details: http://www.bx.psu.edu/hg/galaxy/rev/c1e0a15b5cd5 changeset: 2712:c1e0a15b5cd5 user: Anton Nekrutenko <anton@bx.psu.edu> date: Fri Sep 18 10:29:34 2009 -0400 description: Forgot Ross' tools 1 file(s) affected in this change: tool_conf.xml.sample diffs (102 lines): diff -r 8d3037d55621 -r c1e0a15b5cd5 tool_conf.xml.sample --- a/tool_conf.xml.sample Fri Sep 18 10:27:03 2009 -0400 +++ b/tool_conf.xml.sample Fri Sep 18 10:29:34 2009 -0400 @@ -209,6 +209,25 @@ <tool file="samtools/sam_pileup.xml" /> <tool file="samtools/pileup_parser.xml" /> </section> + <section name="Rg Data" id="rgData1"> + <tool file="rgenetics/rgenetics_import.xml"/> + <tool file="rgenetics/rgLpedPbed.xml"/> + <tool file="rgenetics/rgClean.xml"/> + <tool file="rgenetics/rgQC.xml"/> + </section> + <section name="Rg Simulate" id="rgSim1"> + <tool file="rgenetics/rgfakePhe.xml"/> + </section> + <section name="Rg Visualise" id="rgVis1"> + <tool file="rgenetics/rgQC.xml"/> + <tool file="rgenetics/rgEigPCA2.xml"/> + <tool file="rgenetics/rgQQ.xml"/> + </section> + <section name="Rg Model Data" id="rgModel1"> + <tool file="rgenetics/rgGLM.xml"/> + <tool file="rgenetics/rgCaCo.xml"/> + <tool file="rgenetics/rgTDT.xml"/> + </section> <!-- TODO: uncomment the following EMBOSS section whenever moving to test, but comment it in .sample to eliminate @@ -325,72 +344,5 @@ <tool file="emboss_5/emboss_wordcount.xml" /> <tool file="emboss_5/emboss_wordmatch.xml" /> </section> -<<<<<<< local --> -======= - --> - <section name="SOLiD Data Analysis" id="solid_tools"> - <tool file="solid_tools/solid_qual_stats.xml" /> - <tool file="solid_tools/solid_qual_boxplot.xml" /> - <tool file="solid_tools/maq_cs_wrapper.xml" /> - </section> - <section name="FASTA manipulation" id="fasta_manipulation"> - <tool file="fasta_tools/fasta_compute_length.xml" /> - <tool file="fasta_tools/fasta_filter_by_length.xml" /> - <tool file="fasta_tools/fasta_concatenate_by_species.xml" /> - <tool file="fasta_tools/fasta_to_tabular.xml" /> - <tool file="fasta_tools/tabular_to_fasta.xml" /> - </section> - <section name="FASTA/Q Information" id="cshl_library_information"> - <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="fastx_toolkit/fasta_clipping_histogram.xml" /> - </section> - - <section name="FASTA/Q Preprocessing" id="cshl_fastx_manipulation"> - <tool file="fastx_toolkit/fastq_to_fasta.xml" /> - <tool file="fastx_toolkit/fastq_quality_converter.xml" /> - <tool file="fastx_toolkit/fastx_clipper.xml" /> - <tool file="fastx_toolkit/fastx_trimmer.xml" /> - <tool file="fastx_toolkit/fastx_renamer.xml" /> - <tool file="fastx_toolkit/fastx_reverse_complement.xml" /> - <tool file="fastx_toolkit/fasta_formatter.xml" /> - <tool file="fastx_toolkit/fasta_nucleotide_changer.xml" /> - <tool file="fastx_toolkit/fastx_artifacts_filter.xml" /> - <tool file="fastx_toolkit/fastq_quality_filter.xml" /> - <tool file="fastx_toolkit/fastx_collapser.xml" /> - <!--<tool file="fastx_toolkit/fastx_barcode_splitter.xml" />--> - </section> - <section name="Short Read QC and Manipulation" id="short_read_analysis"> - <tool file="metag_tools/short_reads_figure_score.xml" /> - <tool file="metag_tools/short_reads_figure_high_quality_length.xml" /> - <tool file="metag_tools/short_reads_trim_seq.xml" /> - <tool file="metag_tools/blat_coverage_report.xml" /> - <tool file="metag_tools/split_paired_reads.xml" /> - </section> - <section name="Short Read Mapping" id="solexa_tools"> - <tool file="metag_tools/shrimp_color_wrapper.xml" /> - <tool file="metag_tools/shrimp_wrapper.xml" /> - <tool file="sr_mapping/lastz_wrapper.xml" /> - <tool file="metag_tools/megablast_wrapper.xml" /> - <tool file="metag_tools/megablast_xml_parser.xml" /> - <tool file="metag_tools/blat_wrapper.xml" /> - <tool file="metag_tools/mapping_to_ucsc.xml" /> - <tool file="sr_mapping/bowtie_wrapper.xml" /> - <tool file="sr_mapping/bwa_wrapper.xml" /> - </section> - <section name="Tracks" id="tracks"> - <tool file="visualization/genetrack.xml" /> - </section> - <section name="SAM Tools" id="samtools"> - <tool file="samtools/sam_bitwise_flag_filter.xml" /> - <tool file="samtools/sam2interval.xml" /> - <tool file="samtools/sam_to_bam.xml" /> - <tool file="samtools/sam_merge.xml" /> - <tool file="samtools/sam_pileup.xml" /> - <tool file="samtools/pileup_parser.xml" /> - <tool file="samtools/pileup_interval.xml" /> - </section> ->>>>>>> other </toolbox>