[galaxy-commits] commit/galaxy-central: kellyv: Cleaned up help text across Picard tools (and FastQC) to standardize style as much as possible

1 new changeset in galaxy-central:

http://bitbucket.org/galaxy/galaxy-central/changeset/bee3d356198a/ changeset: r5579:bee3d356198a user: kellyv date: 2011-05-18 03:31:34 summary: Cleaned up help text across Picard tools (and FastQC) to standardize style as much as possible affected #: 12 files (2.2 KB)

--- a/tools/picard/picard_AddOrReplaceReadGroups.xml Tue May 17 18:41:12 2011 -0400 +++ b/tools/picard/picard_AddOrReplaceReadGroups.xml Tue May 17 21:31:34 2011 -0400 @@ -98,12 +98,13 @@

**Purpose**

-Add or Replace Read Groups in an input bam or sam file +Add or Replace Read Groups in an input bam or sam file.

**Picard documentation**

-This is a Galaxy interface for the Picard-tools_ tool AddOrReplaceReadGroups. Picard-tools is supported through the SAMTools_ project. +This is a Galaxy interface for the external package Picard-tools_ tool AddOrReplaceReadGroups_. Picard-tools is supported through the SAMTools_ project.

+ .. _AddOrReplaceReadGroups: http://picard.sourceforge.net/command-line-overview.shtml#AddOrReplaceReadGr... .. _Picard-tools: http://picard.sourceforge.net/index.shtml .. _SAMTools: http://samtools.sourceforge.net/

@@ -129,12 +130,12 @@ RGPL=String Read Group platform (e.g. illumina, solid) RGPU=String Read Group platform unit (eg. run barcode) RGSM=String Read Group sample name + RGID=String Read Group ID; Default value: null (empty)

AddOrReplaceReadGroups OPTIONAL parameters::

Option (Type) Description

- RGID=String Read Group ID; Default value: null (empty) RGCN=String Read Group sequencing center name; Default value: null (empty) RGDS=String Read Group description Default value: null (empty)

--- a/tools/picard/picard_BamIndexStats.xml Tue May 17 18:41:12 2011 -0400 +++ b/tools/picard/picard_BamIndexStats.xml Tue May 17 21:31:34 2011 -0400 @@ -43,8 +43,9 @@

**Picard documentation**

-This is a Galaxy wrapper for BamIndexStats, a part of Picard-tools_, which is closely related to SAMTools_. +This is a Galaxy wrapper for BamIndexStats_, a part of the external package Picard-tools_, which is supported by the SAMTools_ project.

+ .. _BamIndexStats: http://picard.sourceforge.net/command-line-overview.shtml#BamIndexStats .. _Picard-tools: http://picard.sourceforge.net/index.shtml .. _SAMTools: http://samtools.sourceforge.net/

@@ -56,7 +57,8 @@

**Outputs**

-The output from this tool is a simple text file. +This tool outputs an HTML file that contains links to the actual metrics results, as well +as a log file with info on the exact command run.

------

@@ -83,13 +85,13 @@ read7 163 chr7 302 255 10M1D10M5I76M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA I/15445666651/566666553+2/14/I/555512+3/)-'/-I-'*+))*''13+3)'//++''/'))/3+I*5++)I'2+I+/*I-II*)I-./1'1 RG:Z:0 read8 165 * 0 0 * chr7 1 0 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA I/15445666651/566666553+2/14/I/555512+3/)-'/-I-'*+))*''13+3)'//++''/'))/3+I*5++)I'2+I+/*I-II*)I-./1'1 RG:Z:0

-The following file will be produced:: +The following metrics file will be produced::

- chr1 length= 101 Aligned= 0 Unaligned= 0 - chr7 length= 404 Aligned= 7 Unaligned= 0 - chr8 length= 202 Aligned= 0 Unaligned= 0 - chr10 length= 303 Aligned= 0 Unaligned= 0 - chr14 length= 505 Aligned= 0 Unaligned= 0 + chr1 length= 101 Aligned= 0 Unaligned= 0 + chr7 length= 404 Aligned= 7 Unaligned= 0 + chr8 length= 202 Aligned= 0 Unaligned= 0 + chr10 length= 303 Aligned= 0 Unaligned= 0 + chr14 length= 505 Aligned= 0 Unaligned= 0 NoCoordinateCount= 1

