 -r d669408018a1 tools/filters/lav_to_bed.xml --- a/tools/filters/lav_to_bed.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/filters/lav_to_bed.xml Sun Sep 27 23:11:43 2009 -0400 @@ -1,5 +1,5 @@ <tool id="lav_to_bed1" name="LAV to BED"> - <description>Converts a LAV formated file to BED format</description> + <description>Converts a LAV formatted file to BED format</description> <command interpreter="python">lav_to_bed.py $lav_file $bed_file1 $bed_file2</command> <inputs> <param name="lav_file" type="data" format="lav" label="LAV File" optional="False"/> @@ -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 @@ } #:eof
-- To two BED formated files:: +- To two BED formatted files::
chr19 3001011 3001075 hg16_0 0 + chr19 3008278 3008357 hg16_1 0 + diff -r f7459ad62be9 -r d669408018a1 tools/filters/pasteWrapper.xml --- a/tools/filters/pasteWrapper.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/filters/pasteWrapper.xml Sun Sep 27 23:11:43 2009 -0400 @@ -33,7 +33,7 @@
.. class:: infomark
-Paste preserves column assignments of the first dataset +Paste preserves column assignments of the first dataset.
-----
diff -r f7459ad62be9 -r d669408018a1 tools/filters/remove_beginning.xml --- a/tools/filters/remove_beginning.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/filters/remove_beginning.xml Sun Sep 27 23:11:43 2009 -0400 @@ -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.
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diff -r f7459ad62be9 -r d669408018a1 tools/hyphy/hyphy_dnds_wrapper.xml --- a/tools/hyphy/hyphy_dnds_wrapper.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/hyphy/hyphy_dnds_wrapper.xml Sun Sep 27 23:11:43 2009 -0400 @@ -47,7 +47,7 @@
-----
-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 -r f7459ad62be9 -r d669408018a1 tools/hyphy/hyphy_nj_tree_wrapper.xml --- a/tools/hyphy/hyphy_nj_tree_wrapper.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/hyphy/hyphy_nj_tree_wrapper.xml Sun Sep 27 23:11:43 2009 -0400 @@ -16,7 +16,7 @@ <option value="K2P">Kimura 2 parameter</option> <option value="JC69">Jukes-Cantor</option> <!-- <option value="T3P">Tamura 3-parameter (correction for GC content bias and transition/trasversion bias)</option> --> - <!-- <option value="p_Distance">Number of observed substituions per site</option> --> + <!-- <option value="p_Distance">Number of observed substitutions per site</option> --> <!-- <option value="Unaligned_LZ">Distance measure for unaligned sequences based on Lempel Ziv measure of information content</option> --> <!-- <option value="Unaligned_LZ_FR">Distance measure for unaligned sequences based on Lempel Ziv measure of information content using the best choice forward and reverse string orientations</option> --> </param> diff -r f7459ad62be9 -r d669408018a1 tools/maf/genebed_maf_to_fasta.xml --- a/tools/maf/genebed_maf_to_fasta.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/maf/genebed_maf_to_fasta.xml Sun Sep 27 23:11:43 2009 -0400 @@ -48,10 +48,10 @@ </param> </when> </conditional> - <param name="overwrite_with_gaps" type="select" label="Split into Gapless MAF blocks" help="When set to Yes, blocks are divided around gaps appearing in any species. This will prevent gaps occuring in the interior of the sequence for an aligning species from overwriting a nucleotide found for the same position in a lower-scoring block."> + <param name="overwrite_with_gaps" type="select" label="Split into Gapless MAF blocks" help="When set to Yes, blocks are divided around gaps appearing in any species. This will prevent gaps occurring in the interior of the sequence for an aligning species from overwriting a nucleotide found for the same position in a lower-scoring block."> <option value="True" selected="true">No</option> <option value="False">Yes</option> - </param> + </param> </inputs> <outputs> <data format="fasta" name="out_file1" /> @@ -61,7 +61,7 @@ <param name="input1" value="8.bed"/> <param name="maf_source" value="cached"/>in aligning species <param name="maf_identifier" value="8_WAY_MULTIZ_hg17"/> - <param name="species" value="canFam1,hg17,mm5,panTro1,rn3"/> + <param name="species" value="canFam1,hg17,mm5,panTro1,rn3"/> <param name="overwrite_with_gaps" value="True"/> <output name="out_file1" file="gene_bed_maf_to_fasta_out.fasta" /> </test> @@ -69,7 +69,7 @@ <param name="input1" value="8.bed"/> <param name="maf_source" value="user"/> <param name="maf_file" value="4.maf"/> - <param name="species" value="hg17,panTro1"/> + <param name="species" value="hg17,panTro1"/> <param name="overwrite_with_gaps" value="True"/> <output name="out_file1" file="gene_bed_maf_to_fasta_user_out.fasta" /> </test> diff -r f7459ad62be9 -r d669408018a1 tools/maf/interval_maf_to_merged_fasta.xml --- a/tools/maf/interval_maf_to_merged_fasta.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/maf/interval_maf_to_merged_fasta.xml Sun Sep 27 23:11:43 2009 -0400 @@ -49,10 +49,10 @@ </param> </when> </conditional> - <param name="overwrite_with_gaps" type="select" label="Split into Gapless MAF blocks" help="When set to Yes, blocks are divided around gaps appearing in any species. This will prevent gaps occuring in the interior of the sequence for an aligning species from overwriting a nucleotide found for the same position in a lower-scoring block."> + <param name="overwrite_with_gaps" type="select" label="Split into Gapless MAF blocks" help="When set to Yes, blocks are divided around gaps appearing in any species. This will prevent gaps occurring in the interior of the sequence for an aligning species from overwriting a nucleotide found for the same position in a lower-scoring block."