1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/c99af10d79a4/ changeset: r5549:c99af10d79a4 user: kellyv date: 2011-05-12 19:38:00 summary: Updated help section of BWA wrappers to include tags for the RG header record type affected #: 2 files (120 bytes)
--- a/tools/sr_mapping/bwa_color_wrapper.xml Thu May 12 12:20:52 2011 -0400 +++ b/tools/sr_mapping/bwa_color_wrapper.xml Thu May 12 13:38:00 2011 -0400 @@ -137,23 +137,23 @@ <option value="no">No</option></param><when value="yes"> - <param name="rgid" type="text" size="25" label="Read group identifier. Each @RG line must have a unique ID. The value of ID is used in the RG + <param name="rgid" type="text" size="25" label="Read group identifier (ID). Each @RG line must have a unique ID. The value of ID is used in the RG tags of alignment records. Must be unique among all read groups in header section." help="Required if RG specified. Read group IDs may be modified when merging SAM files in order to handle collisions." /> - <param name="rgcn" type="text" size="25" label="Sequencing center that produced the read" help="Optional" /> - <param name="rgds" type="text" size="25" label="Description" help="Optional" /> - <param name="rgdt" type="text" size="25" label="Date that run was produced (ISO8601 format date or date/time, like YYYY-MM-DD)" help="Optional" /> - <param name="rgfo" type="text" size="25" label="Flow order. The array of nucleotide bases that correspond to the nucleotides used for each -flow of each read." help="Optional. Multi-base flows are encoded in IUPAC format, and non-nucleotide flows by + <param name="rgcn" type="text" size="25" label="Sequencing center that produced the read (CN)" help="Optional" /> + <param name="rgds" type="text" size="25" label="Description (DS)" help="Optional" /> + <param name="rgdt" type="text" size="25" label="Date that run was produced (DT)" help="Optional. ISO8601 format date or date/time, like YYYY-MM-DD" /> + <param name="rgfo" type="text" size="25" label="Flow order (FO). The array of nucleotide bases that correspond to the nucleotides used for each +flow of each read." help="Optional. Multi-base flows are encoded in IUPAC format, and non-nucleotide flows by various other characters. Format : /\*|[ACMGRSVTWYHKDBN]+/" /> - <param name="rgks" type="text" size="25" label="The array of nucleotide bases that correspond to the key sequence of each read" help="Optional" /> - <param name="rglb" type="text" size="25" label="Library name" help="Required if RG specified" /> - <param name="rgpg" type="text" size="25" label="Programs used for processing the read group" help="Optional" /> - <param name="rgpi" type="text" size="25" label="Predicted median insert size" help="Optional" /> - <param name="rgpl" type="text" size="25" label="Platform/technology used to produce the reads. Valid values : CAPILLARY, LS454, ILLUMINA, -SOLID, HELICOS, IONTORRENT and PACBIO" help="Required if RG specified" /> - <param name="rgpu" type="text" size="25" label="Platform unit (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD). Unique identifier." help="Optional" /> - <param name="rgsm" type="text" size="25" label="Sample. Use pool name where a pool is being sequenced" help="Required if RG specified" /> + <param name="rgks" type="text" size="25" label="The array of nucleotide bases that correspond to the key sequence of each read (KS)" help="Optional" /> + <param name="rglb" type="text" size="25" label="Library name (LB)" help="Required if RG specified" /> + <param name="rgpg" type="text" size="25" label="Programs used for processing the read group (PG)" help="Optional" /> + <param name="rgpi" type="text" size="25" label="Predicted median insert size (PI)" help="Optional" /> + <param name="rgpl" type="text" size="25" label="Platform/technology used to produce the reads (PL)" help="Required if RG specified. Valid values : CAPILLARY, LS454, ILLUMINA, +SOLID, HELICOS, IONTORRENT and PACBIO" /> + <param name="rgpu" type="text" size="25" label="Platform unit (PU)" help="Optional. Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" /> + <param name="rgsm" type="text" size="25" label="Sample (SM)" help="Required if RG specified. Use pool name where a pool is being sequenced" /></when><when value="no" /></conditional>
