details: http://www.bx.psu.edu/hg/galaxy/rev/f0e32644688b changeset: 3474:f0e32644688b user: Dan Blankenberg <dan@bx.psu.edu> date: Wed Mar 03 15:18:09 2010 -0500 description: Update tool_conf.xml.main to use the new FASTQ tools. Minor updates to help text for a few of the FASTQ tools. diffstat: tool_conf.xml.main | 15 +++++++++++++-- tools/fastq/fastq_filter.xml | 2 +- tools/fastq/fastq_groomer.xml | 5 ++++- tools/fastq/fastq_manipulation.xml | 10 +++++----- tools/fastq/fastq_trimmer.xml | 2 +- 5 files changed, 24 insertions(+), 10 deletions(-) diffs (116 lines): diff -r d6d156b04767 -r f0e32644688b tool_conf.xml.main --- a/tool_conf.xml.main Wed Mar 03 14:34:31 2010 -0500 +++ b/tool_conf.xml.main Wed Mar 03 15:18:09 2010 -0500 @@ -265,20 +265,31 @@ </section> <label text="NGS Toolbox Beta" id="ngs" /> <section name="NGS: QC and manipulation" id="cshl_library_information"> - <label text="Generic FASTQ data" id="fastq" /> + <label text="Illumina data" id="illumina" /> + <tool file="fastq/fastq_groomer.xml" /> + <tool file="fastq/fastq_paired_end_splitter.xml" /> + <tool file="fastq/fastq_paired_end_joiner.xml" /> + <tool file="fastq/fastq_stats.xml" /> + <!--<label text="Deprecated: Generic FASTQ data" id="fastq" /> <tool file="next_gen_conversion/fastq_gen_conv.xml" /> <tool file="fastx_toolkit/fastq_quality_converter.xml" /> <tool file="fastx_toolkit/fastx_quality_statistics.xml" /> <tool file="fastx_toolkit/fastq_quality_boxplot.xml" /> <tool file="fastx_toolkit/fastx_nucleotides_distribution.xml" /> - <tool file="metag_tools/split_paired_reads.xml" /> + <tool file="metag_tools/split_paired_reads.xml" /> --> <label text="Roche-454 data" id="454" /> <tool file="metag_tools/short_reads_figure_score.xml" /> <tool file="metag_tools/short_reads_trim_seq.xml" /> + <tool file="fastq/fastq_combiner.xml" /> <label text="AB-SOLiD data" id="solid" /> <tool file="next_gen_conversion/solid2fastq.xml" /> <tool file="solid_tools/solid_qual_stats.xml" /> <tool file="solid_tools/solid_qual_boxplot.xml" /> + <label text="Generic FASTQ manipulation" id="generic_fastq" /> + <tool file="fastq/fastq_filter.xml" /> + <tool file="fastq/fastq_trimmer.xml" /> + <tool file="fastq/fastq_manipulation.xml" /> + <tool file="fastq/fastq_to_fasta.xml" /> </section> <section name="NGS: Mapping" id="ngs_mapping"> <label text="Illumina" id="illumina"/> diff -r d6d156b04767 -r f0e32644688b tools/fastq/fastq_filter.xml --- a/tools/fastq/fastq_filter.xml Wed Mar 03 14:34:31 2010 -0500 +++ b/tools/fastq/fastq_filter.xml Wed Mar 03 15:18:09 2010 -0500 @@ -16,7 +16,7 @@ <param name="paired_end" label="This is paired end data" type="boolean" truevalue="paired_end" falsevalue="single_end" checked="False"/> <repeat name="fastq_filters" title="Quality Filter on a Range of Bases" help="The above settings do not apply to these filters."> <conditional name="offset_type"> - <param name="base_offset_type" type="select" label="Define Base Offsets as" help="Absolute for e.g. fixed length reads.<br>Percentage for e.g. variable length reads."> + <param name="base_offset_type" type="select" label="Define Base Offsets as" help="Use Absolute for fixed length reads (Illumina, SOLiD)<br>Use Percentage for variable length reads (Roche/454)"> <option value="offsets_absolute" selected="true">Absolute Values</option> <option value="offsets_percent">Percentage of Read Length</option> </param> diff -r d6d156b04767 -r f0e32644688b tools/fastq/fastq_groomer.xml --- a/tools/fastq/fastq_groomer.xml Wed Mar 03 14:34:31 2010 -0500 +++ b/tools/fastq/fastq_groomer.xml Wed Mar 03 15:18:09 2010 -0500 @@ -317,7 +317,7 @@ When converting, if a quality score falls outside of the target score range, it will be coerced to the closest available value (i.e. the minimum or maximum). -When converting between Solexa and the other formats, quality scores are mapped between Solexa and PHRED scales using the equations found in Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res. 2009 Dec 16. +When converting between Solexa and the other formats, quality scores are mapped between Solexa and PHRED scales using the equations found in `Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res. 2009 Dec 16.