</help>

--- a/tools/picard/picard_ReorderSam.xml Tue May 17 18:41:12 2011 -0400 +++ b/tools/picard/picard_ReorderSam.xml Tue May 17 21:31:34 2011 -0400 @@ -110,8 +110,9 @@

**Picard documentation**

-This is a Galaxy interface for Picard-tools_'s ReorderSam tool, a part of Picard-tools_, which is supported by SAMTools_. +This is a Galaxy interface for Picard-tools_ tool ReorderSam_, a part of the external package Picard-tools_, which is supported by the SAMTools_ project.

+ .. _ReorderSam: http://picard.sourceforge.net/command-line-overview.shtml#ReorderSam .. _Picard-tools: http://picard.sourceforge.net/index.shtml .. _SAMTools: http://samtools.sourceforge.net/

--- a/tools/picard/picard_ReplaceSamHeader.xml Tue May 17 18:41:12 2011 -0400 +++ b/tools/picard/picard_ReplaceSamHeader.xml Tue May 17 21:31:34 2011 -0400 @@ -67,8 +67,9 @@

**Picard documentation**

-This is a Galaxy interface to the Picard-tools_'s ReplaceSamHeader tools, which is supported by SAMTools_. +This is a Galaxy interface to the external package Picard-tools_ tool ReplaceSamHeader_, which is supported by the SAMTools_ project.

+ .. _ReplaceSamHeader: http://picard.sourceforge.net/command-line-overview.shtml#ReplaceSamHeader .. _Picard-tools: http://picard.sourceforge.net/index.shtml .. _SAMTools: http://samtools.sourceforge.net/

--- a/tools/picard/rgPicardASMetrics.xml Tue May 17 18:41:12 2011 -0400 +++ b/tools/picard/rgPicardASMetrics.xml Tue May 17 21:31:34 2011 -0400 @@ -95,30 +95,29 @@

**Summary**

-This Galaxy tool uses Picard to report measures of alignment -Picard is supported through the SamTools project. -This tool wraps Picard and is supported through the galaxy-bugs mailing list -or by providing comments through the report form that appears automatically -if a tool fails unexpectedly when you run it in Galaxy. +This Galaxy tool uses Picard to report measures of alignment.

-All the Picard tools are freely available and are documented -at http://picard.sourceforge.net/command-line-overview.shtml#CollectAlignmentSu... -Some of that material is consolidated below from the Picard documentation +**Picard documentation** + +This is a Galaxy wrapper for CollectAlignmentSummaryMetrics_, a part of the external package Picard-tools_, which is supported by the SAMTools_ project. + + .. _CollectAlignmentSummaryMetrics: http://picard.sourceforge.net/command-line-overview.shtml#CollectAlignmentSu... + .. _Picard-tools: http://picard.sourceforge.net/index.shtml + .. _SAMTools: http://samtools.sourceforge.net/

-----

.. class:: infomark

-**Picard Documentation** +**Inputs, outputs, and parameters**

The Picard documentation (reformatted for Galaxy) says:

-***Collect Alignment Summary Metrics*** +**Collect Alignment Summary Metrics**

- Reads a SAM or BAM file and writes a file containing summary alignment metrics. +Reads a SAM or BAM file and writes a file containing summary alignment metrics.

.. csv-table:: ASMDoc - :header-rows: 1

Option,Description @@ -173,16 +172,6 @@ There is a clean sam tool - but only filters what it ignores. The lenient flag allows reads to be discarded if they're empty or don't map. This seems an awful strategy but unfortunately may be needed to run an analysis using badly behaved external packages.

