cleanup of tool_conf.xml

galaxyproject · Oct 17, 2014 · 566fdc9 · 566fdc9
1 parent cf32b45
commit 566fdc9
Showing 1 changed file with 0 additions and 70 deletions.
diff --git a/files/galaxy/test.galaxyproject.org/config/tool_conf.xml b/files/galaxy/test.galaxyproject.org/config/tool_conf.xml
@@ -104,83 +104,13 @@
     <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" />
   </section>
   <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" />
-    <tool file="mutation/visualize.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>