<commit_before><?xml version="1.0"?>
<toolbox>
    <!--
    This is Galaxy's integrated tool panel and should be modified directly only for
    reordering tools inside a section. Each time Galaxy starts up, this file is
    synchronized with the various tool config files: tools, sections and labels
    added to one of these files, will be added also here in the appropriate place,
    while elements removed from the tool config files will be correspondingly
    deleted from this file.
    To modify locally managed tools (e.g. from tool_conf.xml) modify that file
    directly and restart Galaxy. Whenever possible Tool Shed managed tools (e.g.
    from shed_tool_conf.xml) should be managed from within the Galaxy interface or
    via its API - but if changes are necessary (such as to hide a tool or re-assign
    its section) modify that file and restart Galaxy.
    -->
    <label id="basic_tools" text="Basic Tools" version="" />
    <section id="getext" name="Get Data" version="">
    </section>
    <section id="send" name="Send Data" version="">
    </section>
    <section id="liftOver" name="Lift-Over" version="">
    </section>
    <section id="textutil" name="Text Manipulation" version="">
    </section>
    <section id="filter" name="Filter and Sort" version="">
    </section>
    <section id="group" name="Join, Subtract and Group" version="">
    </section>
    <section id="convert" name="Convert Formats" version="">
    </section>
    <section id="bxops" name="Operate on Genomic Intervals" version="">
    </section>
    <section id="features" name="Extract Features" version="">
    </section>
    <label id="statistics_and_visualisation" text="Statistics and Visualisation" version="" />
    <section id="fetchSeq" name="Fetch Sequences" version="">
    </section>
    <section id="fetchAlign" name="Fetch Alignments" version="">
    </section>
    <section id="stats" name="Statistics" version="">
    </section>
    <section id="plots" name="Graph/Display Data" version="">
    </section>
    <label id="ngs_common_toolsets" text="NGS Common Toolsets" version="" />
    <section id="fasta_manipulation" name="FASTA manipulation" version="">
    </section>
    <section id="ngs_picard" name="NGS: Picard" version="">
    </section>
    <section id="samtools" name="NGS: SAM Tools" version="">
    </section>
    <section id="bed_tools" name="BED tools" version="">
    </section>
    <section id="ngs_vcf_tools" name="NGS: VCF Manipulation" version="">
    </section>
    <section id="gatk" name="NGS: GATK Tools 1.4" version="">
    </section>
    <section id="gatk2" name="NGS: GATK Tools 2.8" version="">
    </section>
    <section id="emboss" name="EMBOSS" version="">
    </section>
    <section id="blast+" name="Blast +" version="">
    </section>
    <section id="snpeff" name="snpEff" version="">
    </section>
    <section id="multiple_regression" name="Multiple regression" version="">
    </section>
    <section id="multivariate_analysis" name="Multivariate Analysis" version="">
    </section>
    <section id="regional_variation" name="Regional Variation" version="">
    </section>
    <section id="hgv" name="HGV" version="">
    </section>
    <label id="ngs_analysis" text="NGS Analysis" version="" />
    <section id="ngs_qc" name="NGS: QC and manipulation" version="">
    </section>
    <section id="ngs_mapping" name="NGS: Mapping" version="">
    </section>
    <section id="ngs_assembly" name="NGS: Assembly" version="">
    </section>
    <section id="ngs_rna_tools" name="NGS: RNA Analysis" version="">
    </section>
    <section id="peak_calling" name="NGS: Peak Calling" version="">
    </section>
    <section id="ngs_variant_detection" name="NGS: Variant Detection" version="">
    </section>
    <section id="ngs_variant_analysis" name="NGS: Variant Analysis" version="">
    </section>
    <section id="ngs_annotation" name="NGS: Annotation" version="">
    </section>
    <section id="metagenomics" name="Metagenomic analyses" version="">
    </section>
</toolbox><commit_msg>Added a NGS: Alignment section to integrated_tool_panel.xml file for later use.<commit_after><?xml version="1.0"?>
<toolbox>
    <!--
    This is Galaxy's integrated tool panel and should be modified directly only for
    reordering tools inside a section. Each time Galaxy starts up, this file is
    synchronized with the various tool config files: tools, sections and labels
    added to one of these files, will be added also here in the appropriate place,
    while elements removed from the tool config files will be correspondingly
    deleted from this file.