------ - -.. class:: infomark - -**Attribution** - -Picard and Samtools go together. They are external to and completely independent of Galaxy. We acknowledge that all credit for -their methods and contribution are due to them. - - </help></tool>

--- a/tools/picard/rgPicardFixMate.xml Tue May 17 18:41:12 2011 -0400 +++ b/tools/picard/rgPicardFixMate.xml Tue May 17 21:31:34 2011 -0400 @@ -46,6 +46,12 @@

.. class:: infomark

+**Purpose** + +Ensure that all mate-pair information is in sync between each read and it's mate pair. + +.. class:: warningmark + **Useful for paired data only**

Likely won't do anything helpful for single end sequence data @@ -53,9 +59,14 @@ the data you choose are valid (paired end) sam or bam data - unless you trust this tool not to harm your data.

-**Purpose** +**Picard documentation**

-Ensure that all mate-pair information is in sync between each read and it's mate pair. +This is a Galaxy wrapper for FixMateInformation_, a part of the external package Picard-tools_, which is supported by the SAMTools_ project. + + .. _FixMateInformation: http://picard.sourceforge.net/command-line-overview.shtml#FixMateInformation + .. _Picard-tools: http://picard.sourceforge.net/index.shtml + .. _SAMTools: http://samtools.sourceforge.net/ +

**Why you might want to use this tool**

@@ -77,7 +88,7 @@

.. class:: infomark

-**From the Picard documentation** +**Inputs, outputs, and parameters**

.. csv-table:: Fixmate

@@ -89,20 +100,6 @@ "SORT_ORDER=SortOrder","Optional sort order if the OUTPUT file should be sorted differently than the INPUT file. Default value: null. Possible values: {unsorted, queryname, coordinate}" "CREATE_MD5_FILE=Boolean","Whether to create an MD5 digest for any BAM files created. Default value: false"

------ - -.. class:: infomark - -**Attributions** - -Picard is supported through the SamTools project. -This tool wraps Picard and is supported through the galaxy-bugs mailing list -or by providing comments through the report form that appears automatically -if a tool fails unexpectedly when you run it in Galaxy. - -All the Picard tools are freely available and are documented -at http://picard.sourceforge.net/command-line-overview.shtml - </help></tool>

--- a/tools/picard/rgPicardGCBiasMetrics.xml Tue May 17 18:41:12 2011 -0400 +++ b/tools/picard/rgPicardGCBiasMetrics.xml Tue May 17 21:31:34 2011 -0400 @@ -89,35 +89,36 @@ **Summary**

This Galaxy tool uses Picard to report measures of GC bias. -Picard is supported through the SamTools project. -This tool wraps Picard and is supported through the galaxy-bugs mailing list -or by providing comments through the report form that appears automatically -if a tool fails unexpectedly when you run it in Galaxy.

-All the Picard tools are freely available and are documented -at http://picard.sourceforge.net/command-line-overview.shtml#CollectAlignmentSu... +**Picard documentation** + +This is a Galaxy wrapper for CollectGcBiasMetrics_, a part of the external package Picard-tools_, which is supported by the SAMTools_ project. + + .. _CollectGcBiasMetrics: http://picard.sourceforge.net/command-line-overview.shtml#CollectGcBiasMetri... + .. _Picard-tools: http://picard.sourceforge.net/index.shtml + .. _SAMTools: http://samtools.sourceforge.net/ +

-----

.. class:: infomark

-**Picard Documentation** +**Inputs, outputs, and parameters**

The Picard documentation (reformatted for Galaxy) says:

