From a947686b77286cf4a549237a114e55de1e527613 Mon Sep 17 00:00:00 2001 From: Kanwei Li Date: Fri, 25 Sep 2009 02:06:03 -0400 Subject: [PATCH] fix some typos for tools in folders N-Z --- tools/new_operations/basecoverage.xml | 2 +- tools/new_operations/cluster.xml | 2 +- tools/new_operations/complement.xml | 2 +- tools/new_operations/concat.xml | 2 +- tools/new_operations/coverage.xml | 2 +- tools/new_operations/get_flanks.xml | 2 +- tools/new_operations/intersect.xml | 32 +++++++++---------- tools/new_operations/join.xml | 4 +-- tools/new_operations/merge.xml | 4 +-- tools/new_operations/subtract.xml | 2 +- .../microsats_alignment_level.xml | 4 +-- tools/regVariation/quality_filter.xml | 4 +-- tools/regVariation/substitution_rates.xml | 2 +- tools/samtools/pileup_parser.xml | 31 +++++++++--------- tools/samtools/sam2interval.xml | 2 +- tools/samtools/sam_bitwise_flag_filter.xml | 8 ++--- tools/samtools/sam_pileup.xml | 4 +-- tools/samtools/sam_to_bam.xml | 2 +- tools/solid_tools/maq_cs_wrapper.xml | 2 +- tools/solid_tools/solid_qual_boxplot.xml | 2 +- tools/sr_mapping/bowtie_wrapper.xml | 2 +- tools/sr_mapping/bwa_wrapper.xml | 4 +-- tools/sr_mapping/fastq_statistics.xml | 2 +- tools/sr_mapping/lastz_wrapper.xml | 24 +++++++------- .../aggregate_binned_scores_in_intervals.xml | 2 +- tools/stats/filtering.xml | 2 +- tools/stats/gsummary.xml | 4 +-- tools/stats/wiggle_to_simple.xml | 2 +- tools/taxonomy/find_diag_hits.xml | 4 +-- tools/taxonomy/gi2taxonomy.xml | 2 +- tools/taxonomy/t2ps_wrapper.xml | 2 +- tools/taxonomy/t2t_report.xml | 28 +++++++++++++--- tools/visualization/LAJ.xml | 2 +- tools/visualization/genetrack.xml | 4 +-- 34 files changed, 109 insertions(+), 90 deletions(-) diff --git a/tools/new_operations/basecoverage.xml b/tools/new_operations/basecoverage.xml index 91e68089097..4c95e2b10e7 100644 --- a/tools/new_operations/basecoverage.xml +++ b/tools/new_operations/basecoverage.xml @@ -24,7 +24,7 @@ .. class:: infomark -**TIP:** If your query does not appear in the pulldown menu -> it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns +**TIP:** If your query does not appear in the pulldown menu, it means that it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns. This operation counts the total bases covered by a set of intervals. Bases that are covered by more than one interval are **not** counted more than once towards the total. diff --git a/tools/new_operations/cluster.xml b/tools/new_operations/cluster.xml index a902ad66a31..44cca89c7f6 100644 --- a/tools/new_operations/cluster.xml +++ b/tools/new_operations/cluster.xml @@ -59,7 +59,7 @@ .. class:: infomark -**TIP:** If your query does not appear in the pulldown menu -> it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns +**TIP:** If your query does not appear in the pulldown menu, it means that it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns. ----- diff --git a/tools/new_operations/complement.xml b/tools/new_operations/complement.xml index 4b318fb9787..680720531ee 100644 --- a/tools/new_operations/complement.xml +++ b/tools/new_operations/complement.xml @@ -33,7 +33,7 @@ .. class:: infomark -**TIP:** If your query does not appear in the pulldown menu -> it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns +**TIP:** If your query does not appear in the pulldown menu, it means that it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns. This operation complements the regions of a set of intervals. Regions are returned that represent the empty space in the input interval. diff --git a/tools/new_operations/concat.xml b/tools/new_operations/concat.xml index 1996f516c7f..6e417f3c350 100644 --- a/tools/new_operations/concat.xml +++ b/tools/new_operations/concat.xml @@ -27,7 +27,7 @@ .. class:: infomark -**TIP:** If your query does not appear in the pulldown menu -> it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns +**TIP:** If your query does not appear in the pulldown menu -> it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns. ----- diff --git a/tools/new_operations/coverage.xml b/tools/new_operations/coverage.xml index 979db1e6533..7b0cbaa7470 100644 --- a/tools/new_operations/coverage.xml +++ b/tools/new_operations/coverage.xml @@ -34,7 +34,7 @@ .. class:: infomark -**TIP:** If your query does not appear in the pulldown menu -> it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns +**TIP:** If your query does not appear in the pulldown menu -> it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns. Find the coverage of intervals in the first query on intervals in the second query. The coverage is added as two columns, the first being bases covered, and the second being the fraction of bases covered by that interval. diff --git a/tools/new_operations/get_flanks.xml b/tools/new_operations/get_flanks.xml index eb76d2d31c9..0a0ed359363 100644 --- a/tools/new_operations/get_flanks.xml +++ b/tools/new_operations/get_flanks.xml @@ -41,7 +41,7 @@ -This tool finds the upstream and/or downstream flanking region/s of all the selected regions in the input file. +This tool finds the upstream and/or downstream flanking region(s) of all the selected regions in the input file. **Note:** Every line should contain at least 3 columns: Chromosome number, Start and Stop co-ordinates. If any of these columns is missing or if start and stop co-ordinates are not numerical, the tool may encounter exceptions and such lines are skipped as invalid. The number of invalid skipped lines is documented in the resulting history item as a "Data issue". diff --git a/tools/new_operations/intersect.xml b/tools/new_operations/intersect.xml index 5a755548a42..5a4f660745f 100644 --- a/tools/new_operations/intersect.xml +++ b/tools/new_operations/intersect.xml @@ -21,27 +21,27 @@ - - - - - - - + + + + + + + - + - - - - - - - + + + + + + + @@ -76,7 +76,7 @@ .. class:: infomark -**TIP:** If your query does not appear in the pulldown menu -> it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns +**TIP:** If your query does not appear in the pulldown menu, it means that it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns. ----- diff --git a/tools/new_operations/join.xml b/tools/new_operations/join.xml index ae09d307a05..094fb33d618 100644 --- a/tools/new_operations/join.xml +++ b/tools/new_operations/join.xml @@ -70,7 +70,7 @@ .. class:: infomark -**TIP:** If your query does not appear in the pulldown menu -> it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns +**TIP:** If your query does not appear in the pulldown menu, it means that it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns. ----- @@ -85,7 +85,7 @@ See Galaxy Interval Operation Screencasts_ (right click to open this link in ano **Syntax** - **Where overlap** specifies the minimum overlap between intervals that allows them to be joined. -- **Return only records that are joined** returns only the records of the first query that join to a recond in the second query. This is analogous to an INNER JOIN. +- **Return only records that are joined** returns only the records of the first query that join to a record in the second query. This is analogous to an INNER JOIN. - **Return all records of first query (fill null with ".")** returns all intervals of the first query, and any intervals that do not join an interval from the second query are filled in with a period(.). This is analogous to a LEFT JOIN. - **Return all records of second query (fill null with ".")** returns all intervals of the second query, and any intervals that do not join an interval from the first query are filled in with a period(.). **Note that this may produce an invalid interval file, since a period(.) is not a valid chrom, start, end or strand.** - **Return all records of both queries (fill nulls with ".")** returns all records from both queries, and fills on either the right or left with periods. **Note that this may produce an invalid interval file, since a period(.) is not a valid chrom, start, end or strand.** diff --git a/tools/new_operations/merge.xml b/tools/new_operations/merge.xml index c0118db9d25..39a01f43a77 100644 --- a/tools/new_operations/merge.xml +++ b/tools/new_operations/merge.xml @@ -36,7 +36,7 @@ .. class:: infomark -**TIP:** If your query does not appear in the pulldown menu -> it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns +**TIP:** If your query does not appear in the pulldown menu, it means that it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns. ----- @@ -48,7 +48,7 @@ See Galaxy Interval Operation Screencasts_ (right click to open this link in ano ----- -This operation merges all overlaping intervals into single intervals. +This operation merges all overlapping intervals into single intervals. **Example** diff --git a/tools/new_operations/subtract.xml b/tools/new_operations/subtract.xml index 2a58e1654ee..acba9181dca 100644 --- a/tools/new_operations/subtract.xml +++ b/tools/new_operations/subtract.xml @@ -58,7 +58,7 @@ .. class:: infomark -**TIP:** If your query does not appear in the pulldown menu -> it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns +**TIP:** If your query does not appear in the pulldown menu, it means that it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns. ----- diff --git a/tools/regVariation/microsats_alignment_level.xml b/tools/regVariation/microsats_alignment_level.xml index d5f94aaa0c3..92f913938f8 100644 --- a/tools/regVariation/microsats_alignment_level.xml +++ b/tools/regVariation/microsats_alignment_level.xml @@ -6,8 +6,8 @@ - + -**What is does** +**What it does** -Allows to find sequence variants and/or sites covered by specified number of reads with bases above a set quality threshold. The tool works on six and ten column pileup formats produced with *samtools pileup* command. However, it also allows you to specify columns in the input file manually. The tool assumes the following: +Allows one to find sequence variants and/or sites covered by a specified number of reads with bases above a set quality threshold. The tool works on six and ten column pileup formats produced with *samtools pileup* command. However, it also allows you to specify columns in the input file manually. The tool assumes the following: - the quality scores follow phred33 convention, where input qualities are ASCII characters equal to the Phred quality plus 33. -- the pileup dataset was produced by *samtools pileup* command (although you can override this by setting column assignments manually). +- the pileup dataset was produced by the *samtools pileup* command (although you can override this by setting column assignments manually). -------- **Types of pileup datasets** -The description of pileup format below is largely based on information that can be found on SAMTools_ documentation page. The 6- and 10-column variants are described below. +The descriptions of the following pileup formats are largely based on information that can be found on the SAMTools_ documentation page. The 6- and 10-column variants are described below. .. _SAMTools: http://samtools.sourceforge.net/pileup.shtml @@ -136,7 +136,7 @@ where:: **Ten column pileup** -The `ten-column`__ pileup incoroporates additional consensus information generated with *-c* option of *samtools pileup* command:: +The `ten-column`__ pileup incorporates additional consensus information generated with the *-c* option of the *samtools pileup* command:: 1 2 3 4 5 6 7 8 9 10 @@ -187,7 +187,7 @@ For example, if you are calling variants with base quality above 20 on this data chrM 414 C 4 ...a III2 chrM 415 C 4 TTTt III7 -you will get this:: +you will get:: chrM 413 G 4 ..t, IIIH 0 0 0 1 3 chrM 415 C 4 TTTt III7 0 0 0 4 4 @@ -232,26 +232,26 @@ where:: 12 Quality adjusted coverage -Note that in this case coordinates of SNPs were converted to intervals, where the start coordinate is 0-based and the end coordinate in 1-based using the UCSC Table Browser convention. +Note that in this case the coordinates of SNPs were converted to intervals, where the start coordinate is 0-based and the end coordinate in 1-based using the UCSC Table Browser convention. -Although three positions have variants in the original file (413, 414, and 415), only 413 and 415 are reported, because the quality values associated with these two SNPs are above threshold of 20. In the case of 414 the **a** allele has quality value of 17 ( ord("2")-33 ), and therefore it is not reported. In each of the reported lines the program added five columns. Let's take a look at this line:: +Although three positions have variants in the original file (413, 414, and 415), only 413 and 415 are reported because the quality values associated with these two SNPs are above the threshold of 20. In the case of 414 the **a** allele has a quality value of 17 ( ord("2")-33 ), and is therefore not reported. Note that five columns have been added to each of the reported lines:: chrM 413 G 4 ..t, IIIH 0 0 0 1 3 -here there is one variant, and it is a **t**. Because the fourth column represents **T** counts, it is incremented by 1. The last column shows that at this position three reads