2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/13d9db4d4503/ changeset: r5583:13d9db4d4503 user: jgoecks date: 2011-05-18 22:52:14 summary: Remove obsolete test values for Cufflinks and Cuffdiff tests. affected #: 2 files (121 bytes) --- a/tools/ngs_rna/cuffdiff_wrapper.xml Wed May 18 16:48:02 2011 -0400 +++ b/tools/ngs_rna/cuffdiff_wrapper.xml Wed May 18 16:52:14 2011 -0400 @@ -158,7 +158,6 @@ <param name="aligned_reads2" value="cuffdiff_in2.sam" ftype="sam" /><!-- Defaults. --><param name="fdr" value="0.05" /> - <param name="min_mapqual" value="0" ftype="sam" /><param name="min_alignment_count" value="0" ftype="sam" /><param name="do_bias_correction" value="No" /><param name="do_normalization" value="No" /> --- a/tools/ngs_rna/cufflinks_wrapper.xml Wed May 18 16:48:02 2011 -0400 +++ b/tools/ngs_rna/cufflinks_wrapper.xml Wed May 18 16:52:14 2011 -0400 @@ -109,7 +109,6 @@ <param name="max_intron_len" value="300000"/><param name="min_isoform_fraction" value="0.05"/><param name="pre_mrna_fraction" value="0.05"/> - <param name="min_map_quality" value="0"/><param name="use_ref" value="No"/><param name="do_normalization" value="No" /><param name="do_bias_correction" value="No"/> http://bitbucket.org/galaxy/galaxy-central/changeset/5e72e101e839/ changeset: r5584:5e72e101e839 user: jgoecks date: 2011-05-18 22:52:38 summary: Merge. affected #: 11 files (1.8 KB) --- a/tools/picard/picard_AddOrReplaceReadGroups.xml Wed May 18 16:52:14 2011 -0400 +++ b/tools/picard/picard_AddOrReplaceReadGroups.xml Wed May 18 16:52:38 2011 -0400 @@ -102,23 +102,22 @@ **Picard documentation** -This is a Galaxy interface for the external package Picard-tools_ tool AddOrReplaceReadGroups_. Picard-tools is supported through the SAMTools_ project. +This is a Galaxy wrapper for AddOrReplaceReadGroups, a part of the external package Picard-tools_. - .. _AddOrReplaceReadGroups: http://picard.sourceforge.net/command-line-overview.shtml#AddOrReplaceReadGr... - .. _Picard-tools: http://picard.sourceforge.net/index.shtml - .. _SAMTools: http://samtools.sourceforge.net/ + .. _Picard-tools: http://www.google.com/search?q=picard+samtools ------ -**Inputs** +.. class:: infomark -Either a sam file or a bam file must be supplied. If a bam file is used, it must be coordinate-sorted. Galaxy currently coordinate-sorts all bam files. +**Inputs, outputs, and parameters** -**Outputs** +Either a sam file or a bam file must be supplied. If a bam file is used, it must +be coordinate-sorted. Galaxy currently coordinate-sorts all bam files. -The output file is either bam (the default) or sam, according to user selection, and contains the same information as the input file except for the appropraite additional (or modified) read group tags. Bam is recommended since it is smaller. - -**AddOrReplaceReadGroups parameters** +The output file is either bam (the default) or sam, according to user selection, +and contains the same information as the input file except for the appropraite +additional (or modified) read group tags. Bam is recommended since it is smaller. From the Picard documentation. @@ -139,7 +138,17 @@ RGCN=String Read Group sequencing center name; Default value: null (empty) RGDS=String Read Group description Default value: null (empty) -One parameter that Picard's AddOrReplaceReadGroups offers that is automatically set by Galaxy is the SORT_ORDER, which is set to coordinate. +One parameter that Picard's AddOrReplaceReadGroups offers that is automatically +set by Galaxy is the SORT_ORDER, which is set to coordinate. + +.. class:: warningmark + +**Warning on Sam quality** + +Unfortunately some packages seem perfectly capable of producing sam and bam files +that Picard will be picky about otherwise. Galaxy deals with this by using the lenient +flag, which allows reads to be discarded if they're empty or don't map. This appears +to be the only way to deal with sam that cannot be parsed. </help> --- a/tools/picard/picard_BamIndexStats.xml Wed May 18 16:52:14 2011 -0400 +++ b/tools/picard/picard_BamIndexStats.xml Wed May 18 16:52:38 2011 -0400 @@ -39,27 +39,35 @@ **Purpose** -Generate Bam Index Stats for a provided bam file +Generate Bam Index Stats for a provided bam file. **Picard documentation** -This is a Galaxy wrapper for BamIndexStats_, a part of the external package