details: http://www.bx.psu.edu/hg/galaxy/rev/5db45e48f954 changeset: 2773:5db45e48f954 user: Kanwei Li <kanwei@gmail.com> date: Fri Sep 25 02:06:03 2009 -0400 description: fix some typos for tools in folders N-Z 34 file(s) affected in this change: tools/new_operations/basecoverage.xml tools/new_operations/cluster.xml tools/new_operations/complement.xml tools/new_operations/concat.xml tools/new_operations/coverage.xml tools/new_operations/get_flanks.xml tools/new_operations/intersect.xml tools/new_operations/join.xml tools/new_operations/merge.xml tools/new_operations/subtract.xml tools/regVariation/microsats_alignment_level.xml tools/regVariation/quality_filter.xml tools/regVariation/substitution_rates.xml tools/samtools/pileup_parser.xml tools/samtools/sam2interval.xml tools/samtools/sam_bitwise_flag_filter.xml tools/samtools/sam_pileup.xml tools/samtools/sam_to_bam.xml tools/solid_tools/maq_cs_wrapper.xml tools/solid_tools/solid_qual_boxplot.xml tools/sr_mapping/bowtie_wrapper.xml tools/sr_mapping/bwa_wrapper.xml tools/sr_mapping/fastq_statistics.xml tools/sr_mapping/lastz_wrapper.xml tools/stats/aggregate_binned_scores_in_intervals.xml tools/stats/filtering.xml tools/stats/gsummary.xml tools/stats/wiggle_to_simple.xml tools/taxonomy/find_diag_hits.xml tools/taxonomy/gi2taxonomy.xml tools/taxonomy/t2ps_wrapper.xml tools/taxonomy/t2t_report.xml tools/visualization/LAJ.xml tools/visualization/genetrack.xml diffs (744 lines): diff -r 210e048e7ec7 -r 5db45e48f954 tools/new_operations/basecoverage.xml --- a/tools/new_operations/basecoverage.xml Fri Sep 25 00:39:29 2009 -0400 +++ b/tools/new_operations/basecoverage.xml Fri Sep 25 02:06:03 2009 -0400 @@ -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 -r 210e048e7ec7 -r 5db45e48f954 tools/new_operations/cluster.xml --- a/tools/new_operations/cluster.xml Fri Sep 25 00:39:29 2009 -0400 +++ b/tools/new_operations/cluster.xml Fri Sep 25 02:06:03 2009 -0400 @@ -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 -r 210e048e7ec7 -r 5db45e48f954 tools/new_operations/complement.xml --- a/tools/new_operations/complement.xml Fri Sep 25 00:39:29 2009 -0400 +++ b/tools/new_operations/complement.xml Fri Sep 25 02:06:03 2009 -0400 @@ -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 -r 210e048e7ec7 -r 5db45e48f954 tools/new_operations/concat.xml --- a/tools/new_operations/concat.xml Fri Sep 25 00:39:29 2009 -0400 +++ b/tools/new_operations/concat.xml Fri Sep 25 02:06:03 2009 -0400 @@ -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 -r 210e048e7ec7 -r 5db45e48f954 tools/new_operations/coverage.xml --- a/tools/new_operations/coverage.xml Fri Sep 25 00:39:29 2009 -0400 +++ b/tools/new_operations/coverage.xml Fri Sep 25 02:06:03 2009 -0400 @@ -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 -r 210e048e7ec7 -r 5db45e48f954 tools/new_operations/get_flanks.xml --- a/tools/new_operations/get_flanks.xml Fri Sep 25 00:39:29 2009 -0400 +++ b/tools/new_operations/get_flanks.xml Fri Sep 25 02:06:03 2009 -0400 @@ -41,7 +41,7 @@ </tests> <help> -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 -r 210e048e7ec7 -r 5db45e48f954 tools/new_operations/intersect.xml --- a/tools/new_operations/intersect.xml Fri Sep 25 00:39:29 2009 -0400 +++ b/tools/new_operations/intersect.xml Fri Sep 25 02:06:03 2009 -0400 @@ -21,27 +21,27 @@ <data format="input" name="output" metadata_source="input1" /> </outputs> <code file="operation_filter.py"/> - <tests> - <test> - <param name="input1" value="1.bed" /> - <param name="input2" value="2.bed" /> - <param name="min" value="1" /> - <param name="returntype" value="" /> - <output name="output" file="gops_intersect_out.bed" /> + <tests> + <test> + <param name="input1" value="1.bed" /> + <param name="input2" value="2.bed" /> + <param