integrated_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="flowfileupload" name="Upload Files" version="">

        <tool id="upload1" />

    </section>

    <section id="fcsfiletools" name="FCS File Tools" version="">

        <tool id="extract_fcs_keywords" />

        <tool id="get_fcs_headers" />

        <tool id="get_fcs_stats" />

        <tool id="gen_density_plots" />

        <tool id="ggcyto_1d_density_plots" />

        <tool id="flowviz_density_plots" />

        <tool id="edit_fcs_markers" />

        <tool id="fcs_merge_downsample" />

        <tool id="metacyto_preprocess" />

        <tool id="metacyto_checkpanel" />

        <tool id="flowAI" />

        <tool id="fcs_gate_trans_convert" />

        <tool id="convert_fcs_to_text" />

    </section>

    <section id="flowfiletools" name="Flow Text File Tools" version="">

        <tool id="get_headers" />

        <tool id="get_txt_fcs_stats" />

        <tool id="gen_density_plots_txt" />

        <tool id="edit_rearrange_columns" />

        <tool id="fcstxt_merge_downsample" />

        <tool id="txt_diagnosis" />

        <tool id="extract_pop" />

        <tool id="collapse_populations" />

        <tool id="auto_collapse_populations" />

        <tool id="flowclr_stats" />

    </section>

    <section id="flowanalysistools" name="Flow Analysis Tools" version="">

        <tool id="run_flock" />

        <tool id="generate_mfi" />

        <tool id="run_cross_sample" />

        <tool id="flowsom_tree" />

        <tool id="flowsom_cross_comp" />

        <tool id="flowsom_compare" />

        <tool id="metacyto_autocluster" />

        <tool id="metacyto_search_clr" />

        <tool id="get_cell_ontology" />

        <tool id="get_profiles_cell_ontology" />

    </section>

    <section id="flowvisualizationtools" name="Flow Visualization Tools" version="">

        <tool id="gen_flow_overview" />

        <tool id="cross_sample_overview" />

        <tool id="clustergrammer_flow" />

        <tool id="metacyto_histogram" />

    </section>

    <section id="metadataanalysis" name="Phenotype Correlation Analysis" version="">

        <tool id="metacyto_glm_all" />

        <tool id="metacyto_glm_clr" />

    </section>

</toolbox>