{# #######################
  toolbox.html
##########################

This block codes the markup used by the toolbar on the right hand side
of the report.

#}

<div class="mqc-toolbox collapse">

  <!-- Toolbar show/hide buttons -->
  <div class="mqc-toolbox-buttons hidden-xs">
    <a class="mqc-toolbox-label" href="#mqc_cols" title="Open Toolbox">Toolbox</a>
    <ul>
      <li><a href="#mqc_cols" title="Highlight" data-placement="left" data-toggle="tooltip"><span class="glyphicon glyphicon-pushpin"></span></a></li>
      <li><a href="#mqc_renamesamples" title="Rename" data-placement="left" data-toggle="tooltip"><span class="glyphicon glyphicon-font"></span></a></li>
      <li><a href="#mqc_hidesamples" title="Hide" data-placement="left" data-toggle="tooltip"><span class="glyphicon glyphicon-eye-close"></span></a></li>
      <li><a href="#mqc_exportplots" title="Export" data-placement="left" data-toggle="tooltip"><span class="glyphicon glyphicon-download-alt"></span></a></li>
      <li><a href="#mqc_saveconfig" title="Save" data-placement="left" data-toggle="tooltip"><span class="glyphicon glyphicon-floppy-disk"></span></a></li>
      <li><a href="#mqc_citations" title="Citations" data-placement="left" data-toggle="tooltip"><span class="glyphicon glyphicon-education"></span></a></li>
      <li><a href="#mqc_about" title="About" data-placement="left" data-toggle="tooltip"><span class="glyphicon glyphicon-question-sign"></span></a></li>
    </ul>
  </div>

  <div class="mqc-toolbox-wrapper">
    <!-- Header - always visible -->
    <div class="mqc-toolbox-header hidden-xs">
      <h3>MultiQC Toolbox</h3>
    </div>

    <!-- Highlighting -->
    <div id="mqc_cols" class="mqc_filter_section">
      <h4>
        <button id="mqc_cols_apply" class="btn btn-xs btn-default pull-right" disabled>Apply</button>
        Highlight Samples
      </h4>
      {% if report.num_flat_plots > 0 %}
      <p>
        <span class="glyphicon glyphicon-warning-sign" aria-hidden="true"></span>
        This report has flat image plots that won't be highlighted.<br/>
        See the <a href="https://docs.seqera.io/multiqc/development/plots/#interactive--flat-image-plots" target="_blank">documentation</a>
        for help.
      </p>
      {% endif %}
      <form class="form-inline" id="mqc_color_form">
        <input id="mqc_colour_filter" type="text" placeholder="Custom Pattern" class="form-control input-sm">
        <input id="mqc_colour_filter_color" type="color" value="#e41a1c" class="form-control input-sm">
        <button type="submit" id="mqc_colour_filter_update" class="btn btn-default btn-sm">+</button>
      </form>
      <p class="mqc_regex_mode_p">
        <span class="mqc_switch_wrapper mqc_regex_mode" data-target="mqc_cols">Regex mode <span class="mqc_switch re_mode off">off</span></span>
        <button class="btn btn-sm btn-link" data-toggle="modal" data-target="#regex_help_modal">help</button>
        <button class="btn btn-default btn-xs mqc_toolbox_clear"><span class="glyphicon glyphicon-trash"></span> Clear</button>
      </p>
      <ul id="mqc_col_filters" class="mqc_filters"></ul>
    </div>