name="min" value="1" /> + <param name="returntype" value="" /> + <output name="output" file="gops_intersect_out.bed" /> </test> <test> <param name="input1" value="1.bed" /> <param name="input2" value="2_mod.bed" ftype="interval"/> <param name="min" value="1" /> - <param name="returntype" value="" /> + <param name="returntype" value="" /> <output name="output" file="gops_intersect_diffCols.bed" /> - </test> - <test> - <param name="input1" value="1.bed" /> - <param name="input2" value="2_mod.bed" ftype="interval"/> - <param name="min" value="1" /> - <param name="returntype" value="Overlapping pieces of Intervals" /> - <output name="output" file="gops_intersect_p_diffCols.bed" /> + </test> + <test> + <param name="input1" value="1.bed" /> + <param name="input2" value="2_mod.bed" ftype="interval"/> + <param name="min" value="1" /> + <param name="returntype" value="Overlapping pieces of Intervals" /> + <output name="output" file="gops_intersect_p_diffCols.bed" /> </test> <test> <param name="input1" value="1.bed" /> @@ -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 -r 210e048e7ec7 -r 5db45e48f954 tools/new_operations/join.xml --- a/tools/new_operations/join.xml Fri Sep 25 00:39:29 2009 -0400 +++ b/tools/new_operations/join.xml Fri Sep 25 02:06:03 2009 -0400 @@ -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 @@ **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 -r 210e048e7ec7 -r 5db45e48f954 tools/new_operations/merge.xml --- a/tools/new_operations/merge.xml Fri Sep 25 00:39:29 2009 -0400 +++ b/tools/new_operations/merge.xml Fri Sep 25 02:06:03 2009 -0400 @@ -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 @@ ----- -This operation merges all overlaping intervals into single intervals. +This operation merges all overlapping intervals into single intervals. **Example** diff -r 210e048e7ec7 -r 5db45e48f954 tools/new_operations/subtract.xml --- a/tools/new_operations/subtract.xml Fri Sep 25 00:39:29 2009 -0400 +++ b/tools/new_operations/subtract.xml Fri Sep 25 02:06:03 2009 -0400 @@ -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 -r 210e048e7ec7 -r 5db45e48f954 tools/regVariation/microsats_alignment_level.xml --- a/tools/regVariation/microsats_alignment_level.xml Fri Sep 25 00:39:29 2009 -0400 +++ b/tools/regVariation/microsats_alignment_level.xml Fri Sep 25 02:06:03 2009 -0400 @@ -6,8 +6,8 @@ <inputs> <page> <param format="fasta" name="input1" type="data" label="Select data"/> - <param name="separation" size="10" type="integer" value="10" label="Minimum basepair distance between adjacent microsatellites" - help="A value of 10 means: Adjacent microsatellites separated by less than 10 basepairs will be excluded from the output."/> + <param name="separation" size="10" type="integer" value="10" label="Minimum base pair distance between adjacent microsatellites" + help="A value of 10 means: Adjacent microsatellites separated by less than 10 base pairs will be excluded from the output."/> <param name="mono_threshold" size="10" type="integer" value="9" label="Minimum Threshold for the number of repeats for mononucleotide microsatellites" help="A value of 9 means: All mononucleotide microsatellites having fewer than 9 repeats will be excluded from the output."