--- a/tools/sr_mapping/bwa_wrapper.xml Thu May 12 12:20:52 2011 -0400 +++ b/tools/sr_mapping/bwa_wrapper.xml Thu May 12 13:38:00 2011 -0400 @@ -130,23 +130,23 @@ <option value="no">No</option></param><when value="yes"> - <param name="rgid" type="text" size="25" label="Read group identifier. Each @RG line must have a unique ID. The value of ID is used in the RG + <param name="rgid" type="text" size="25" label="Read group identifier (ID). Each @RG line must have a unique ID. The value of ID is used in the RG tags of alignment records. Must be unique among all read groups in header section." help="Required if RG specified. Read group IDs may be modified when merging SAM files in order to handle collisions." /> - <param name="rgcn" type="text" size="25" label="Sequencing center that produced the read" help="Optional" /> - <param name="rgds" type="text" size="25" label="Description" help="Optional" /> - <param name="rgdt" type="text" size="25" label="Date that run was produced (ISO8601 format date or date/time, like YYYY-MM-DD)" help="Optional" /> - <param name="rgfo" type="text" size="25" label="Flow order. The array of nucleotide bases that correspond to the nucleotides used for each + <param name="rgcn" type="text" size="25" label="Sequencing center that produced the read (CN)" help="Optional" /> + <param name="rgds" type="text" size="25" label="Description (DS)" help="Optional" /> + <param name="rgdt" type="text" size="25" label="Date that run was produced (DT)" help="Optional. ISO8601 format date or date/time, like YYYY-MM-DD" /> + <param name="rgfo" type="text" size="25" label="Flow order (FO). The array of nucleotide bases that correspond to the nucleotides used for each flow of each read." help="Optional. Multi-base flows are encoded in IUPAC format, and non-nucleotide flows by various other characters. Format : /\*|[ACMGRSVTWYHKDBN]+/" /> - <param name="rgks" type="text" size="25" label="The array of nucleotide bases that correspond to the key sequence of each read" help="Optional" /> - <param name="rglb" type="text" size="25" label="Library name" help="Required if RG specified" /> - <param name="rgpg" type="text" size="25" label="Programs used for processing the read group" help="Optional" /> - <param name="rgpi" type="text" size="25" label="Predicted median insert size" help="Optional" /> - <param name="rgpl" type="text" size="25" label="Platform/technology used to produce the reads. Valid values : CAPILLARY, LS454, ILLUMINA, -SOLID, HELICOS, IONTORRENT and PACBIO" help="Required if RG specified" /> - <param name="rgpu" type="text" size="25" label="Platform unit (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD). Unique identifier." help="Optional" /> - <param name="rgsm" type="text" size="25" label="Sample. Use pool name where a pool is being sequenced" help="Required if RG specified" /> + <param name="rgks" type="text" size="25" label="The array of nucleotide bases that correspond to the key sequence of each read (KS)" help="Optional" /> + <param name="rglb" type="text" size="25" label="Library name (LB)" help="Required if RG specified" /> + <param name="rgpg" type="text" size="25" label="Programs used for processing the read group (PG)" help="Optional" /> + <param name="rgpi" type="text" size="25" label="Predicted median insert size (PI)" help="Optional" /> + <param name="rgpl" type="text" size="25" label="Platform/technology used to produce the reads (PL)" help="Required if RG specified. Valid values : CAPILLARY, LS454, ILLUMINA, +SOLID, HELICOS, IONTORRENT and PACBIO" /> + <param name="rgpu" type="text" size="25" label="Platform unit (PU)" help="Optional. Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" /> + <param name="rgsm" type="text" size="25" label="Sample (SM)" help="Required if RG specified. Use pool name where a pool is being sequenced" /></when><when value="no" /></conditional>
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