has bases above the quality threshold of 20. +Here, there is one variant, **t**. Because the fourth column represents **T** counts, it is incremented by 1. The last column shows that at this position, three reads have bases above the quality threshold of 20. ----- **Example 1**: Just variants -In this mode the tool outputs only those lines from the input datasets where at least one read contains a sequence variant with quality above the limit set by the **Do not consider read bases with quality lower than** option. For example, suppose one has a pileup dataset like this:: +In this mode, the tool only outputs the lines from the input datasets where at least one read contains a sequence variant with quality above the threshold set by the **Do not consider read bases with quality lower than** option. For example, suppose one has a pileup dataset like the following:: chrM 412 A 2 ., II chrM 413 G 4 ..t, III2 chrM 414 C 4 ...a III2 chrM 415 C 4 TTTt III7 -to call all variants (with no restriction by coverage) with quality above phred value of 20 we will need to set parameters as follows: +To call all variants (with no restriction by coverage) with quality above phred value of 20, we will need to set the parameters as follows: .. image:: ../static/images/pileup_parser_help1.png @@ -260,13 +260,13 @@ Running the tool with these parameters will return:: chrM 413 G 4 ..t, IIIH 0 0 0 1 3 chrM 415 C 4 TTTt III7 0 0 0 4 4 -**Note** that position 414 is not reported because the *a* variant has associated quality value of 17 (because ord('2')-33 = 17) in is below the phred threshold 20 set by the **Count variants with quality above this value** parameter. +**Note** that position 414 is not reported because the *a* variant has associated quality value of 17 (because ord('2')-33 = 17) and is below the phred threshold of 20 set by the **Count variants with quality above this value** parameter. ----- **Example 2**: Report everything -In addition to calling variants it is often useful to know the quality adjusted coverage. Running the tool with these parameters: +In addition to calling variants, it is often useful to know the quality adjusted coverage. Running the tool with these parameters: .. image:: ../static/images/pileup_parser_help2.png @@ -277,10 +277,9 @@ will report everything from the original file:: chrM 414 C 4 ...a III2 0 0 0 0 3 chrM 415 C 4 TTTt III7 0 0 0 4 4 -Here, for instance, you can see that although the total coverage at position 414 is 4 (column 4) the quality adjusted coverage is 3 (last column). This is because inly three reads out of four have bases with quality above the set threshold of 20 (the actual qualities are III2 or, after conversion, 40, 40, 40, 17). - -Now, one can use the last column of this dataset to filter out (using Galaxy's filter tool) positions where quality adjusted coverage (last column) is below a set threshold. +Here, you can see that although the total coverage at position 414 is 4 (column 4), the quality adjusted coverage is 3 (last column). This is because only three out of four reads have bases with quality above the set threshold of 20 (the actual qualities are III2 or, after conversion, 40, 40, 40, 17). +One can use the last column of this dataset to filter out (using Galaxy's **Filter** tool) positions where quality adjusted coverage (last column) is below a set threshold. diff --git a/tools/samtools/sam2interval.xml b/tools/samtools/sam2interval.xml index 682beab2059..7d2660d50c9 100644 --- a/tools/samtools/sam2interval.xml +++ b/tools/samtools/sam2interval.xml @@ -31,7 +31,7 @@ **What it does** -Converts positional information from a SAM dataset into interval format with 0-based start and 1-based end. CIGAR string of SAM format is usd to compute the end coordinate. +Converts positional information from a SAM dataset into interval format with 0-based start and 1-based end. CIGAR string of SAM format is used to compute the end coordinate. ----- diff --git a/tools/samtools/sam_bitwise_flag_filter.xml b/tools/samtools/sam_bitwise_flag_filter.xml index e432443ee61..d09116da060 100644 --- a/tools/samtools/sam_bitwise_flag_filter.xml +++ b/tools/samtools/sam_bitwise_flag_filter.xml @@ -46,7 +46,7 @@ **What it does** -Allows parsing SAM datasets using bitwise flag (the second column). The bits in the flag are defined as follows:: +Allows parsing of SAM datasets