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tool_conf.xml
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<?xml version='1.0' encoding='utf-8'?>
<toolbox monitor="true">
<label id="Pre-analysis" text="Pre-analysis"/>
<section id="Data_Preparation" name="Data Preparation">
<tool id="Obtain_Genome_or_Transcriptome_Sequences_and_Annotation" file="1-PRE-ANALYSIS/Data_Preparation/01_Obtain_Genome_Sequences_and_Annotation.xml"/>
<tool id="Obtain_Epitranscriptome_Sequencing_Reads" file="1-PRE-ANALYSIS/Data_Preparation/02_Obtain_Epitranscriptome_Sequencing_Reads.xml"/>
<tool id="Convert_Format" file="1-PRE-ANALYSIS/Data_Preparation/03_Sequencing_Data_Preprocessing.xml"/>
</section>
<section id="Quality_Control" name="Quality Control">
<tool id="Reads_Quality_Check" file="1-PRE-ANALYSIS/Quality_Assessment/00_Assess_Reads_Quality.xml"/>
<tool id="Assess_Alignment_Quality" file="1-PRE-ANALYSIS/Quality_Assessment/01_Assess_Alignment_Quality.xml"/>
<tool id="Assess_CMR_Regions_Quality" file="1-PRE-ANALYSIS/Quality_Assessment/02_Assess_CMR_Regions_Quality.xml"/>
</section>
<label id="Core_analysis" text="Core Analysis"/>
<section id="Identify" name="Identification of RNA Modifications">
<label id="Align" text="Align Reads to Genome"/>
<tool id="tophat2" file="2-CORE-ANALYSIS/Align_reads_to_genome/00_tophat2.xml"/>
<tool id="bowtie2" file="2-CORE-ANALYSIS/Align_reads_to_genome/01_bowtie2.xml"/>
<tool id="star" file="2-CORE-ANALYSIS/Align_reads_to_genome/02_star.xml"/>
<tool id="hisat2" file="2-CORE-ANALYSIS/Align_reads_to_genome/03_hisat2.xml"/>
<tool id="bwa-mem" file="2-CORE-ANALYSIS/Align_reads_to_genome/04_bwa-mem.xml"/>
<label id="CMR_identification" text="Identify RNA Modifications"/>
<tool id="Calling_peaks" file="2-CORE-ANALYSIS/CMR_Calling/00_PeakCalling.xml"/>
<tool id="peakcalling_m5C" file="2-CORE-ANALYSIS/CMR_Calling/01_m5C_calling.xml"/>
<tool id="Calling_pseudoU" file="2-CORE-ANALYSIS/CMR_Calling/02_pseudouridylation.xml"/>
</section>
<section id="Functional_annotation" name="Functional Annotation">
<tool id="CMR_distribution" file="2-CORE-ANALYSIS/Functional_Annotation/00_CMR_distribution.xml"/>
<tool id="De_novo_motif_discovery" file="2-CORE-ANALYSIS/Functional_Annotation/01_De_novo_motif_discovery.xml"/>
<tool id="Gene_annotation" file="2-CORE-ANALYSIS/Functional_Annotation/04_gene_annotation.xml" />
<tool id="Functional_enrichment_analysis" file="2-CORE-ANALYSIS/Functional_Annotation/03_Functional_enrichment_analysis.xml" />
</section>
<label id="Advanced_analysis" text="Advanced Analysis"/>
<section id="Multi_omics_analysis" name="Multi-omics Integrative Analysis">
<tool id="Gene_Labeling_Analysis" file="3-ADVANCED-ANALYSIS/Multi-omics_Integrative_Analysis/01_Gene_Labeling_Analysis.xml"/>
<tool id="Multi-omics-integration" file="3-ADVANCED-ANALYSIS/Multi-omics_Integrative_Analysis/02_Multi-omics_Integration.xml"/>
</section>
<section id="Machine_learning_based_CMR_Prediction " name="Prediction Analysis Based on Machine Learning">
<tool id="samples_generation" file="3-ADVANCED-ANALYSIS/ML-based_Modelling_Analysis/01_samples_generation.xml"/>
<tool id="feature_encoding" file="3-ADVANCED-ANALYSIS/ML-based_Modelling_Analysis/02_feature_encoding.xml"/>
<tool id="ML_prediction" file="3-ADVANCED-ANALYSIS/ML-based_Modelling_Analysis/03_ML_cassification.xml"/>
</section>
<label id="Useful_tools" text="Useful Tools"/>
<section id="merge_rep" name="Merge biological replicates">
<tool file="merge_two_replicates.xml" />
<tool file="merge_three_replicates.xml" />
</section>
<section id="convert" name="Convert Formats">
<tool file="filters/bed2gff.xml" />
<tool file="filters/gff2bed.xml" />
<tool file="maf/maf_to_bed.xml" />
<tool file="maf/maf_to_interval.xml" />
<tool file="maf/maf_to_fasta.xml" />
<tool file="filters/sff_extractor.xml" />
<tool file="filters/wig_to_bigwig.xml" />
<tool file="filters/bed_to_bigbed.xml" />
</section>
<section id="filter" name="Filter and Sort">
<tool file="stats/filtering.xml" />
<tool file="filters/sorter.xml" />
<tool file="filters/grep.xml" />
<label id="gff" text="GFF" />
<tool file="filters/gff/extract_GFF_Features.xml" />
<tool file="filters/gff/gff_filter_by_attribute.xml" />
<tool file="filters/gff/gff_filter_by_feature_count.xml" />
<tool file="filters/gff/gtf_filter_by_attribute_values_list.xml" />
</section>
<section id="getext" name="Get Data">
<tool file="data_source/upload.xml" />
<tool file="data_source/ucsc_tablebrowser.xml" />
</section>
</toolbox>