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Anonymous committed ea8f66d

changes made to the tool_conf_ci file for GATK2.8

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File tool_conf_ci.xml

 <?xml version="1.0"?>
 <toolbox>
   <!-- keep our tools at the top for now? -->
-  <section name="Tool Installer" id="ToolInstaller">
-    <tool file="tool_installer/repo_installer.xml"/>
-    <tool file="tool_installer/tool_info_grabber.xml"/>
-  </section>
-
   <label text="Data Transfer" id="data_transfer" />
-  <section name="Amazon S3" id="globus_s3_get_data">
-    <tool file="globus/from_s3.xml"/>
-  </section>
-
   <section name="Globus Data Transfer" id="globus">
     <tool file="globus/from_go.xml" />
     <tool file="globus/from_go_text.xml" />
     <tool file="globus/to_go.xml" />
+    <tool file="globus/from_go_plain.xml" />
+    <tool file="globus/to_go_plain.xml" />
     <tool file="globus/transfer.xml" />
     <tool file="globus/directory_dataset_hack.xml" />
   </section>
     
     <label text="Illumina fastq" id="illumina" />
     <tool file="fastq/fastq_groomer.xml" />
-    <tool file="fastq/fastq_groomer_parallel.xml" />
     <tool file="fastq/fastq_paired_end_splitter.xml" />
     <tool file="fastq/fastq_paired_end_joiner.xml" />
     <tool file="fastq/fastq_stats.xml" />
     <tool file="solid_tools/solid_qual_stats.xml" />
     <tool file="solid_tools/solid_qual_boxplot.xml" />
     
-    <label text="FASTQ manipulation" id="generic_fastq" />
+    <label text="Generic FASTQ manipulation" id="generic_fastq" />
     <tool file="fastq/fastq_filter.xml" />
     <tool file="fastq/fastq_trimmer.xml" />
     <tool file="fastq/fastq_trimmer_by_quality.xml" />
     <tool file="fastq/fastq_to_fasta.xml" />
     <tool file="fastq/fastq_to_tabular.xml" />
     <tool file="fastq/tabular_to_fastq.xml" />
-    <tool file="fastq_validator/fastqvalidator.xml" />    
-    <tool file="ea_utils/fastq-join.xml" />
-    <tool file="fastq_mcf/fastq-mcf.xml" />
-    <tool file="scythe/scythe.xml" />
     <tool file="sickle/sickle.xml" />
-    <tool file="cutadapt/cutadapt.xml" />
-
+    
     <label text="FASTX-Toolkit for FASTQ data" id="fastx_toolkit" />
     <tool file="fastx_toolkit/fastq_quality_converter.xml" />
     <tool file="fastx_toolkit/fastx_quality_statistics.xml" />
     <label text="ROCHE-454" id="mapping_454" />
     <tool file="metag_tools/megablast_wrapper.xml" />
     <tool file="metag_tools/megablast_xml_parser.xml" />
+    <label text="Ion-Torrent" id="ion_torrent" />
+    <tool file="tmap/tmap_wrapper.xml" />
 <!--    <tool file="sr_mapping/lastz_wrapper.xml" />
     <tool file="sr_mapping/lastz_paired_reads_wrapper.xml" />
     <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"/> -->
-    <label id="bgi" text="BGI SOAP Package Beta"/>
-    <tool file="bgisoap/soap1.xml"/>
-    <tool file="bgisoap/soap2.xml"/>
   </section>
 
   <section name="NGS: Mapping QC" id="cov_qc">
     <tool file="coverage/findLowCovPositions.xml" />
     <tool file="coverage/summarizeLowCovAreas.xml" />
     <tool file="coverage/coverageStats.xml" />
-    <tool file="ea_utils/sam-stats.xml" />
   </section>
 
   <section name="NGS: RNA Analysis" id="ngs-rna-tools">
     <label text="Transcriptome Alignment" id="rna_seq_alignment" />
     <tool file="ngs_rna/tophat_wrapper.xml" />
+    <tool file="ngs_rna/tophat2_wrapper.xml" />
     <tool file="ngs_rna/tophat_color_wrapper.xml" />
     <label text="Cufflinks Package " id="rna_seq_tools" />
     <tool file="ngs_rna/cufflinks_wrapper.xml" />
     <tool file="miso/miso_compute_events_psi.xml"/>
     <tool file="miso/miso_summarize_samples.xml"/>
     <tool file="miso/miso_compare_samples.xml"/>
+    <label text="RSeqC" id="rseqc"/>
+    <tool file="rseqc/bam2wig.xml"/>
+    <tool file="rseqc/bam_stat.xml"/>
+    <tool file="rseqc/clipping_profile.xml"/>
+    <tool file="rseqc/geneBody_coverage2.xml"/>
+    <tool file="rseqc/geneBody_coverage.xml"/>
+    <tool file="rseqc/infer_experiment.xml"/>
+    <tool file="rseqc/inner_distance.xml"/>
+    <tool file="rseqc/junction_annotation.xml"/>
+    <tool file="rseqc/junction_saturation.xml"/>
+    <tool file="rseqc/read_distribution.xml"/>
+    <tool file="rseqc/read_duplication.xml"/>
+    <tool file="rseqc/read_GC.xml"/>
+    <tool file="rseqc/read_NVC.xml"/>
+    <tool file="rseqc/read_quality.xml"/>
+    <tool file="rseqc/RPKM_count.xml"/>
+    <tool file="rseqc/RPKM_saturation.xml"/>
+    <label text="HTseq" id="htseq"/>
+    <tool file="htseq/htseq-count.xml"/>
+
     <!-- Trinity is very memory-intensive and should only be enabled/run
     on instances with sufficient resources. 
     <label text="De novo Assembly" id="de_novo_assembly "/>
     -->
     <label text="Filtering" id="filtering" />
     <tool file="ngs_rna/filter_transcripts_via_tracking.xml" />
+    <tool file="deseq/sam2counts.xml" />
+    <tool file="deseq/deseq.xml" />
+    <tool file="dexseq/dexseq_prepare_annotation.xml" />
+    <tool file="dexseq/dexseq_counts.xml" />
+    <tool file="dexseq/dexseq.xml" />
     <label text="Visualization" id="visualization" />
     <tool file="ngs_rna/cummerbund_wrapper.xml" />
-    <label text="Fusion Sites" id="fusion" />
-    <tool file="defuse/defuse.xml" />
   </section>
 