> <option value="True" selected="true">No</option> <option value="False">Yes</option> - </param> + </param> </page> </inputs> <outputs> @@ -63,7 +63,7 @@ <param name="input1" value="13.bed" dbkey="hg18" ftype="bed"/> <param name="maf_source" value="cached"/> <param name="maf_identifier" value="17_WAY_MULTIZ_hg18"/> - <param name="species" value="hg18,mm8"/> + <param name="species" value="hg18,mm8"/> <param name="overwrite_with_gaps" value="True"/> <output name="out_file1" file="interval_maf_to_merged_fasta_out3.fasta" /> </test> @@ -71,7 +71,7 @@ <param name="input1" value="1.bed" dbkey="hg17" ftype="bed"/> <param name="maf_source" value="cached"/> <param name="maf_identifier" value="8_WAY_MULTIZ_hg17"/> - <param name="species" value="canFam1,hg17,mm5,panTro1,rn3"/> + <param name="species" value="canFam1,hg17,mm5,panTro1,rn3"/> <param name="overwrite_with_gaps" value="True"/> <output name="out_file1" file="interval_maf_to_merged_fasta_out.dat" /> </test> @@ -79,7 +79,7 @@ <param name="input1" value="1.bed" dbkey="hg17" ftype="bed"/> <param name="maf_source" value="user"/> <param name="maf_file" value="5.maf"/> - <param name="species" value="canFam1,hg17,mm5,panTro1,rn3"/> + <param name="species" value="canFam1,hg17,mm5,panTro1,rn3"/> <param name="overwrite_with_gaps" value="True"/> <output name="out_file1" file="interval_maf_to_merged_fasta_user_out.dat" /> </test> diff -r f7459ad62be9 -r d669408018a1 tools/maf/maf_to_bed.xml --- a/tools/maf/maf_to_bed.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/maf/maf_to_bed.xml Sun Sep 27 23:11:43 2009 -0400 @@ -36,12 +36,12 @@ * **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 -r f7459ad62be9 -r d669408018a1 tools/maf/maf_to_fasta.xml --- a/tools/maf/maf_to_fasta.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/maf/maf_to_fasta.xml Sun Sep 27 23:11:43 2009 -0400 @@ -71,7 +71,7 @@ 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 -r f7459ad62be9 -r d669408018a1 tools/maf/maf_to_interval.xml --- a/tools/maf/maf_to_interval.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/maf/maf_to_interval.xml Sun Sep 27 23:11:43 2009 -0400 @@ -1,5 +1,5 @@ <tool id="MAF_To_Interval1" name="MAF to Interval" force_history_refresh="True"> - <description>Converts a MAF formated file to the Interval format</description> + <description>Converts a MAF formatted file to the Interval format</description> <command interpreter="python">maf_to_interval.py $input1 $out_file1 $out_file1.id $__new_file_path__ $input1.dbkey $species $input1.metadata.species $complete_blocks $remove_gaps</command> <inputs> <param format="maf" name="input1" type="data" label="MAF file to convert"/> diff -r f7459ad62be9 -r d669408018a1 tools/metag_tools/blat_wrapper.xml --- a/tools/metag_tools/blat_wrapper.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/metag_tools/blat_wrapper.xml Sun Sep 27 23:11:43 2009 -0400 @@ -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 @@ >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 -r f7459ad62be9 -r d669408018a1 tools/metag_tools/convert_SOLiD_color2nuc.xml --- a/tools/metag_tools/convert_SOLiD_color2nuc.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/metag_tools/convert_SOLiD_color2nuc.xml Sun Sep 27 23:11:43 2009 -0400 @@ -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 -r f7459ad62be9 -r d669408018a1 tools/metag_tools/mapping_to_ucsc.xml --- a/tools/metag_tools/mapping_to_ucsc.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/metag_tools/mapping_to_ucsc.xml Sun Sep 27 23:11:43 2009 -0400 @@ -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 -r f7459ad62be9 -r d669408018a1 tools/metag_tools/megablast_xml_parser.xml --- a/tools/metag_tools/megablast_xml_parser.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/metag_tools/megablast_xml_parser.xml Sun Sep 27 23:11:43 2009 -0400 @@ -26,13 +26,13 @@ **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 -r f7459ad62be9 -r d669408018a1 tools/metag_tools/short_reads_figure_high_quality_length.xml --- a/tools/metag_tools/short_reads_figure_high_quality_length.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/metag_tools/short_reads_figure_high_quality_length.xml Sun Sep 27 23:11:43 2009 -0400 @@ -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 @@ >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 -r f7459ad62be9 -r d669408018a1 tools/metag_tools/short_reads_figure_score.xml --- a/tools/metag_tools/short_reads_figure_score.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/metag_tools/short_reads_figure_score.xml Sun Sep 27 23:11:43 2009 -0400 @@ -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 @@
.. 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 -r f7459ad62be9 -r d669408018a1 tools/metag_tools/short_reads_trim_seq.xml --- a/tools/metag_tools/short_reads_trim_seq.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/metag_tools/short_reads_trim_seq.xml Sun Sep 27 23:11:43 2009 -0400 @@ -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 -r f7459ad62be9 -r d669408018a1 tools/metag_tools/shrimp_color_wrapper.xml --- a/tools/metag_tools/shrimp_color_wrapper.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/metag_tools/shrimp_color_wrapper.xml Sun Sep 27 23:11:43 2009 -0400 @@ -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 @@ -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 -r f7459ad62be9 -r d669408018a1 tools/metag_tools/shrimp_wrapper.xml --- a/tools/metag_tools/shrimp_wrapper.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/metag_tools/shrimp_wrapper.xml Sun Sep 27 23:11:43 2009 -0400 @@ -219,7 +219,7 @@ 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 @@ -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.
-----