tool_panel.xml

<?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.
    -->
    <section id="getext" name="Get Data" version="">

        <tool id="kallistobus" />

        <tool id="starsolo" />

        <tool id="alevin" />

        <tool id="upload1" />

        <tool id="ucsc_table_direct1" />

        <tool id="ucsc_table_direct_archaea1" />

        <tool id="ebi_sra_main" />

        <tool id="modENCODEfly" />

        <tool id="intermine" />

        <tool id="flymine" />

        <tool id="modmine" />

        <tool id="mousemine" />

        <tool id="ratmine" />

        <tool id="yeastmine" />

        <tool id="modENCODEworm" />

        <tool id="wormbase" />

        <tool id="zebrafishmine" />

        <tool id="eupathdb" />

        <tool id="genomespace_importer" />

        <tool id="genomespace_push" />

    </section>

    <section id="send" name="Send Data" version="">

        <tool id="send_to_cloud" />

        <tool id="genomespace_exporter" />

    </section>

    <section id="collection_operations" name="Collection Operations" version="">

        <tool id="__UNZIP_COLLECTION__" />

        <tool id="__ZIP_COLLECTION__" />

        <tool id="__FILTER_FAILED_DATASETS__" />

        <tool id="__FLATTEN__" />

        <tool id="__MERGE_COLLECTION__" />

        <tool id="__RELABEL_FROM_FILE__" />

        <tool id="__FILTER_FROM_FILE__" />

        <tool id="__SORTLIST__" />

        <tool id="__APPLY_RULES__" />

    </section>

    <section id="expression_tools" name="Expression Tools" version="">

    </section>

    <section id="liftOver" name="Lift-Over" version="">

        <tool id="liftOver1" />

    </section>

    <section id="textutil" name="Text Manipulation" version="">

        <tool id="addValue" />

        <tool id="cat1" />

        <tool id="Condense characters1" />

        <tool id="Cut1" />

        <tool id="mergeCols1" />

        <tool id="Convert characters1" />

        <tool id="createInterval" />

        <tool id="ChangeCase" />

        <tool id="Paste1" />

        <tool id="Remove beginning1" />

        <tool id="random_lines1" />

        <tool id="Show beginning1" />

        <tool id="Show tail1" />

        <tool id="trimmer" />

        <tool id="wc_gnu" />

        <tool id="secure_hash_message_digest" />

    </section>

    <section id="convert" name="Convert Formats" version="">

        <tool id="bed2gff1" />

        <tool id="gff2bed1" />

        <tool id="MAF_To_BED1" />

        <tool id="MAF_To_Interval1" />

        <tool id="MAF_To_Fasta1" />

        <tool id="Sff_extractor" />

        <tool id="wig_to_bigWig" />

        <tool id="bed_to_bigBed" />

    </section>

    <section id="filter" name="Filter and Sort" version="">

        <tool id="Filter1" />

        <tool id="sort1" />

        <tool id="Grep1" />

        <label id="gff" text="GFF" version="" />

        <tool id="Extract_features1" />

        <tool id="gff_filter_by_attribute" />

        <tool id="gff_filter_by_feature_count" />

        <tool id="gtf_filter_by_attribute_values_list" />

    </section>

    <section id="group" name="Join, Subtract and Group" version="">

        <tool id="join1" />

        <tool id="comp1" />

        <tool id="Grouping1" />

    </section>

    <section id="fetchAlignSeq" name="Fetch Alignments/Sequences" version="">

        <tool id="Interval2Maf_pairwise1" />

        <tool id="Interval2Maf1" />

        <tool id="Interval_Maf_Merged_Fasta2" />

        <tool id="GeneBed_Maf_Fasta2" />

        <tool id="maf_stats1" />

        <tool id="MAF_Thread_For_Species1" />

        <tool id="MAF_Limit_To_Species1" />

        <tool id="maf_limit_size1" />

        <tool id="maf_by_block_number1" />

        <tool id="MAF_Reverse_Complement_1" />

        <tool id="Extract genomic DNA 1" />

        <tool id="MAF_filter" />

    </section>

    <section id="bxops" name="Operate on Genomic Intervals" version="">

        <tool id="wiggle2simple1" />

        <tool id="aggregate_scores_in_intervals2" />

        <tool id="gene2exon1" />

    </section>

    <section id="stats" name="Statistics" version="">

        <tool id="Summary_Statistics1" />

        <tool id="Count1" />

    </section>

    <section id="plots" name="Graph/Display Data" version="">

        <tool id="qual_stats_boxplot" />

        <tool id="vcf_to_maf_customtrack1" />

    </section>

    <section id="cshl_library_information" name="NGS: QC and manipulation" version="">

        <label id="illumina" text="Illumina data" version="" />

        <label id="454" text="Roche-454 data" version="" />

        <label id="solid" text="AB-SOLiD data" version="" />

        <tool id="solid2fastq" />

        <tool id="solid_qual_stats" />

        <tool id="solid_qual_boxplot" />

        <label id="generic_fastq" text="Generic FASTQ manipulation" version="" />

        <label id="fastx_toolkit_fastq" text="FASTX-Toolkit for FASTQ data" version="" />

    </section>

    <section id="ngs_mapping" name="NGS: Mapping" version="">

        <label id="illumina" text="Illumina" version="" />

        <label id="roche_454" text="Roche-454" version="" />

        <label id="ab_solid" text="AB-SOLiD" version="" />

    </section>

    <section id="testing" name="Testing tools" version="">

        <tool id="alevin" />

        <tool id="salmon" />

        <tool id="bustools" />

        <tool id="kallistobus" />

        <tool id="seurat" />

        <tool id="anndata_export" />

        <tool id="anndata_import" />

    </section>

    <label id="deprecated" text="DEPRECATED" version="" />

    <section id="gatk" name="NGS: GATK Tools (beta)" version="">

    </section>

    <section id="hgv" name="Phenotype Association" version="">

        <tool id="hgv_linkToGProfile" />

        <tool id="hgv_david" />

        <tool id="hgv_ldtools" />

        <tool id="master2pgSnp" />

        <tool id="hgv_pass" />

        <tool id="hgv_gpass" />

        <tool id="hgv_beam" />

        <tool id="hgv_lps" />

    </section>

    <tool id="toolshed.g2.bx.psu.edu/repos/cole_easson/assembly/velvetg/1.2.10.0" />

    <tool id="toolshed.g2.bx.psu.edu/repos/cole_easson/assembly/velveth/1.2.10.0" />

</toolbox>