1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d519ad654358/ Changeset: d519ad654358 User: martenson Date: 2014-11-11 17:26:45+00:00 Summary: Merged in anton/galaxy-central-anton (pull request #539) Initial tweaks to tool_conf.xml sample and one of the tools. Affected #: 2 files diff -r 932f4bbf2c317fc5dc735777d167765d907a0e0d -r d519ad65435883112008e90ec06ebf44a91586e7 config/tool_conf.xml.sample --- a/config/tool_conf.xml.sample +++ b/config/tool_conf.xml.sample @@ -104,10 +104,6 @@ <tool file="maf/maf_reverse_complement.xml" /><tool file="maf/maf_filter.xml" /></section> - <section id="scores" name="Get Genomic Scores"> - <tool file="filters/wiggle_to_simple.xml" /> - <tool file="stats/aggregate_binned_scores_in_intervals.xml" /> - </section><section id="stats" name="Statistics"><tool file="stats/gsummary.xml" /><tool file="filters/uniq.xml" /> @@ -115,71 +111,6 @@ <section id="plots" name="Graph/Display Data"><tool file="plotting/bar_chart.xml" /><tool file="plotting/boxplot.xml" /> - <tool file="visualization/LAJ.xml" /><tool file="maf/vcf_to_maf_customtrack.xml" /></section> - <section id="hyphy" name="Evolution"> - <tool file="evolution/codingSnps.xml" /> - <tool file="evolution/add_scores.xml" /> - </section> - <section id="motifs" name="Motif Tools"> - <tool file="meme/meme.xml" /> - <tool file="meme/fimo.xml" /> - </section> - <section id="NGS_QC" name="NGS: QC and manipulation"> - - <label id="fastqcsambam" text="FastQC: fastq/sam/bam" /> - - <label id="illumina" text="Illumina fastq" /> - - <label id="454" text="Roche-454 data" /> - <label id="solid" text="AB-SOLiD data" /> - <tool file="next_gen_conversion/solid2fastq.xml" /> - <tool file="solid_tools/solid_qual_stats.xml" /> - <tool file="solid_tools/solid_qual_boxplot.xml" /> - - <label id="generic_fastq" text="Generic FASTQ manipulation" /> - - <label id="fastx_toolkit" text="FASTX-Toolkit for FASTQ data" /> - </section> - <!-- - Keep this section commented until it includes tools that - will be hosted on test/main. The velvet wrappers have been - included in the distribution but will not be hosted on our - public servers for the current time. - <section name="NGS: Assembly" id="ngs_assembly"> - <label text="Velvet" id="velvet"/> - <tool file="sr_assembly/velvetg.xml" /> - <tool file="sr_assembly/velveth.xml" /> - </section> - --> - <section id="solexa_tools" name="NGS: Mapping"> - <tool file="sr_mapping/bfast_wrapper.xml" /> - <tool file="sr_mapping/PerM.xml" /> - <tool file="sr_mapping/srma_wrapper.xml" /> - <tool file="sr_mapping/mosaik.xml" /> - </section> - <section id="ngs-rna-tools" name="NGS: RNA Analysis"> - - <label id="rna_seq" text="RNA-seq" /> - <label id="filtering" text="Filtering" /> - </section> - <section id="samtools" name="NGS: SAM Tools"> - </section> - <section id="ngs-simulation" name="NGS: Simulation"> - <tool file="ngs_simulation/ngs_simulation.xml" /> - </section> - <section id="hgv" name="Phenotype Association"> - <tool file="evolution/codingSnps.xml" /> - <tool file="evolution/add_scores.xml" /> - <tool file="phenotype_association/sift.xml" /> - <tool file="phenotype_association/linkToGProfile.xml" /> - <tool file="phenotype_association/linkToDavid.xml" /> - <tool file="phenotype_association/ldtools.xml" /> - <tool file="phenotype_association/pass.xml" /> - <tool file="phenotype_association/gpass.xml" /> - <tool file="phenotype_association/beam.xml" /> - <tool file="phenotype_association/lps.xml" /> - <tool file="phenotype_association/master2pg.xml" /> - </section></toolbox> diff -r 932f4bbf2c317fc5dc735777d167765d907a0e0d -r d519ad65435883112008e90ec06ebf44a91586e7 tools/filters/uniq.xml --- a/tools/filters/uniq.xml +++ b/tools/filters/uniq.xml @@ -26,8 +26,7 @@ </test></tests><help> - - .. class:: infomark +.. class:: infomark **TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert* 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.