`_ When converting between color space (csSanger) and base/sequence space (Sanger, Illumina, Solexa) formats, adapter bases are lost or gained; if gained, the base 'G' is used as the adapter. You cannot convert a color space read to base space if there is no adapter present in the color space sequence. Any masked or ambiguous nucleotides in base space will be converted to 'N's when determining color space encoding. @@ -340,5 +340,8 @@ Diagram adapted from http://en.wikipedia.org/wiki/FASTQ_format + +.. _Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res. 2009 Dec 16.: http://www.ncbi.nlm.nih.gov/pubmed/20015970 + </help> </tool> diff -r d6d156b04767 -r f0e32644688b tools/fastq/fastq_manipulation.xml --- a/tools/fastq/fastq_manipulation.xml Wed Mar 03 14:34:31 2010 -0500 +++ b/tools/fastq/fastq_manipulation.xml Wed Mar 03 15:18:09 2010 -0500 @@ -89,25 +89,25 @@ </when> <when value="trim"> <conditional name="offset_type"> - <param name="base_offset_type" type="select" label="Define Base Offsets as" help="Absolute for e.g. fixed length reads.<br>Percentage for e.g. variable length reads."> + <param name="base_offset_type" type="select" label="Define Base Offsets as" help="Use Absolute for fixed length reads (Illumina, SOLiD)<br>Use Percentage for variable length reads (Roche/454)"> <option value="offsets_absolute" selected="true">Absolute Values</option> <option value="offsets_percent">Percentage of Read Length</option> </param> <when value="offsets_absolute"> - <param name="left_column_offset" label="Absolute Left Base Offset" value="0" type="integer" help="Values start at 0, increasing from the left"> + <param name="left_column_offset" label="Offset from 5' end" value="0" type="integer" help="Values start at 0, increasing from the left"> <validator type="in_range" message="Base Offsets must be positive" min="0" max="inf"/> <validator type="expression" message="An integer is required.">int( float( value ) ) == float( value )</validator> </param> - <param name="right_column_offset" label="Absolute Right Base Offset" value="0" type="integer" help="Values start at 0, increasing from the right"> + <param name="right_column_offset" label="Offset from 3' end" value="0" type="integer" help="Values start at 0, increasing from the right"> <validator type="in_range" message="Base Offsets must be positive" min="0" max="inf"/> <validator type="expression" message="An integer is required.">int( float( value ) ) == float( value )</validator> </param> </when> <when value="offsets_percent"> - <param name="left_column_offset" label="Percentage Left Base Offset" value="0" type="float"> + <param name="left_column_offset" label="Offset from 5' end" value="0" type="float"> <validator type="in_range" message="Base Offsets must be between 0 and 100" min="0" max="100"/> </param> - <param name="right_column_offset" label="Percentage Right Base Offset" value="0" type="float"> + <param name="right_column_offset" label="Offset from 3' end" value="0" type="float"> <validator type="in_range" message="Base Offsets must be between 0 and 100" min="0" max="100"/> </param> </when> diff -r d6d156b04767 -r f0e32644688b tools/fastq/fastq_trimmer.xml --- a/tools/fastq/fastq_trimmer.xml Wed Mar 03 14:34:31 2010 -0500 +++ b/tools/fastq/fastq_trimmer.xml Wed Mar 03 15:18:09 2010 -0500 @@ -4,7 +4,7 @@ <inputs> <param name="input_file" type="data" format="fastqsanger,fastqcssanger" label="FASTQ File"/> <conditional name="offset_type"> - <param name="base_offset_type" type="select" label="Define Base Offsets as"> + <param name="base_offset_type" type="select" label="Define Base Offsets as" help="Use Absolute for fixed length reads (Illumina, SOLiD)<br>Use Percentage for variable length reads (Roche/454)"> <option value="offsets_absolute" selected="true">Absolute Values</option> <option value="offsets_percent">Percentage of Read Length</option> </param>