Picard-tools_, which is supported by the SAMTools_ project. +This is a Galaxy wrapper for BamIndexStats, a part of the external package Picard-tools_. - .. _BamIndexStats: http://picard.sourceforge.net/command-line-overview.shtml#BamIndexStats - .. _Picard-tools: http://picard.sourceforge.net/index.shtml - .. _SAMTools: http://samtools.sourceforge.net/ + .. _Picard-tools: http://www.google.com/search?q=picard+samtools ------ -**Inputs** +.. class:: infomark -The only input is the bam file you wish to obtain statistics for, which is required. Note that it must be coordinate-sorted. Galaxy currently coordinate-sorts all bam files. +**Inputs and outputs** -**Outputs** +The only input is the bam file you wish to obtain statistics for, which is required. +Note that it must be coordinate-sorted. Galaxy currently coordinate-sorts all bam files. 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. +.. class:: warningmark + +**Warning on Sam quality** + +Unfortunately some packages seem perfectly capable of producing sam and bam files +that Picard will be picky about otherwise. Galaxy deals with this by using the lenient +flag, which allows reads to be discarded if they're empty or don't map. This appears +to be the only way to deal with sam that cannot be parsed. + ------ **Example** --- a/tools/picard/picard_ReorderSam.xml Wed May 18 16:52:14 2011 -0400 +++ b/tools/picard/picard_ReorderSam.xml Wed May 18 16:52:38 2011 -0400 @@ -106,29 +106,49 @@ **Purpose** -Reorder Sam to match contig ordering in a particular reference file. Note that this is not the same as sorting as done by the SortSam tool, which sorts by either coordinate values or query name. The ordering in ReorderSam is based on exact name matching of contigs. Reads that are mapped to a contig that is not in the new reference file are not included in the output. +Reorder Sam to match contig ordering in a particular reference file. Note that this is +not the same as sorting as done by the SortSam tool, which sorts by either coordinate +values or query name. The ordering in ReorderSam is based on exact name matching of +contigs. Reads that are mapped to a contig that is not in the new reference file are +not included in the output. **Picard documentation** -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. +This is a Galaxy wrapper for ReorderSam, a part of the external package Picard-tools_. - .. _ReorderSam: http://picard.sourceforge.net/command-line-overview.shtml#ReorderSam - .. _Picard-tools: http://picard.sourceforge.net/index.shtml - .. _SAMTools: http://samtools.sourceforge.net/ + .. _Picard-tools: http://www.google.com/search?q=picard+samtools ------ -**Inputs** +.. class:: infomark -For the file that needs to be reordered, either a sam file or a bam file must be supplied. If a bam file is used, it must be coordinate-sorted. A reference file is also required, so either a fasta file should be supplied or a built-in reference can be selected. +**Inputs, outputs, and parameters** -**Outputs** +For the file that needs to be reordered, either a sam file or a bam file must be supplied. +If a bam file is used, it must be coordinate-sorted. A reference file is also required, +so either a fasta file should be supplied or a built-in reference can be selected. -The output contains the same reads as the input file but the reads have been rearranged so they appear in the same order as the provided reference file. The tool will output either bam (the default) or sam, according to user selection. Bam is recommended since it is smaller. +The output contains the same reads as the input file but the reads have been rearranged so +they appear in the same order as the provided reference file. The tool will output either +bam (the default) or sam, according to user selection. Bam is recommended since it is smaller. -**ReorderSam parameters** +The only extra parameters that can be set are flags for allowing incomplete dict concordance +and allowing contig length discordance. If incomplete dict concordance is allowed, only a +partial overlap of the bam contigs with the new reference sequence contigs is required. By +default it is off, requiring a corresponding contig in the new reference for each read contig. +If contig length discordance is allowed, contig names that are the same between a read