using bitwise flag (the second column). The bits in the flag are defined as follows:: Bit Info ------ -------------------------------------------------------------------------- @@ -67,7 +67,7 @@ Allows parsing SAM datasets using bitwise flag (the second column). The bits in Note the following: - Flag 0x02, 0x08, 0x20, 0x40 and 0x80 are only meaningful when flag 0x01 is present. -- If in a read pair the information on which read is the first in the pair is lost in the upstream analysis, flag 0x01 should be present and 0x40 and 0x80 are both zero. +- If in a read pair the information on which read is the first in the pair is lost in the upstream analysis, flag 0x01 should be set, while 0x40 and 0x80 should both be zero. ----- @@ -82,12 +82,12 @@ Suppose the following dataset was generated with BWA mapper:: r003 16 ref 29 30 6H5M * 0 0 TAGGC * NM:i:0 r001 83 ref 37 30 9M = 7 -39 CAGCGCCAT * -To select properly mapped pairs click the **Add new Flag** button and set *Read mapped in a proper pair* to **Yes**. The following two reads will be returned:: +To select properly mapped pairs, click the **Add new Flag** button and set *Read mapped in a proper pair* to **Yes**. The following two reads will be returned:: r001 163 ref 7 30 8M2I4M1D3M = 37 39 TTAGATAAAGGATACTA * r001 83 ref 37 30 9M = 7 -39 CAGCGCCAT * -For more information please consult the `SAM format description`__. +For more information, please consult the `SAM format description`__. .. __: http://www.ncbi.nlm.nih.gov/pubmed/19505943 diff --git a/tools/samtools/sam_pileup.xml b/tools/samtools/sam_pileup.xml index 668834ed4ca..e4bd9ed2101 100644 --- a/tools/samtools/sam_pileup.xml +++ b/tools/samtools/sam_pileup.xml @@ -77,7 +77,7 @@ **What it does** -Uses SAMTools_' pileup command to produce a pileup dataset from a provided BAM dataset. It generated two types of pileup datasets depending on chosen options. If *Call consensus according to MAQ model?* option is set to **No**, the tool produces simple pileup. If the option is set to **Yes**, a ten column pileup dataset with consensus is generated. Both types of datasets are briefly summarized below. +Uses SAMTools_' pileup command to produce a pileup dataset from a provided BAM dataset. It generates two types of pileup datasets depending on the specified options. If *Call consensus according to MAQ model?* option is set to **No**, the tool produces simple pileup. If the option is set to **Yes**, a ten column pileup dataset with consensus is generated. Both types of datasets are briefly summarized below. .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml @@ -111,7 +111,7 @@ where:: **Ten column pileup** -The `ten-column`__ pileup incoroporates additional consensus information generated with *-c* option of *samtools pileup* command:: +The `ten-column`__ pileup incorporates additional consensus information generated with *-c* option of *samtools pileup* command:: 1 2 3 4 5 6 7 8 9 10 diff --git a/tools/samtools/sam_to_bam.xml b/tools/samtools/sam_to_bam.xml index 99cd40b98d6..ed977074c7c 100644 --- a/tools/samtools/sam_to_bam.xml +++ b/tools/samtools/sam_to_bam.xml @@ -51,7 +51,7 @@ **What it does** -This tool uses the SAMTools_ toolkit to produce a indexed BAM file based on a sorted input SAM file. +This tool uses the SAMTools_ toolkit to produce an indexed BAM file based on a sorted input SAM file. .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml diff --git a/tools/solid_tools/maq_cs_wrapper.xml b/tools/solid_tools/maq_cs_wrapper.xml index 03fa50d83d4..8fe3fb7e68e 100644 --- a/tools/solid_tools/maq_cs_wrapper.xml +++ b/tools/solid_tools/maq_cs_wrapper.xml @@ -71,7 +71,7 @@ **What it does** -This tool maps SOLiD colour-space reads against the target genome using MAQ. It produces three output datasets: +This tool maps SOLiD color-space reads against the target genome using MAQ. It produces three output datasets: **ALIGNMENT INFO** : contains the read alignment information, diff --git a/tools/solid_tools/solid_qual_boxplot.xml b/tools/solid_tools/solid_qual_boxplot.xml index c208de6bb62..8fc5dabcd74 100644 --- a/tools/solid_tools/solid_qual_boxplot.xml +++ b/tools/solid_tools/solid_qual_boxplot.xml @@ -26,7 +26,7 @@ Creates a boxplot graph for the quality scores in the library. * Black horizontal lines are medians * Rectangular red boxes show the Inter-quartile Range (IQR) (top