.. csv-table:: GC Bias Doc :header-rows: 1

- Option,Description - "REFERENCE_SEQUENCE=File","The reference sequence fasta file. Required." - "INPUT=File","The BAM or SAM file containing aligned reads. Required." - "OUTPUT=File","The text file to write the metrics table to. Required." - "CHART_OUTPUT=File","The PDF file to render the chart to. Required." - "SUMMARY_OUTPUT=File","The text file to write summary metrics to. Default value: null." - "WINDOW_SIZE=Integer","The size of windows on the genome that are used to bin reads. Default value: 100." - "MINIMUM_GENOME_FRACTION=Double","For summary metrics, exclude GC windows that include less than this fraction of the genome. Default value: 1.0E-5." - "CREATE_MD5_FILE=Boolean","Whether to create an MD5 digest for any BAM files created. Default value: false." - + Option,Description + "REFERENCE_SEQUENCE=File","The reference sequence fasta file. Required." + "INPUT=File","The BAM or SAM file containing aligned reads. Required." + "OUTPUT=File","The text file to write the metrics table to. Required." + "CHART_OUTPUT=File","The PDF file to render the chart to. Required." + "SUMMARY_OUTPUT=File","The text file to write summary metrics to. Default value: null." + "WINDOW_SIZE=Integer","The size of windows on the genome that are used to bin reads. Default value: 100." + "MINIMUM_GENOME_FRACTION=Double","For summary metrics, exclude GC windows that include less than this fraction of the genome. Default value: 1.0E-5." + "CREATE_MD5_FILE=Boolean","Whether to create an MD5 digest for any BAM files created. Default value: false."

GcBiasDetailMetrics

@@ -136,7 +137,6 @@

.. class:: infomark

- **Typical tool invocation without Galaxy is on a command line - eg:**

java -jar /share/shared/galaxy/tool-data/shared/jars/CollectGcBiasMetrics.jar REFERENCE_SEQUENCE="hg18.fasta" @@ -151,15 +151,5 @@ This seems an awful strategy but unfortunately may be needed to run an analysis using badly behaved external packages.

------ - -.. class:: infomark - -**Attributions** - -Picard and Samtools go together. -They are external to and completely independent of Galaxy. We acknowledge that all credit for -their methods and contribution are due to them. - </help></tool>

--- a/tools/picard/rgPicardHsMetrics.xml Tue May 17 18:41:12 2011 -0400 +++ b/tools/picard/rgPicardHsMetrics.xml Tue May 17 21:31:34 2011 -0400 @@ -40,21 +40,27 @@

**Summary**

-This tool provides a Galaxy interface to one of the Picard tools freely -available at http://picard.sourceforge.net/command-line-overview.shtml#CalculateHsMetrics +Calculates a set of Hybrid Selection specific metrics from an aligned SAM or BAM file. + +**Picard documentation** + +This is a Galaxy wrapper for CalculateHsMetrics_, a part of the external package Picard-tools_, which is supported by the SAMTools_ project. + + .. _CalculateHsMetrics: http://picard.sourceforge.net/command-line-overview.shtml#CalculateHsMetrics + .. _Picard-tools: http://picard.sourceforge.net/index.shtml + .. _SAMTools: http://samtools.sourceforge.net/ +

-----

.. class:: infomark

-**Picard Documentation** +**Inputs, outputs, and parameters**

-Picard documentation says: - +Picard documentation says (reformatted for Galaxy):

Calculates a set of Hybrid Selection specific metrics from an aligned SAM or BAM file.

- .. csv-table:: HsDoc :header-rows: 1

@@ -125,20 +131,5 @@ The lenient flag means reads are discarded if empty or off the end of the map - or whatever. Suggestions for improvement are welcome.

------ - -.. class:: infomark - -**Attribution** - -This tool takes interval files in the usual Galaxy interval (bed) format as bait and target sequences rather than -the special format Picard requires - the tool provides reliable reformatting for Picard. - -Picard is a project associated with the SamTools project. -This Galaxy tool uses part of Picard to report measures of hybridization selection in your -aligned short read sequence data. Sequence data must be chosen from the sam/bam format files in your current history. -Target and bait files must be selected from the UCSC BED format in your current history. - - </help></tool>

--- a/tools/picard/rgPicardInsertSize.xml Tue May 17 18:41:12 2011 -0400 +++ b/tools/picard/rgPicardInsertSize.xml Tue May 17 21:31:34 2011 -0400 @@ -41,16 +41,30 @@

**Purpose**

-This tool works for PAIRED DATA ONLY and can be expected to fail for single end data. +Reads a SAM or BAM file and describes the distribution +of insert size (excluding duplicates) with metrics and a histogram plot.