    <!-- Renaming -->
    <div id="mqc_renamesamples" class="mqc_filter_section">
      <h4>
        <button id="mqc_rename_apply" class="btn btn-xs btn-default pull-right" disabled>Apply</button>
        Rename Samples
      </h4>
      {% if report.num_flat_plots > 0 %}
      <p>
        <span class="glyphicon glyphicon-warning-sign" aria-hidden="true"></span>
        This report has flat image plots that won't be renamed.<br/>
        See the <a href="https://docs.seqera.io/multiqc/development/plots/#interactive--flat-image-plots" target="_blank">documentation</a>
        for help.
      </p>
      {% endif %}
      <form class="form-inline" id="mqc_renamesamples_form">
        <input id="mqc_renamesamples_from" type="text" placeholder="From" class="form-control input-sm">
        <input id="mqc_renamesamples_to" type="text" placeholder="To" class="form-control input-sm">
        <button type="submit" id="mqc_renamesamples_filter_update" class="btn btn-default btn-sm">+</button>
      </form>
      <p><a data-toggle="collapse" href="#mqc_renamesamples_bulk_collapse">Click here for bulk input.</a></p>
      <div class="collapse" id="mqc_renamesamples_bulk_collapse">
        <p>Paste two columns of a tab-delimited table here (eg. from Excel).</p>
        <p>First column should be the old name, second column the new name.</p>
        <form id="mqc_renamesamples_bulk_form">
          <textarea class="form-control" rows="5"></textarea>
          <button type="submit" id="mqc_renamesamples_bulk_update" class="btn btn-default btn-sm">Add</button>
        </form>
      </div>
      <p class="mqc_regex_mode_p">
        <span class="mqc_switch_wrapper mqc_regex_mode" data-target="mqc_renamesamples">Regex mode <span class="mqc_switch re_mode off">off</span></span>
        <button class="btn btn-sm btn-link" data-toggle="modal" data-target="#regex_help_modal">help</button>
        <button class="btn btn-default btn-xs mqc_toolbox_clear"><span class="glyphicon glyphicon-trash"></span> Clear</button>
      </p>
      <ul id="mqc_renamesamples_filters" class="mqc_filters"></ul>
    </div>

    <!-- Hiding -->
    <div id="mqc_hidesamples" class="mqc_filter_section">
      <h4>
        <button id="mqc_hide_apply" class="btn btn-xs btn-default pull-right" disabled>Apply</button>
        Show / Hide Samples
      </h4>
      {% if report.num_flat_plots > 0 %}
      <p>
        <span class="glyphicon glyphicon-warning-sign" aria-hidden="true"></span>
        This report has flat image plots that won't be hidden.<br/>
        See the <a href="https://docs.seqera.io/multiqc/development/plots/#interactive--flat-image-plots" target="_blank">documentation</a>
        for help.
      </p>
      {% endif %}
      <form id="mqc_hidesamples_form">
        <div class="radio input-sm">
          <label><input type="radio" name="mqc_hidesamples_showhide" class="mqc_hidesamples_showhide" value="hide" checked> Hide matching samples</label>
        </div>
        <div class="radio input-sm">
          <label><input type="radio" name="mqc_hidesamples_showhide" class="mqc_hidesamples_showhide" value="show"> Show only matching samples</label>
        </div>
        <div class="form-inline">
          <input id="mqc_hidesamples_filter" type="text" placeholder="Custom Pattern" class="form-control input-sm">
          <button type="submit" id="mqc_hidesamples_filter_update" class="btn btn-default btn-sm">+</button>
        </div>
      </form>
      {% if report.general_stats_data | length > 10 %}<p>Warning! This can take a few seconds.</p>{% endif %}
      <p class="mqc_regex_mode_p">
        <span class="mqc_switch_wrapper mqc_regex_mode" data-target="mqc_hidesamples">Regex mode <span class="mqc_switch re_mode off">off</span></span>
        <button class="btn btn-sm btn-link" data-toggle="modal" data-target="#regex_help_modal">help</button>
        <button class="btn btn-default btn-xs mqc_toolbox_clear"><span class="glyphicon glyphicon-trash"></span> Clear</button>
      </p>
      <ul id="mqc_hidesamples_filters" class="mqc_filters"></ul>
    </div>