and the +new reference contig are allowed even if they have different lengths. This is usually not a +good idea, unless you know exactly what you're doing. It's off by default. -The only extra parameters that can be set are flags for allowing incomplete dict concordance and allowing contig length discordance. If incomplete dict concordance is allowed, only a partial overlap of the bam contigs with the new reference sequence contigs is required. By default it is off, requiring a corresponding contig in the new reference for each read contig. If contig length discordance is allowed, contig names that are the same between a read and the new reference contig are allowed even if they have different lengths. This is usually not a good idea, unless you know exactly what you're doing. It's off by default. +.. class:: warningmark + +**Warning on Sam quality** + +Unfortunately some packages seem perfectly capable of producing sam and bam files +that Picard will be picky about otherwise. Galaxy deals with this by using the lenient +flag, which allows reads to be discarded if they're empty or don't map. This appears +to be the only way to deal with sam that cannot be parsed. + </help></tool> --- a/tools/picard/picard_ReplaceSamHeader.xml Wed May 18 16:52:14 2011 -0400 +++ b/tools/picard/picard_ReplaceSamHeader.xml Wed May 18 16:52:38 2011 -0400 @@ -61,28 +61,42 @@ **Purpose** -Replace Sam Header with the header from another sam file. The tool does not do any significant validation, so it's up to the user to make sure that the elements in the header are relevant and that the new header has all the required things. +Replace Sam Header with the header from another sam file. The tool does not do any +significant validation, so it's up to the user to make sure that the elements in +the header are relevant and that the new header has all the required things. -Replace the SAMFileHeader in a SAM file with the given header. Validation is minimal. It is up to the user to ensure that all the elements referred to in the SAMRecords are present in the new header. Sort order of the two input files must be the same. +Replace the SAMFileHeader in a SAM file with the given header. Validation is +minimal. It is up to the user to ensure that all the elements referred to in the +SAMRecords are present in the new header. Sort order of the two input files must +be the same. **Picard documentation** -This is a Galaxy interface to the external package Picard-tools_ tool ReplaceSamHeader_, which is supported by the SAMTools_ project. +This is a Galaxy wrapper for ReplaceSamHeader, a part of the external package Picard-tools_. - .. _ReplaceSamHeader: http://picard.sourceforge.net/command-line-overview.shtml#ReplaceSamHeader - .. _Picard-tools: http://picard.sourceforge.net/index.shtml - .. _SAMTools: http://samtools.sourceforge.net/ + .. _Picard-tools: http://www.google.com/search?q=picard+samtools ------ -**Inputs** +.. class:: infomark -Either a sam file or a bam file is required as the file whose header will be replaced. The header file is also required and can also be either sam or bam (it does not have to be the same type as the other file). In both cases, if a bam file is used, it must be coordinate-sorted. Galaxy currently coordinate-sorts all bam files. +**Inputs and outputs** -**Outputs** +Either a sam file or a bam file is required as the file whose header will be replaced. +The header file is also required and can also be either sam or bam (it does not have +to be the same type as the other file). In both cases, if a bam file is used, it must +be coordinate-sorted. Galaxy currently coordinate-sorts all bam files. The tool will output either bam (the default) or sam. Bam is recommended since it is smaller. +.. class:: warningmark + +**Warning on Sam quality** + +Unfortunately some packages seem perfectly capable of producing sam and bam files +that Picard will be picky about otherwise. Galaxy deals with this by using the lenient +flag, which allows reads to be discarded if they're empty or don't map. This appears +to be the only way to deal with sam that cannot be parsed. </help> --- a/tools/picard/rgPicardASMetrics.xml Wed May 18 16:52:14 2011 -0400 +++ b/tools/picard/rgPicardASMetrics.xml Wed May 18 16:52:38 2011 -0400 @@ -76,6 +76,19 @@ </tests><help> +.. class:: infomark + +**Summary** + +This Galaxy tool uses Picard to report high-level measures of alignment based on a provided sam or bam file. + +**Picard documentation** + +This is a Galaxy wrapper for CollectAlignmentSummaryMetrics, a part of the external package Picard-tools_. + + .. _Picard-tools: http://www.google.com/search?q=picard+samtools + +----- .. class:: infomark @@ -88,23 +101,6 @@ - **Bisulphite data** see Picard documentation http://picard.sourceforge.net/command-line-overview.shtml#CollectAlignmentSu... - **Maximum acceptable insertion length** See Picard documentation at http://picard.sourceforge.net/command-line-overview.shtml#CollectAlignmentSu... - ------ - -.. class:: infomark - -**Summary** - -This Galaxy tool uses Picard to report measures of alignment. - -**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 @@ -113,10 +109,6 @@ The Picard documentation (reformatted for Galaxy) says: -**Collect Alignment Summary Metrics** - -Reads a SAM or BAM file and writes a file containing summary alignment metrics. - .. csv-table:: ASMDoc :header-rows: 1 @@ -130,13 +122,7 @@ "IS_BISULFITE_SEQUENCED=Boolean","Whether the SAM or BAM file consists of bisulfite sequenced reads. Default value: false. " "CREATE_MD5_FILE=Boolean","Whether to create an MD5 digest for any BAM files created." - -AlignmentSummaryMetrics - -High level metrics about the alignment of reads within a SAM file, produced by the CollectAlignmentSummaryMetrics program and usually stored in a file -with the extension ".alignment_summary_metrics". - -Output Column Definitions +The output produced by the tool has the following columns: #. CATEGORY: One of either UNPAIRED (for a fragment run), FIRST_OF_PAIR when metrics are for only the first read in a paired run, SECOND_OF_PAIR when the metrics are for only the second read in a paired run or PAIR when the metrics are aggregeted for both first and second reads in a pair. #. TOTAL_READS: The total number of reads including all PF and non-PF reads. When CATEGORY equals PAIR this value will be 2x the number of clusters. @@ -158,6 +144,15 @@ #. PCT_CHIMERAS: The percentage of reads that map outside of a maximum insert size (usually 100kb) or that have the two ends mapping to different chromosomes. #. PCT_ADAPTER: The percentage of PF reads that are unaligned and match to a known adapter sequence right from the start of the read. +.. class:: warningmark + +**Warning on Sam quality** + +Unfortunately some packages seem perfectly capable of producing sam and bam files +that Picard will be picky about otherwise. Galaxy deals with this by using the lenient +flag, which allows reads to be discarded if they're empty or don't map. This appears +to be the only way to deal with sam that cannot be parsed. + ----- .. class:: infomark @@ -168,9 +163,6 @@ Note that last parameter - your life will be far easier if you use it. -Unfortunately some packages seem perfectly capable of producing sam and bam files that Picard will be picky about otherwise. -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. </help></tool> --- a/tools/picard/rgPicardFixMate.xml Wed May 18 16:52:14 2011 -0400 +++ b/tools/picard/rgPicardFixMate.xml Wed May 18 16:52:38 2011 -0400 @@ -50,6 +50,12 @@ Ensure that all mate-pair information is in sync between each read and it's mate pair. +**Picard documentation** + +This is a Galaxy wrapper for FixMateInformation, a part of the external package Picard-tools_. + + .. _Picard-tools: http://www.google.com/search?q=picard+samtools + .. class:: warningmark **Useful for paired data only** @@ -59,20 +65,6 @@ the data you choose are valid (paired end) sam or bam data - unless you trust this tool not to harm your data. -**Picard documentation** - -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** - -This tool provides a Galaxy interface to one of the Picard tools. -If you need to repair broken paired read sam/bam files, the Picard tool may help. - ----- .. class:: infomark @@ -100,6 +92,16 @@ "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:: warningmark + +**Warning on Sam quality** + +Unfortunately some packages seem perfectly capable of producing sam and bam files +that Picard will be picky about otherwise. Galaxy deals with this by using the lenient +flag, which allows reads to be discarded if they're