-Reads a SAM or BAM file and describes the distribution -of insert size (excluding duplicates). Generates a histogram plot. +.. class:: warningmark + +**Useful for paired data only** + +This tool works for paired data only and can be expected to fail for single end data. + +**Picard documentation** + +This is a Galaxy wrapper for CollectInsertSizeMetrics_, a part of the external package Picard-tools_, which is supported by the SAMTools_ project. + + .. _CollectInsertSizeMetrics: http://picard.sourceforge.net/command-line-overview.shtml#CollectInsertSizeM... + .. _Picard-tools: http://picard.sourceforge.net/index.shtml + .. _SAMTools: http://samtools.sourceforge.net/

-----

.. class:: infomark

-**From the Picard documentation** +**Inputs, outputs, and parameters** + +Picard documentation says (reformatted for Galaxy):

.. csv-table:: Insert size metrics docs :header-rows: 1 @@ -65,21 +79,5 @@ "STOP_AFTER=Integer","Stop after processing N reads, mainly for debugging. Default value: 0." "CREATE_MD5_FILE=Boolean","Whether to create an MD5 digest for any BAM files created. Default value: false."

- ------ - -.. class:: infomark - -**Attributions** - -Picard is supported through the SamTools project. -This tool wraps Picard and is supported through the galaxy-bugs mailing list -or by providing comments through the report form that appears automatically -if a tool fails unexpectedly when you run it in Galaxy. - -All the Picard tools are freely available and are documented -at http://picard.sourceforge.net/command-line-overview.shtml - - </help></tool>

--- a/tools/picard/rgPicardLibComplexity.xml Tue May 17 18:41:12 2011 -0400 +++ b/tools/picard/rgPicardLibComplexity.xml Tue May 17 21:31:34 2011 -0400 @@ -55,42 +55,51 @@

**Purpose**

- EstimateLibraryComplexity - Attempts to estimate library complexity from sequence alone. - Does so by sorting all reads by the first N bases (5 by default) of each read and then - comparing reads with the first N bases identical to each other for duplicates. Reads are considered to be - duplicates if they match each other with no gaps and an overall mismatch rate less than or equal to MAX_DIFF_RATE (0.03 by default). +Attempts to estimate library complexity from sequence alone. +Does so by sorting all reads by the first N bases (5 by default) of each read and then +comparing reads with the first N bases identical to each other for duplicates. Reads are considered to be +duplicates if they match each other with no gaps and an overall mismatch rate less than or equal to MAX_DIFF_RATE (0.03 by default).

- Reads of poor quality are filtered out so as to provide a more accurate estimate. - The filtering removes reads with any no-calls in the first N bases or with a mean base quality lower than - MIN_MEAN_QUALITY across either the first or second read. +Reads of poor quality are filtered out so as to provide a more accurate estimate. +The filtering removes reads with any no-calls in the first N bases or with a mean base quality lower than +MIN_MEAN_QUALITY across either the first or second read.

- The algorithm attempts to detect optical duplicates separately from PCR duplicates and excludes these in the - calculation of library size. Also, since there is no alignment to screen out technical reads one - further filter is applied on the data. After examining all reads a histogram is built of - [#reads in duplicate set -> #of duplicate sets]; - all bins that contain exactly one duplicate set are then removed from the histogram as outliers before library size is estimated. +The algorithm attempts to detect optical duplicates separately from PCR duplicates and excludes these in the +calculation of library size. Also, since there is no alignment to screen out technical reads one +further filter is applied on the data. After examining all reads a histogram is built of +[#reads in duplicate set -> #of duplicate sets]; all bins that contain exactly one duplicate set are +then removed from the histogram as outliers before library size is estimated. + +**Picard documentation** + +This is a Galaxy wrapper for EstimateLibraryComplexity_, a part of the external package Picard-tools_, which is supported by the SAMTools_ project. + + .. _EstimateLibraryComplexity: http://picard.sourceforge.net/command-line-overview.shtml#EstimateLibraryCom... + .. _Picard-tools: http://picard.sourceforge.net/index.shtml + .. _SAMTools: http://samtools.sourceforge.net/ +

**Why you might want to use this tool**

- This tool provides a Galaxy interface to one of the Picard tools. - If you need to estimate library complexity from sequences, the Picard tool may help. +This tool provides a Galaxy interface to one of the Picard tools. +If you need to estimate library complexity from sequences, the Picard tool may help.