/> <param name="non_mono_threshold" size="10" type="integer" value="4" label="Minimum Threshold for the number of repeats for non-mononucleotide microsatellites" diff -r 210e048e7ec7 -r 5db45e48f954 tools/regVariation/quality_filter.xml --- a/tools/regVariation/quality_filter.xml Fri Sep 25 00:39:29 2009 -0400 +++ b/tools/regVariation/quality_filter.xml Fri Sep 25 02:06:03 2009 -0400 @@ -91,8 +91,8 @@ **Note** -Any block/s not containing the primary species(species whose quality scores is to be used), will be omitted. -Also, any primary species whose quality scores are not available in galaxy, will be considered as a non-primary species. This info will appear as a message in the job history panel. +Any block/s not containing the primary species (species whose quality scores is to be used), will be omitted. +Also, any primary species whose quality scores are not available in Galaxy will be considered as a non-primary species. This info will appear as a message in the job history panel. ----- diff -r 210e048e7ec7 -r 5db45e48f954 tools/regVariation/substitution_rates.xml --- a/tools/regVariation/substitution_rates.xml Fri Sep 25 00:39:29 2009 -0400 +++ b/tools/regVariation/substitution_rates.xml Fri Sep 25 02:06:03 2009 -0400 @@ -43,7 +43,7 @@ **What it does** -This tool takes a pairwise MAF file as input and estimates substitution rate according to Jukes-Cantor JC69 model. The 3 new columns appended to the output are explanied below: +This tool takes a pairwise MAF file as input and estimates substitution rate according to Jukes-Cantor JC69 model. The 3 new columns appended to the output are explained below: - L: number of nucleotides compared - N: number of different nucleotides diff -r 210e048e7ec7 -r 5db45e48f954 tools/samtools/pileup_parser.xml --- a/tools/samtools/pileup_parser.xml Fri Sep 25 00:39:29 2009 -0400 +++ b/tools/samtools/pileup_parser.xml Fri Sep 25 02:06:03 2009 -0400 @@ -99,18 +99,18 @@ </tests> <help> -**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 @@ **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 @@ 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 @@ 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 @@ 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 @@ 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). +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). -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. - +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. </help> </tool> diff -r 210e048e7ec7 -r 5db45e48f954 tools/samtools/sam2interval.xml --- a/tools/samtools/sam2interval.xml Fri Sep 25 00:39:29 2009 -0400 +++ b/tools/samtools/sam2interval.xml Fri Sep 25 02:06:03 2009 -0400 @@ -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 -r 210e048e7ec7 -r 5db45e48f954 tools/samtools/sam_bitwise_flag_filter.xml --- a/tools/samtools/sam_bitwise_flag_filter.xml Fri Sep 25 00:39:29 2009 -0400 +++ b/tools/samtools/sam_bitwise_flag_filter.xml Fri Sep 25 02:06:03 2009 -0400 @@ -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 @@ 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 @@ 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 -r 210e048e7ec7 -r 5db45e48f954 tools/samtools/sam_pileup.xml --- a/tools/samtools/sam_pileup.xml Fri Sep 25 00:39:29 2009 -0400 +++ b/tools/samtools/sam_pileup.xml Fri Sep 25 02:06:03 2009 -0400 @@ -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 @@ **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 -r 210e048e7ec7 -r 5db45e48f954 tools/samtools/sam_to_bam.xml --- a/tools/samtools/sam_to_bam.xml Fri Sep 25 00:39:29 2009 -0400 +++ b/tools/samtools/sam_to_bam.xml Fri Sep 25 02:06:03 2009 -0400 @@ -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 -r 210e048e7ec7 -r 5db45e48f954 tools/solid_tools/maq_cs_wrapper.xml --- a/tools/solid_tools/maq_cs_wrapper.xml Fri Sep 25 00:39:29 2009 -0400 +++ b/tools/solid_tools/maq_cs_wrapper.xml Fri Sep 25 02:06:03 2009 -0400 @@ -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 -r 210e048e7ec7 -r 5db45e48f954 tools/solid_tools/solid_qual_boxplot.xml --- a/tools/solid_tools/solid_qual_boxplot.xml Fri Sep 25 00:39:29 2009 -0400 +++ b/tools/solid_tools/solid_qual_boxplot.xml Fri Sep 25 02:06:03 2009 -0400 @@ -26,7 +26,7 @@ * 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 -r 