   <section name="NGS: Peak Calling" id="peak_calling">
     <tool file="samtools/pileup_interval.xml" />
     <tool file="samtools/samtools_flagstat.xml" />
     <tool file="samtools/samtools_rmdup.xml" />
-    <tool file="samtools/samtools_fixmate.xml" />
     <tool file="samtools/samtools_slice_bam.xml" />
     <tool file="samtools/samtools_sort.xml" />
     <tool file="samtools/samtools_varfilter.xml" />
     <tool file="indels/indel_sam2interval.xml" />
     <tool file="indels/indel_table.xml" />
     <tool file="indels/indel_analysis.xml" />
-    <label text="BGI SOAP indel tools" id="soapindel" />
-    <tool file="bgisoap/msort.xml"/>
-    <tool file="bgisoap/soapsnp.xml"/>
-    <tool file="bgisoap/soappopindel.xml"/>
   </section>
 
   <section name="NGS: GATK Tools" id="gatk">
   <section name="NGS: GATK2 Tools" id="gatk2">
     <label text="Alignment Utilities" id="gatk2_bam_utilities"/>
     <tool file="gatk2/gatk2_depth_of_coverage.xml" />
-    <tool file="gatk2/gatk2_print_reads.xml" />
+    <tool file="gatk2/gatk2_reduce_reads.xml" />
     
     <label text="Realignment" id="gatk2_realignment" />
     <tool file="gatk2/gatk2_realigner_target_creator.xml" />
     <tool file="gatk2/gatk2_indel_realigner.xml" />
     
     <label text="Base Recalibration" id="gatk2_recalibration" />
-    <tool file="gatk2/count_covariates.xml" />
-    <tool file="gatk2/table_recalibration.xml" />
-    <tool file="gatk2/analyze_covariates.xml" />
+    <tool file="gatk2/gatk2_base_recalibrator.xml" />
+    <tool file="gatk2/gatk2_print_reads.xml" />
+<!--    <tool file="gatk2/analyze_covariates.xml" /> -->
     
     <label text="Genotyping" id="gatk2_genotyping" />
     <tool file="gatk2/gatk2_unified_genotyper.xml" />
     <!-- <tool file="variant_detection/freebayes.xml" /> -->
     <tool file="freebayes/freebayes_DirectoryInput.xml"/>
 
-    <label text="Additional" id="others"/>
+    <label text="Polymutt" id="polymutt"/>
     <tool file="polymutt/polymutt.xml"/>
-    <tool file="somatic_sniper/somatic_sniper.xml" />
+
+    <label text="somatic" id="somatic"/>
     <tool file="mutect/muTect.xml"/>
-    <tool file="bgisoap/soappileup.xml"/>
-    <tool file="bgisoap/snvtest.xml"/>
-    <tool file="bgisoap/alleleqc.xml"/>
-    <tool file="bgisoap/snvdetect.xml"/>
-
-    <label text="Structural: SVDetect" id="svdetect"/>
-    <tool file="svdetect/BAM_preprocessingPairs.xml"/>
-    <tool file="svdetect/SVDetect_run_parallel.xml"/>
-    <tool file="svdetect/SVDetect_compare.xml"/>
-
   </section>
 
   <section name="NGS: Interval Tools" id="interval_tools">
     <tool file="kent_tools/bedIntersect.xml" /> -->
     <label text="BEDTools" id="bedtools"/>
     <tool file="bedtools/intersectBed_bed.xml" />
-    <tool file="bedtools/intersectBed_bam.xml" />
-    <tool file="bedtools/multiIntersectBed.xml" />
-    <tool file="bedtools/bamToBed.xml" />
-    <tool file="bedtools/coverageBed_counts.xml" />
-    <tool file="bedtools/genomeCoverageBed_bedgraph.xml" />
-    <tool file="bedtools/genomeCoverageBed_histogram.xml" />
-    <tool file="bedtools/unionBedGraphs.xml" />
   </section>
 
   <section name="NGS: VCF Tools" id="vcf_tools">
     <label text="Formatting" id="vcf_formatting" /> 
     <tool file="variant_detection/pileup2vcf.xml" />
-    <tool file="vcf_tools/vcftools.xml" />
-    <tool file="tabix/bgzip.xml" />
-    <tool file="tabix/tabix.xml" />
 
     <label text="Filtering" id="vcf_filtering" /> 
     <tool file="vcf_tools/intersect.xml" />
   </section>
   <section name="Join, Subtract and Group" id="group">
     <tool file="filters/joiner.xml" />
+    <tool file="filters/joiner_multiple.xml" />
     <tool file="filters/compare.xml"/>
     <tool file="new_operations/subtract_query.xml"/>
     <tool file="stats/grouping.xml" />