    <!-- Export Plots -->
    <div id="mqc_exportplots" class="mqc_filter_section">
      <h4>Export Plots</h4>
      <form>
        <ul class="nav nav-tabs" role="tablist">
          <li class="active"><a href="#mqc_image_download" data-toggle="tab">Images</a></li>
          <li><a href="#mqc_data_download" data-toggle="tab">Data</a></li>
        </ul>
        <div class="tab-content">
          <div role="tabpanel" class="tab-pane fade in active" id="mqc_image_download">
            <div class="row">
              <div class="form-group col-sm-6">
                <div class="input-group input-group-sm">
                  <input type="text" class="form-control input-sm" id="mqc_exp_width" placeholder="Width" value="1200">
                  <span class="input-group-addon">px</span>
                </div>
              </div>
              <div class="form-group col-sm-6">
                <div class="input-group input-group-sm">
                  <input type="text" class="form-control input-sm" id="mqc_exp_height" placeholder="Height" value="800">
                  <span class="input-group-addon">px</span>
                </div>
              </div>
            </div>
            <div class="row">
              <div class="form-group col-sm-6 checkbox">
                <label><input type="checkbox" id="mqc_export_aspratio" checked> Aspect ratio</label>
              </div>
              <div class="form-group col-sm-6">
                <select id="mqc_export_ft" class="form-control input-sm">
                  <option value="image/png">PNG</option>
                  <option value="image/svg+xml">SVG</option>
                </select>
              </div>
            </div>
            <div class="row">
              <div class="col-sm-6 checkbox">
                <label for="mqc_export_scaling">Plot scaling</label>
              </div>
              <div class="col-sm-6">
                <div class="input-group input-group-sm">
                  <input type="text" class="form-control" id="mqc_export_scaling" placeholder="Scale" value="1.5">
                  <span class="input-group-addon">X</span>
                </div>
              </div>
            </div>
          </div>

          <div role="tabpanel" class="tab-pane fade" id="mqc_data_download">
            <p>Download the raw data used to create the plots in this report below:</p>
            <div class="row">
              <div class="form-group col-sm-4 checkbox">
                <label>Format:</label>
              </div>
              <div class="form-group col-sm-8">
                <select id="mqc_export_data_ft" class="form-control input-sm">
                  <option value="tsv">Tab-separated</option>
                  <option value="csv">Comma-separated</option>
                  <option value="json">JSON</option>
                </select>
              </div>
            </div>
            {% if config.make_data_dir %}
            <p>Note that additional data was saved in <code>{{ config.data_dir_name }}</code> when this report was generated.</p>
            {% endif %}
            <div id="mqc_export_data_log"></div>
          </div>
        </div>

        <hr>
        <h5>Choose Plots</h5>
        <button class="btn btn-sm btn-default" id="mqc_export_sall"><span class="glyphicon glyphicon-check"></span> All</button>
        <button class="btn btn-sm btn-default" id="mqc_export_snone"><span class="glyphicon glyphicon-unchecked"></span> None</button>
        <div id="mqc_export_selectplots"></div>

        <hr>
        <button type="submit" class="btn btn-block btn-default" id="mqc-dl-plot-btn">
          <span class="glyphicon glyphicon-download-alt"></span> &nbsp; Download Plot <span id="mqc-dl-plot-txt">Images</span>
        </button>
        <p><small>If you use plots from MultiQC in a publication or presentation, please cite:</small></p>
        <blockquote>
          <strong>MultiQC: Summarize analysis results for multiple tools and samples in a single report</strong><br>
          <em>Philip Ewels, M&aring;ns Magnusson, Sverker Lundin and Max K&auml;ller</em><br>
          Bioinformatics (2016)<br>
          doi: <a href="http://dx.doi.org/10.1093/bioinformatics/btw354" target="_blank">10.1093/bioinformatics/btw354</a><br>
          PMID: <a href="http://www.ncbi.nlm.nih.gov/pubmed/27312411" target="_blank">27312411</a>
        </blockquote>
      </form>
    </div>