value is Q3, bottom value is Q1) -* Whiskers show outlier at max. 1.5*IQR +* Whiskers show outliers at max. 1.5*IQR .. image:: ../static/images/solid_qual.png diff --git a/tools/sr_mapping/bowtie_wrapper.xml b/tools/sr_mapping/bowtie_wrapper.xml index 165c606c14b..acbc1c7719e 100644 --- a/tools/sr_mapping/bowtie_wrapper.xml +++ b/tools/sr_mapping/bowtie_wrapper.xml @@ -181,7 +181,7 @@ - + diff --git a/tools/sr_mapping/bwa_wrapper.xml b/tools/sr_mapping/bwa_wrapper.xml index 42754a4e597..ccfb55bb26b 100644 --- a/tools/sr_mapping/bwa_wrapper.xml +++ b/tools/sr_mapping/bwa_wrapper.xml @@ -141,7 +141,7 @@ - + @@ -293,7 +293,7 @@ **What it does** -**BWA** is a high performance sequence aligner that succeeds MAQ. It is based on BWT-SW but uses a completely different algorithm, and it is aimed toward short read alignments. It is fast--it can map the human genome in only 15-25 minutes. Heng Li of the Sanger Institute wrote the majority of the code, with contributions by Chi-Kwong Wong at the University of Hong Kong, Nong Ge at Sun Yat-Sen University, and Yuta Mori. +**BWA** is a high performance sequence aligner that succeeds MAQ. It is based on BWT-SW but uses a completely different algorithm and is aimed towards short read alignments. It is fast--it can map the human genome in only 15-25 minutes. Heng Li of the Sanger Institute wrote the majority of the code, with contributions by Chi-Kwong Wong at the University of Hong Kong, Nong Ge at Sun Yat-Sen University, and Yuta Mori. ------ diff --git a/tools/sr_mapping/fastq_statistics.xml b/tools/sr_mapping/fastq_statistics.xml index 9b82bd0db51..6c87fee6441 100755 --- a/tools/sr_mapping/fastq_statistics.xml +++ b/tools/sr_mapping/fastq_statistics.xml @@ -2,7 +2,7 @@ for Solexa file cat $input | solexa_quality_statistics -o $output - + diff --git a/tools/sr_mapping/lastz_wrapper.xml b/tools/sr_mapping/lastz_wrapper.xml index 48e0eec12ea..4efba932afd 100644 --- a/tools/sr_mapping/lastz_wrapper.xml +++ b/tools/sr_mapping/lastz_wrapper.xml @@ -76,20 +76,20 @@ - + - + lastz - - - + + + @@ -98,10 +98,10 @@ - + - - + + @@ -111,18 +111,18 @@ - + - + **What it does** -**LASTZ** is a high perfomance pairwise sequence aligner derived from BLASTZ. It is written by Bob Harris in Webb Miller's laboratory at Penn State. Special scoring sets were derived to improve the performance, both in runtime and quality. The Galaxy version of LASTZ is geared towards aligning of short (Illumina/Solexa, AB/SOLiD) and medium (Roche/454) reads against a reference sequence. +**LASTZ** is a high performance pairwise sequence aligner derived from BLASTZ. It is written by Bob Harris in Webb Miller's laboratory at Penn State. Special scoring sets were derived to improve runtime performance and quality. The Galaxy version of LASTZ is geared towards aligning of short (Illumina/Solexa, AB/SOLiD) and medium (Roche/454) reads against a reference sequence. .. class:: warningmark -At present this tools supports aligning reads against a single reference sequence no longer than 1 Megabase. This limitation will be lifted in the coming months as our short read analysis hardware capacity is expanding. +This tool presently supports aligning reads against a single reference sequence no longer than 1 Megabase. This limitation will be lifted in the coming months as our short read analysis hardware capacity expands. ------ diff --git a/tools/stats/aggregate_binned_scores_in_intervals.xml b/tools/stats/aggregate_binned_scores_in_intervals.xml index 14535ae3189..8faef96ce0b 100644 --- a/tools/stats/aggregate_binned_scores_in_intervals.xml +++ b/tools/stats/aggregate_binned_scores_in_intervals.xml @@ -62,7 +62,7 @@ .. class:: warningmark -This tool currently only has cached data for genome builds hg16, hg17 and hg18. However, you may use your own data point (wiggle) data, such as is available from UCSC. If you are trying to use your own data point file and it is not appearing as an option, make sure that the builds for your history items are the same. +This tool currently only has cached data for genome builds hg16, hg17 and hg18. However, you may use your own data point (wiggle) data, such as those available from UCSC. If you are trying to use your own data point file and it is not appearing as an option, make sure that the builds for your history items are the same. .. class:: warningmark diff --git a/tools/stats/filtering.xml b/tools/stats/filtering.xml index 22d3de76460..b33f72c1e9d 100644 --- a/tools/stats/filtering.xml +++ b/tools/stats/filtering.xml @@ -42,7 +42,7 @@ Double equal signs, ==, must be used as *"equal to"* (e.g., **c1 == 'chr22'**) **Syntax** -The filter tool allows you to restrict the datset using simple conditional statements +The filter tool allows you to restrict the dataset using simple conditional statements. - Columns are referenced with **c** and a **number**. For example, **c1** refers to the first column of a tab-delimited file - Make sure that multi-character operators contain no white space ( e.g., **<=** is valid while **< =** is not valid ) diff --git a/tools/stats/gsummary.xml b/tools/stats/gsummary.xml index e30e79cf395..1074b0ede78 100644 --- a/tools/stats/gsummary.xml +++ b/tools/stats/gsummary.xml @@ -24,7 +24,7 @@ .. class:: warningmark -This tool expects input datasets to consist of tab-delimited columns (blank or comment lines beginning with a # character are automatically skipped). +This tool expects input datasets consisting of tab-delimited columns (blank or comment lines beginning with a # character are automatically skipped). .. class:: infomark @@ -48,7 +48,7 @@ This tool computes basic summary statistics on a given column, or on a valid exp - Columns are referenced with **c** and a **number**. For example, **c1** refers to the first column of a tab-delimited file. -- Examples of expressions: +- For example: - **log(c5)** calculates the summary statistics for the natural log of column 5 - **(c5 + c6 + c7) / 3** calculates the summary statistics on the average of columns 5-7 diff --git a/tools/stats/wiggle_to_simple.xml b/tools/stats/wiggle_to_simple.xml index fe0d07a68c9..de881574f0f 100644 --- a/tools/stats/wiggle_to_simple.xml +++ b/tools/stats/wiggle_to_simple.xml @@ -18,7 +18,7 @@ This tool converts wiggle data into interval type. -- **Wiggle format**: The .wig format is line-oriented. Wiggle data is preceeded by a UCSC track definition line. Following the track definition line is the track data, which can be entered in three different formats described below. +- **Wiggle format**: The .wig format is line-oriented. Wiggle data is preceded by a UCSC track definition line. Following the track definition line is the track data, which can be entered in three different formats described below. - **BED format** with no declaration line and four columns of data:: diff --git a/tools/taxonomy/find_diag_hits.xml b/tools/taxonomy/find_diag_hits.xml index ca559f10115..fd0da7edce2 100644 --- a/tools/taxonomy/find_diag_hits.xml +++ b/tools/taxonomy/find_diag_hits.xml @@ -67,7 +67,7 @@ Running this tool with the following parameters: * *Select column with sequence id* set to **c1** * *Select taxonomic ranks* with **order**, and **genus** checked - * *Output format* set to **Dignostic read list** + * *Output format* set to **Diagnostic read list** will return:: @@ -89,7 +89,7 @@ Note that **read1** is omitted because it is non-unique: it hits Mammals and Ins .. class:: warningmark -This tool omits "**n**" corresponding to ranks missing from NCBI taxonomy. In the above example *Home sapiens* conatains the order name (Primates) while *Bos taurus* does not. +This tool omits "**n**" corresponding to ranks missing from NCBI taxonomy. In the above example *Home sapiens* contains the order name (Primates) while *Bos taurus* does not. diff --git a/tools/taxonomy/gi2taxonomy.xml b/tools/taxonomy/gi2taxonomy.xml index 0985cd99cb0..35cdbc6c469 100644 --- a/tools/taxonomy/gi2taxonomy.xml +++ b/tools/taxonomy/gi2taxonomy.xml @@ -45,7 +45,7 @@ Suppose you have BLAST output that looks like this:: | 1L_EYKX4VC01BXWX1_265 | 1430919 | 90.09 | 212 | 15 | 6 | 252.00 | +-----------------------+----------+----------+-----------------+------------+------+--------+ -and you want to obtain full taxonomic representation for GIs listed in *targetGI* column. If you set paramenters as shown here: +and you want to obtain full taxonomic representation for GIs listed in *targetGI* column. If you set parameters as shown here: .. image:: ../static/images/fetchTax.png diff --git a/tools/taxonomy/t2ps_wrapper.xml b/tools/taxonomy/t2ps_wrapper.xml index 81b3c67c654..8af421ed517 100644 --- a/tools/taxonomy/t2ps_wrapper.xml +++ b/tools/taxonomy/t2ps_wrapper.xml @@ -108,7 +108,7 @@ Here