empty or don't map. This appears +to be the only way to deal with sam that cannot be parsed. + + </help></tool> --- a/tools/picard/rgPicardGCBiasMetrics.xml Wed May 18 16:52:14 2011 -0400 +++ b/tools/picard/rgPicardGCBiasMetrics.xml Wed May 18 16:52:38 2011 -0400 @@ -74,6 +74,20 @@ .. class:: infomark +**Summary** + +This Galaxy tool uses Picard to report detailed metrics about reads that fall within windows of a certain GC bin on the reference genome. + +**Picard documentation** + +This is a Galaxy wrapper for CollectGcBiasMetrics, a part of the external package Picard-tools_. + + .. _Picard-tools: http://www.google.com/search?q=picard+samtools + +----- + +.. class:: infomark + **Syntax** - **Input** is sam/bam format aligned short read data in your current history @@ -86,23 +100,6 @@ .. class:: infomark -**Summary** - -This Galaxy tool uses Picard to report measures of GC bias. - -**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 - **Inputs, outputs, and parameters** The Picard documentation (reformatted for Galaxy) says: @@ -120,11 +117,7 @@ "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 - - Class that holds detailed metrics about reads that fall within windows of a certain GC bin on the reference genome. - -Output Column Definitions +The output produced by the tool has the following columns: #. GC: The G+C content of the reference sequence represented by this bin. Values are from 0% to 100% #. WINDOWS: The number of windows on the reference genome that have this G+C content. @@ -133,6 +126,15 @@ #. NORMALIZED_COVERAGE: The ration of "coverage" in this GC bin vs. the mean coverage of all GC bins. A number of 1 represents mean coverage, a number less than one represents lower than mean coverage (e.g. 0.5 means half as much coverage as average) while a number greater than one represents higher than mean coverage (e.g. 3.1 means this GC bin has 3.1 times more reads per window than average). #. ERROR_BAR_WIDTH: The radius of error bars in this bin based on the number of observations made. For example if the normalized coverage is 0.75 and the error bar width is 0.1 then the error bars would be drawn from 0.65 to 0.85. +.. class:: warningmark + +**Warning on Sam quality** + +Unfortunately some packages seem perfectly capable of producing sam and bam files +that Picard will be picky about otherwise. Galaxy deals with this by using the lenient +flag, which allows reads to be discarded if they're empty or don't map. This appears +to be the only way to deal with sam that cannot be parsed. + ----- .. class:: infomark @@ -143,13 +145,5 @@ MINIMUM_GENOME_FRACTION=0.00001 INPUT=test.bam OUTPUT=picardASMetrics.txt OUTPUT=test.txt CHART_OUTPUT=test.pdf WINDOW_SIZE=100 VALIDATION_STRINGENCY=LENIENT -Note that last parameter - your life will be far easier if you use it. -Unfortunately some packages seem perfectly capable of producing sam and bam -files that Picard will be picky about otherwise. -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. - </help></tool> --- a/tools/picard/rgPicardHsMetrics.xml Wed May 18 16:52:14 2011 -0400 +++ b/tools/picard/rgPicardHsMetrics.xml Wed May 18 16:52:38 2011 -0400 @@ -114,22 +114,23 @@ #. HS_PENALTY_20X: The "hybrid selection penalty" incurred to get 80% of target bases to 20X. This metric should be interpreted as: if I have a design with 10 megabases of target, and want to get 20X coverage I need to sequence until PF_ALIGNED_BASES = 10^6 * 20 * HS_PENALTY_20X. #. HS_PENALTY_30X: The "hybrid selection penalty" incurred to get 80% of target bases to 10X. This metric should be interpreted as: if I have a design with 10 megabases of target, and want to get 30X coverage I need to sequence until PF_ALIGNED_BASES = 10^6 * 30 * HS_PENALTY_30X. +.. class:: warningmark + +**Warning on Sam quality** + +Unfortunately some packages seem perfectly capable of producing sam and bam files +that Picard will be picky about otherwise. Galaxy deals with this by using the lenient +flag, which allows reads to be discarded if they're empty or don't map. This appears +to be the only way to deal with sam that cannot be parsed. + ----- .. class:: infomark - -*Typical tool invocation without Galaxy is on a command line - eg:* +**Typical tool invocation without Galaxy is on a command line - eg:** java -jar /share/shared/galaxy/tool-data/shared/jars/CalculateHsMetrics.jar BAIT_INTERVALS=test.pic TARGET_INTERVALS=test.pic INPUT=test.bam OUTPUT=picardHsMetrics.txt VALIDATION_STRINGENCY=LENIENT -Note that last parameter - your life will be far easier if you use it as some of the external packages that -Galaxy relies upon are capable of producing sam/bam -files that Picard will refuse to parse. - -The lenient flag means reads are discarded if empty or off the end of the map - or whatever. Suggestions for -improvement are welcome. - </help></tool> --- a/tools/picard/rgPicardInsertSize.xml Wed May 18 16:52:14 2011 -0400 +++ b/tools/picard/rgPicardInsertSize.xml Wed May 18 16:52:38 2011 -0400 @@ -44,20 +44,18 @@ Reads a SAM or BAM file and describes the distribution of insert size (excluding duplicates) with metrics and a histogram plot. +**Picard documentation** + +This is a Galaxy wrapper for CollectInsertSizeMetrics, a part of the external package Picard-tools_. + + .. _Picard-tools: http://www.google.com/search?q=picard+samtools + .. 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 @@ -79,5 +77,14 @@ "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:: warningmark + +**Warning on Sam quality** + +Unfortunately some packages seem perfectly capable of producing sam and bam files +that Picard will be picky about otherwise. Galaxy deals with this by using the lenient +flag, which allows reads to be discarded if they're empty or don't map. This appears +to be the only way to deal with sam that cannot be parsed. + </help></tool> --- a/tools/picard/rgPicardLibComplexity.xml Wed May 18 16:52:14 2011 -0400 +++ b/tools/picard/rgPicardLibComplexity.xml Wed May 18 16:52:38 2011 -0400 @@ -72,26 +72,9 @@ **Picard documentation** -This is a Galaxy wrapper for EstimateLibraryComplexity_, a part of the external package Picard-tools_, which is supported by the SAMTools_ project. +This is a Galaxy wrapper for EstimateLibraryComplexity, a part of the external package Picard-tools_. - .. _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. - - -**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]+).*. + .. _Picard-tools: http://www.google.com/search?q=picard+samtools ----- @@ -114,6 +97,26 @@ "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:: warningmark + +**Warning on Sam quality** + +Unfortunately some packages seem perfectly capable of producing sam and bam files +that Picard will be picky about otherwise. Galaxy deals with this by using the lenient +flag, which allows reads to be discarded if they're empty or don't map. This appears +to be the only way to deal with sam that cannot be parsed. + +.. class:: infomark + +**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]+).*. + + </help></tool> --- a/tools/picard/rgPicardMarkDups.xml Wed May 18 16:52:14 2011 -0400 +++ b/tools/picard/rgPicardMarkDups.xml Wed May 18 16:52:38 2011 -0400 @@ -72,11 +72,13 @@ **Picard documentation** -This is a Galaxy interface to the external package Picard-tools_ tool MarkDuplicates, which is supported by the SAMTools_ project. +This is a Galaxy wrapper for MarkDuplicates, a part of the external package Picard-tools_. - .. _MarkDuplicates: http://picard.sourceforge.net/command-line-overview.shtml#MarkDuplicates - .. _Picard-tools: http://picard.sourceforge.net/index.shtml - .. _SAMTools: http://samtools.sourceforge.net/ + .. _Picard-tools: http://www.google.com/search?q=picard+samtools + +----- + +.. class:: infomark **Inputs, outputs, and parameters** @@ -96,6 +98,17 @@ "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" +.. class:: warningmark + +**Warning on Sam quality** + +Unfortunately some packages seem perfectly capable of producing sam and bam files +that Picard will be picky about otherwise. Galaxy deals with this by using the lenient +flag, which allows reads to be discarded if they're empty or don't map. This appears +to be the only way to deal with sam that cannot be parsed. + +.. class:: infomark + **Note on the Regular Expression** (from the Picard docs) @@ -109,12 +122,6 @@ remove duplicates option is selected. In some cases you may want to do this, but please only do this if you really understand what you are doing. -**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. - - </help></tool> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.