210e048e7ec7 -r 5db45e48f954 tools/sr_mapping/bowtie_wrapper.xml --- a/tools/sr_mapping/bowtie_wrapper.xml Fri Sep 25 00:39:29 2009 -0400 +++ b/tools/sr_mapping/bowtie_wrapper.xml Fri Sep 25 02:06:03 2009 -0400 @@ -181,7 +181,7 @@ <param name="dcv" type="integer" value="1024" label="The period for the difference-cover sample (--dcv)" /> </when> </conditional> - <param name="nodc" type="select" label="Whether or not to disable the use of the difference-cover sample (--nodc)" help="Suffix sorting becomes quadratic-time in the worst case (a very repetetive reference)"> + <param name="nodc" type="select" label="Whether or not to disable the use of the difference-cover sample (--nodc)" help="Suffix sorting becomes quadratic-time in the worst case (a very repetitive reference)"> <option value="dc">Use difference-cover sample</option> <option value="nodc">Disable difference-cover sample</option> </param> diff -r 210e048e7ec7 -r 5db45e48f954 tools/sr_mapping/bwa_wrapper.xml --- a/tools/sr_mapping/bwa_wrapper.xml Fri Sep 25 00:39:29 2009 -0400 +++ b/tools/sr_mapping/bwa_wrapper.xml Fri Sep 25 02:06:03 2009 -0400 @@ -141,7 +141,7 @@ <param name="mismatchPenalty" type="integer" value="3" label="Mismatch penalty" help="BWA will not search for suboptimal hits with a score lower than [value]" /> <param name="gapOpenPenalty" type="integer" value="11" label="Gap open penalty" /> <param name="gapExtensPenalty" type="integer" value="4" label="Gap extension penalty" /> - <param name="colorSpaceRev" type="select" label="Reverse query but don't compement it" help="Reverse query for all alignment in color space"> + <param name="colorSpaceRev" type="select" label="Reverse query but don't complement it" help="Reverse query for all alignment in color space"> <option value="false">Don't reverse query</option> <option value="true">Reverse query</option> </param> @@ -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 -r 210e048e7ec7 -r 5db45e48f954 tools/sr_mapping/fastq_statistics.xml --- a/tools/sr_mapping/fastq_statistics.xml Fri Sep 25 00:39:29 2009 -0400 +++ b/tools/sr_mapping/fastq_statistics.xml Fri Sep 25 02:06:03 2009 -0400 @@ -2,7 +2,7 @@ <description>for Solexa file</description> <command>cat $input | solexa_quality_statistics -o $output</command> <inputs> - <param format="fastqsolexa" name="input" type="data" label="Library to analyse" /> + <param format="fastqsolexa" name="input" type="data" label="Library to analyze" /> </inputs> <outputs> <data format="txt" name="output" /> diff -r 210e048e7ec7 -r 5db45e48f954 tools/sr_mapping/lastz_wrapper.xml --- a/tools/sr_mapping/lastz_wrapper.xml Fri Sep 25 00:39:29 2009 -0400 +++ b/tools/sr_mapping/lastz_wrapper.xml Fri Sep 25 02:06:03 2009 -0400 @@ -76,20 +76,20 @@ <param name="max_ident" type="integer" size="3" value="100" label="Do not report matches above this identity (%)"/> <param name="min_cvrg" type="integer" size="3" value="0" label="Do not report matches that cover less than this fraction (%) of each read"/> </inputs> - <outputs> + <outputs> <data format="tabular" name="output1"> <change_format> <when input="out_format" value="maf" format="maf" /> </change_format> </data> - <data format="coverage" name="output2" /> + <data format="coverage" name="output2" /> </outputs> <requirements> <requirement type="binary">lastz</requirement> </requirements> - <tests> - <test> - <param name="input1" value="phiX.fa" ftype="fasta" /> + <tests> + <test> + <param name="input1" value="phiX.fa" ftype="fasta" /> <param name="input2" value="B1.fa" ftype="fasta" /> <param name="source_select" value="pre_set" /> <param name="pre_set_options" value="yasra95short" /> @@ -98,10 +98,10 @@ <param name="max_ident" value="100" /> <param name="min_cvrg" value="0" /> <param name="out_format" value="diffs" /> - <output