**Note on the Regular Expression**

- (from the Picard docs) - This tool requires a valid regular expression to parse out the read names in the incoming SAM or BAM file. - These values are used to estimate the rate of optical duplication in order to give a more accurate estimated library size. - The regular expression should contain three capture groups for the three variables, in order. - Default value: [a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*. - +(from the Picard docs) +This tool requires a valid regular expression to parse out the read names in the incoming SAM or BAM file. +These values are used to estimate the rate of optical duplication in order to give a more accurate estimated library size. +The regular expression should contain three capture groups for the three variables, in order. +Default value: [a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*.

-----

.. class:: infomark

-**From the Picard documentation** +**Inputs, outputs, and parameters** + +Picard documentation says (reformatted for Galaxy):

.. csv-table:: Estimate complexity docs :header-rows: 1 @@ -105,21 +114,6 @@ "OPTICAL_DUPLICATE_PIXEL_DISTANCE=Integer","The maximum offset between two duplicte clusters in order to consider them optical duplicates. This should usually be set to some fairly small number (e.g. 5-10 pixels) unless using later versions of the Illumina pipeline that multiply pixel values by 10, in which case 50-100 is more normal. Default value: 100" "CREATE_MD5_FILE=Boolean","Whether to create an MD5 digest for any BAM files created. Default value: false. This option can be set to 'null' to clear the default value. "

- ------ - -.. class:: infomark - -**Attributions** - -Picard is supported through the SamTools project. -This tool wraps Picard and is supported through the galaxy-bugs mailing list -Please help us by completing the report form that appears automatically -if a tool fails unexpectedly when you run it in Galaxy. - -All the Picard tools are freely available and are documented -at http://picard.sourceforge.net/command-line-overview.shtml#CollectInsertSizeM... - </help></tool>

--- a/tools/picard/rgPicardMarkDups.xml Tue May 17 18:41:12 2011 -0400 +++ b/tools/picard/rgPicardMarkDups.xml Tue May 17 21:31:34 2011 -0400 @@ -56,7 +56,7 @@ <param name="remDups" value="true" /><param name="assumeSorted" value="true" /><param name="readRegex" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*" /> - <param name="optDupeDist" value="100" /> + <param name="optDupeDist" value="100" /><output name="out_file" file="picard_output_markdups_remdupes.bam" ftype="bam" compare="diff" /><output name="html_file" file="picard_output_markdups_sortedpairsam.html" ftype="html" lines_diff="75" /></test> @@ -68,9 +68,19 @@

**Purpose**

-MarkDuplicates +Marks all duplicate reads in a provided sam or bam file and either removes them or flags them.

-**From the Picard documentation** +**Picard documentation** + +This is a Galaxy interface to the external package Picard-tools_ tool MarkDuplicates, which is supported by the SAMTools_ project. + + .. _MarkDuplicates: http://picard.sourceforge.net/command-line-overview.shtml#MarkDuplicates + .. _Picard-tools: http://picard.sourceforge.net/index.shtml + .. _SAMTools: http://samtools.sourceforge.net/ + +**Inputs, outputs, and parameters** + +Picard documentation says (reformatted for Galaxy):

.. csv-table:: Mark Duplicates docs :header-rows: 1 @@ -86,7 +96,6 @@ "READ_NAME_REGEX=String","Regular expression that can be used to parse read names in the incoming SAM file. Read names are parsed to extract three variables: tile/region, x coordinate and y coordinate. " "OPTICAL_DUPLICATE_PIXEL_DISTANCE=Integer","The maximum offset between two duplicte clusters in order to consider them optical duplicates. This should usually be set to some fairly small number (e.g. 5-10 pixels) unless using later versions of the Illumina pipeline that multiply pixel values by 10, in which case 50-100 is more normal. Default value: 100"

- **Note on the Regular Expression**

(from the Picard docs) @@ -105,19 +114,6 @@ This tool provides a Galaxy interface to one of the Picard tools. If you need to estimate library complexity from sequences, the Picard tool may help.