    <!-- Save Config -->
    <div id="mqc_saveconfig" class="mqc_filter_section">
      <h4>Save Settings</h4>
      <p>You can save the toolbox settings for this report to the browser.</p>
      <form class="form-inline" id="mqc_saveconfig_form">
        <input type="text" class="form-control input-sm" placeholder="Config Name">
        <button type="submit" class="btn btn-sm btn-default"><span class="glyphicon glyphicon-floppy-disk"></span> Save</button>
      </form>
      <hr>

      <h4>Load Settings</h4>
      <p>Choose a saved report profile from the dropdown box below:</p>
      <form id="mqc_loadconfig_form">
        <div class="form-group">
          <select class="form-control input-sm">
            <option value="">[ select ]</option>
          </select>
        </div>
        <div class="form-group actions">
          <button type="submit" class="btn btn-sm btn-default"><span class="glyphicon glyphicon-floppy-open"></span> Load</button>
          <button class="mqc_config_clear btn btn-sm btn-default"><span class="glyphicon glyphicon-trash"></span> Delete</button>
          <button class="mqc_config_set_default btn btn-sm btn-default"><span class="glyphicon glyphicon-floppy-saved"></span> Set default</button>
          <button class="mqc_config_clear_default btn btn-sm btn-default"><span class="glyphicon glyphicon-floppy-remove"></span> Clear default</button>
        </div>
      </form>
    </div>

    <!-- Tool citations -->
    <div id="mqc_citations" class="mqc_filter_section">
      <h4>Tool Citations</h4>
      <p>Please remember to cite the tools that you use in your analysis.</p>
      <p>To help with this, you can download publication details of the tools mentioned in this report:</p>
      <p><button class="btn btn-sm btn-default download-citations-btn" data-format="doi"><span class="glyphicon glyphicon-barcode"></span> List of DOIs</button></p>
      <p><button class="btn btn-sm btn-default download-citations-btn" data-format="bibtex"><span class="glyphicon glyphicon-bold"></span> BibTeX file</button></p>
    </div>

    <!-- Help / About -->
    <div id="mqc_about" class="mqc_filter_section">
      <h4>About MultiQC</h4>
      <p>This report was generated using MultiQC, version {{ config.version }}</p>
      <p>You can see a YouTube video describing how to use MultiQC reports here:
        <a href="https://youtu.be/qPbIlO_KWN0?list=PLIA2-lqNuhvFGAsB92N0v7Qi5xCxCNsYM" target="_blank">https://youtu.be/qPbIlO_KWN0</a></p>
      <p>For more information about MultiQC, including other videos and
        extensive documentation, please visit <a href="http://multiqc.info/?ref=mqc_report" target="_blank">http://multiqc.info</a></p>
      <p>You can report bugs, suggest improvements and find the source code for MultiQC on GitHub:
        <a href="https://github.com/MultiQC/MultiQC" target="_blank">https://github.com/MultiQC/MultiQC</a></p>
      <p>MultiQC is published in Bioinformatics:</p>
      <blockquote>
        <strong>MultiQC: Summarize analysis results for multiple tools and samples in a single report</strong><br>
        <em>Philip Ewels, M&aring;ns Magnusson, Sverker Lundin and Max K&auml;ller</em><br>
        Bioinformatics (2016)<br>
        doi: <a href="http://dx.doi.org/10.1093/bioinformatics/btw354" target="_blank">10.1093/bioinformatics/btw354</a><br>
        PMID: <a href="http://www.ncbi.nlm.nih.gov/pubmed/27312411" target="_blank">27312411</a>
      </blockquote>
      <hr>
      <p class="text-center seqera-logo">
        MultiQC is developed by:<br>
        <a href="https://seqera.io" target="_blank"><img src="data:image/png;base64,{{ include_file('assets/img/seqera_logo_mono.png', b64=True) }}"></a>
      </p>

    </div>

  </div>
  <a href="#top" class="mqc-toplink hidden-xs" title="Go to top"><span class="glyphicon glyphicon-chevron-up"></span></a>
</div>