name="output1" file="lastz_diffs.txt" /> + <output name="output1" file="lastz_diffs.txt" /> </test> - <test> - <param name="input1" value="phiX.fa" ftype="fasta" /> + <test> + <param name="input1" value="phiX.fa" ftype="fasta" /> <param name="input2" value="B1.fa" ftype="fasta" /> <param name="source_select" value="pre_set" /> <param name="pre_set_options" value="yasra95short" /> @@ -111,18 +111,18 @@ <param name="max_ident" value="100" /> <param name="min_cvrg" value="0" /> <param name="out_format" value="diffs" /> - <output name="output1" file="lastz_diffs_ref_name.txt" /> + <output name="output1" file="lastz_diffs_ref_name.txt" /> </test> - </tests> + </tests> <help> **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 -r 210e048e7ec7 -r 5db45e48f954 tools/stats/aggregate_binned_scores_in_intervals.xml --- a/tools/stats/aggregate_binned_scores_in_intervals.xml Fri Sep 25 00:39:29 2009 -0400 +++ b/tools/stats/aggregate_binned_scores_in_intervals.xml Fri Sep 25 02:06:03 2009 -0400 @@ -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 -r 210e048e7ec7 -r 5db45e48f954 tools/stats/filtering.xml --- a/tools/stats/filtering.xml Fri Sep 25 00:39:29 2009 -0400 +++ b/tools/stats/filtering.xml Fri Sep 25 02:06:03 2009 -0400 @@ -42,7 +42,7 @@ **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 -r 210e048e7ec7 -r 5db45e48f954 tools/stats/gsummary.xml --- a/tools/stats/gsummary.xml Fri Sep 25 00:39:29 2009 -0400 +++ b/tools/stats/gsummary.xml Fri Sep 25 02:06:03 2009 -0400 @@ -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 @@ - 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 -r 210e048e7ec7 -r 5db45e48f954 tools/stats/wiggle_to_simple.xml --- a/tools/stats/wiggle_to_simple.xml Fri Sep 25 00:39:29 2009 -0400 +++ b/tools/stats/wiggle_to_simple.xml Fri Sep 25 02:06:03 2009 -0400 @@ -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 -r 210e048e7ec7 -r 5db45e48f954 tools/taxonomy/find_diag_hits.xml --- a/tools/taxonomy/find_diag_hits.xml Fri Sep 25 00:39:29 2009 -0400 +++ b/tools/taxonomy/find_diag_hits.xml Fri Sep 25 02:06:03 2009 -0400 @@ -67,7 +67,7 @@ * *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 @@ .. 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. </help> diff -r 210e048e7ec7 -r 5db45e48f954 tools/taxonomy/gi2taxonomy.xml --- a/tools/taxonomy/gi2taxonomy.xml Fri Sep 25 00:39:29 2009 -0400 +++ b/tools/taxonomy/gi2taxonomy.xml Fri Sep 25 02:06:03 2009 -0400 @@ -45,7 +45,7 @@ | 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 -r 210e048e7ec7 -r 5db45e48f954 tools/taxonomy/t2ps_wrapper.xml --- a/tools/taxonomy/t2ps_wrapper.xml Fri Sep 25 00:39:29 2009 -0400 +++ b/tools/taxonomy/t2ps_wrapper.xml Fri Sep 25 02:06:03 2009 -0400 @@ -108,7 +108,7 @@ **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 -r 210e048e7ec7 -r 5db45e48f954 tools/taxonomy/t2t_report.xml --- a/tools/taxonomy/t2t_report.xml Fri Sep 25 00:39:29 2009 -0400 +++ b/tools/taxonomy/t2t_report.xml Fri Sep 25 02:06:03 2009 -0400 @@ -30,19 +30,39 @@ 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. </help> diff -r 210e048e7ec7 -r 5db45e48f954 tools/visualization/LAJ.xml --- a/tools/visualization/LAJ.xml Fri Sep 25 00:39:29 2009 -0400 +++ b/tools/visualization/LAJ.xml Fri Sep 25 02:06:03 2009 -0400 @@ -15,7 +15,7 @@ <data name="out_file1" format="laj"/> </outputs> <help> -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 -r 210e048e7ec7 -r 5db45e48f954 tools/visualization/genetrack.xml --- a/tools/visualization/genetrack.xml Fri Sep 25 00:39:29 2009 -0400 +++ b/tools/visualization/genetrack.xml Fri Sep 25 02:06:03 2009 -0400 @@ -48,7 +48,7 @@ </requirements> <help> 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 @@ - **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.