------ - -.. class:: infomark - -**Attributions** - -Picard is supported through the SamTools project. -This tool wraps Picard and is supported through the galaxy-bugs mailing list -or by providing comments through the report form that appears automatically -if a tool fails unexpectedly when you run it in Galaxy. - -All the Picard tools are freely available and are documented -at http://picard.sourceforge.net/command-line-overview.shtml#CollectInsertSizeM...

</help></tool>

--- a/tools/rgenetics/rgFastQC.xml Tue May 17 18:41:12 2011 -0400 +++ b/tools/rgenetics/rgFastQC.xml Tue May 17 21:31:34 2011 -0400 @@ -6,7 +6,9 @@ -c "$contaminants" #end if </command> -<requirements><requirement type="package">FastQC</requirement></requirements> + <requirements> + <requirement type="package">FastQC</requirement> + </requirements><inputs><param format="fastqsanger,fastq,bam,sam" name="input_file" type="data" label="Short read data from your current history" /><param name="out_prefix" value="FastQC" type="text" label="Title for the output file - to remind you what the job was for" size="80" /> @@ -30,35 +32,57 @@

**Purpose**

-FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. -It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of +FastQC aims to provide a simple way to do some quality control checks on raw +sequence data coming from high throughput sequencing pipelines. +It provides a modular set of analyses which you can use to give a quick +impression of whether your data has any problems of which you should be aware before doing any further analysis.

-The main functions of FastQC are +The main functions of FastQC are:

-Import of data from BAM, SAM or FastQ files (any variant) -Providing a quick overview to tell you in which areas there may be problems -Summary graphs and tables to quickly assess your data -Export of results to an HTML based permanent report -Offline operation to allow automated generation of reports without running the interactive application +- Import of data from BAM, SAM or FastQ files (any variant) +- Providing a quick overview to tell you in which areas there may be problems +- Summary graphs and tables to quickly assess your data +- Export of results to an HTML based permanent report +- Offline operation to allow automated generation of reports without running the interactive application + +**FastQC documentation** + +This is a Galaxy interface to the external package FastQC_. +Specific documentation on FastQC can be found on that site. +FastQC incorporates the Picard-tools_ libraries for sam/bam processing. + + .. _FastQC: http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/ + .. _Picard-tools: http://picard.sourceforge.net/index.shtml + +The contaminants file parameter was borrowed from the independently developed +fastqcwrapper contributed to the Galaxy Community Tool Shed by J. Johnson.

-----

.. class:: infomark

-**Attribution** +**Inputs and outputs**

-FastQC comes from http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/ -Please see that site for all documentation - this is just a Galaxy wrapper. -This tool wraps the fastqc package to report some QC metrics on fastq, groomed fastq (fastqsanger) in Galaxy +This wrapper will accept any fastq file as well as sam or bam as the primary file to check. +It will also take an optional file containing a list of contaminants information, in the form of +a tab-delimited file with 2 columns, name and sequence.

-This Galaxy tool wrapper is part of the rgenetics toolkit. +The tool produces a single HTML output file that contains all of the results, including the following:

-Contaminants file parameter borrowed from the independently -developed fastqcwrapper_ contributed to the galaxy community tool shed -by j johnson +- Basic Statistics +- Per base sequence quality +- Per sequence quality scores +- Per base sequence content +- Per base GC content +- Per sequence GC content +- Per base N content +- Sequence Length Distribution +- Sequence Duplication Levels +- Overrepresented sequences +- Kmer Content

-.. _fastqcwrapper: http%3A//community.g2.bx.psu.edu/tool/browse_tools%3F%26webapp%3Dcommunity%26operation%3Dview_tool%26id%3D256f9f17b153ce60 +All except Basic Statistics and Overrepresented sequences are plots.

</help></tool>

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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