    To modify locally managed tools (e.g. from tool_conf.xml) modify that file
    directly and restart Galaxy. Whenever possible Tool Shed managed tools (e.g.
    from shed_tool_conf.xml) should be managed from within the Galaxy interface or
    via its API - but if changes are necessary (such as to hide a tool or re-assign
    its section) modify that file and restart Galaxy.
    -->
    <label id="basic_tools" text="Basic Tools" version="" />
    <section id="getext" name="Get Data" version="">
    </section>
    <section id="send" name="Send Data" version="">
    </section>
    <section id="liftOver" name="Lift-Over" version="">
    </section>
    <section id="textutil" name="Text Manipulation" version="">
    </section>
    <section id="filter" name="Filter and Sort" version="">
    </section>
    <section id="group" name="Join, Subtract and Group" version="">
    </section>
    <section id="convert" name="Convert Formats" version="">
    </section>
    <section id="bxops" name="Operate on Genomic Intervals" version="">
    </section>
    <section id="features" name="Extract Features" version="">
    </section>
    <label id="statistics_and_visualisation" text="Statistics and Visualisation" version="" />
    <section id="fetchSeq" name="Fetch Sequences" version="">
    </section>
    <section id="fetchAlign" name="Fetch Alignments" version="">
    </section>
    <section id="stats" name="Statistics" version="">
    </section>
    <section id="plots" name="Graph/Display Data" version="">
    </section>
    <label id="ngs_common_toolsets" text="NGS Common Toolsets" version="" />
    <section id="fasta_manipulation" name="FASTA manipulation" version="">
    </section>
    <section id="ngs_picard" name="NGS: Picard" version="">
    </section>
    <section id="samtools" name="NGS: SAM Tools" version="">
    </section>
    <section id="bed_tools" name="BED tools" version="">
    </section>
    <section id="ngs_vcf_tools" name="NGS: VCF Manipulation" version="">
    </section>
    <section id="gatk" name="NGS: GATK Tools 1.4" version="">
    </section>
    <section id="gatk2" name="NGS: GATK Tools 2.8" version="">
    </section>
    <section id="emboss" name="EMBOSS" version="">
    </section>
    <section id="blast+" name="Blast +" version="">
    </section>
    <section id="snpeff" name="snpEff" version="">
    </section>
    <section id="multiple_regression" name="Multiple regression" version="">
    </section>
    <section id="multivariate_analysis" name="Multivariate Analysis" version="">
    </section>
    <section id="regional_variation" name="Regional Variation" version="">
    </section>
    <section id="hgv" name="HGV" version="">
    </section>
    <section id="alignment" name="NGS: Alignment" version="">
    </section>
    <label id="ngs_analysis" text="NGS Analysis" version="" />
    <section id="ngs_qc" name="NGS: QC and manipulation" version="">
    </section>
    <section id="ngs_mapping" name="NGS: Mapping" version="">
    </section>
    <section id="ngs_assembly" name="NGS: Assembly" version="">
    </section>
    <section id="ngs_rna_tools" name="NGS: RNA Analysis" version="">
    </section>
    <section id="peak_calling" name="NGS: Peak Calling" version="">
    </section>
    <section id="ngs_variant_detection" name="NGS: Variant Detection" version="">
    </section>
    <section id="ngs_variant_analysis" name="NGS: Variant Analysis" version="">
    </section>
    <section id="ngs_annotation" name="NGS: Annotation" version="">
    </section>
    <section id="metagenomics" name="Metagenomic analyses" version="">
    </section>
</toolbox>
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