the tree is automatically trimmed at a taxonomic rank that will only have 3 **Explanation of phylogenetic tree markup** -Branches of the tree are colored according to the heatmap below. The "bluer" the branch the lesser the numer of leaves it leads to and vice versa. +Branches of the tree are colored according to the heatmap below. The "bluer" the branch the lesser the number of leaves it leads to and vice versa. .. image:: ../static/images/t2ps_heatmap.png diff --git a/tools/taxonomy/t2t_report.xml b/tools/taxonomy/t2t_report.xml index 29416bb8a68..2f953fa98bf 100644 --- a/tools/taxonomy/t2t_report.xml +++ b/tools/taxonomy/t2t_report.xml @@ -30,19 +30,39 @@ Given taxonomy representation (produced by *Taxonomy manipulation->Fetch Taxonom Suppose the *Taxonomy manipulation->Fetch Taxonomic Ranks* generated the following taxonomy representation:: - 9916 2 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Laurasiatheria n Ruminantia n Bovidae Bovinae n n Bos n Bos taurus n 9606 12585 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Primates Haplorrhini Hominoidea Hominidae n n n Homo n Homo sapiens n + 9916 2 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Laurasiatheria n Ruminantia n Bovidae Bovinae n n Bos n Bos taurus n + 9606 12585 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Primates Haplorrhini Hominoidea Hominidae n n n Homo n Homo sapiens n Running this tool will generate the following output:: Rank Rank Name Count ------------------------------------- - root root 2 superkingdom Eukaryota 2 kingdom Metazoa 2 phylum Chordata 2 subphylum Craniata 2 superclass Gnathostomata 2 class Mammalia 2 superorder Euarchontoglires 1 superorder Laurasiatheria 1 order Primates 1 suborder Haplorrhini 1 suborder Ruminantia 1 superfamily Hominoidea 1 family Bovidae 1 family Hominidae 1 subfamily Bovinae 1 genus Bos 1 genus Homo 1 species Bos taurus 1 species Homo sapiens 1 + root root 2 + superkingdom Eukaryota 2 + kingdom Metazoa 2 + phylum Chordata 2 + subphylum Craniata 2 + superclass Gnathostomata 2 + class Mammalia 2 + superorder Euarchontoglires 1 + superorder Laurasiatheria 1 + order Primates 1 + suborder Haplorrhini 1 + suborder Ruminantia 1 + superfamily Hominoidea 1 + family Bovidae 1 + family Hominidae 1 + subfamily Bovinae 1 + genus Bos 1 + genus Homo 1 + species Bos taurus 1 + species Homo sapiens 1 -The outoput is sorted on Rank and then on Rank Name. +The output is sorted on Rank and then on Rank Name. .. class:: warningmark -**Note** that this tool omits "**n**" corresponding to ranks missing from NCBI taxonomy. In the above example *Home sapiens* conatains the order name (Primates) while *Bos taurus* does not. +**Note** that this tool omits "**n**" corresponding to ranks missing from NCBI taxonomy. In the above example *Home sapiens* contains the order name (Primates) while *Bos taurus* does not. diff --git a/tools/visualization/LAJ.xml b/tools/visualization/LAJ.xml index 46644c1cb07..972941a5768 100644 --- a/tools/visualization/LAJ.xml +++ b/tools/visualization/LAJ.xml @@ -15,7 +15,7 @@ -You can use this tool to view a set of LAV alignments. You may include FASTA formated sequences for both species. +You can use this tool to view a set of LAV alignments. You may include FASTA formatted sequences for both species. For detailed information on LAJ, click here_. diff --git a/tools/visualization/genetrack.xml b/tools/visualization/genetrack.xml index d48d4999953..d60fd527fe7 100644 --- a/tools/visualization/genetrack.xml +++ b/tools/visualization/genetrack.xml @@ -48,7 +48,7 @@ This tool takes the input Fit Data and creates a peak and curve plot -showing the reads and fitness on each basepair. Features can be +showing the reads and fitness on each base pair. Features can be plotted below as tracks. Fit data is coverage output from tools like the Lastz tool. Features are simply interval datasets that may be plotted as tracks below the optional fit data. Both the fit data and @@ -62,7 +62,7 @@ to generate a track. - **Track Label** is the name of the generated track. - **Fit Data** is the dataset to calculate coverage/reads across - basepairs and generate a curve. This is optional, and tracks may + base pairs and generate a curve. This is optional, and tracks may be created simply showing features. - **Features** are datasets (interval format) to be plotted as tracks.