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    <title>GLAM2 - Submission form</title>
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    <!-- Help Popups -->

    <!--{help/}-->

    <div class="pop_content" id="pop_sequences">
      <p>Please enter the sequences which you believe share one or more motifs.</p>
      <p>The sequences may contain no more than <b>60,000 characters total</b>
      and must be in <a href="../doc/fasta-format.html">FASTA format</a>.</p>
      <p>See the <a href="@SITE_URL@/doc/examples/example-datasets/At.faa"
      >example protein sequences</a> which were used to create the <a 
      href="../doc/examples/glam2_example_output_files/glam2.html">sample_output</a>.
      <div class="pop_close">[ <a href="javascript:help_popup()">close</a> ]</div>
    </div>

    <div class="pop_content" id="pop_min_seqs">
      <p>This is the minimum aligned sequence count. It must be at least 2.</p>
      <div class="pop_close">[ <a href="javascript:help_popup()">close</a> ]</div>
    </div>

    <div class="pop_content" id="pop_aligned_cols">
      <p>GLAM2 allows you to set limits on the number of "key positions"
      (the aligned columns) in motifs. GLAM2 automatically adjusts the number
      of key positions so as to maximize the alignment score, but it sometimes
      has trouble with this. You can help GLAM2 by changing the initial number
      of aligned columns to a ballpark value. You can also set lower and upper
      bounds on the number of aligned columns in the motif.</p>
      <p>Note that the minimum possible value for aligned columns is 2 and the
      maximum possible value is 300.</p>
      <p>Both protein and DNA motifs are often shorter than the default
      maximum number of aligned columns (50). It is often advisable for you to
      reduce that parameter to a much smaller value (in the range
      10 - 20).</p>
      <div class="pop_close">[ <a href="javascript:help_popup()">close</a> ]</div>
    </div>

    <div class="pop_content" id="pop_pseudo_delete">
      <p>This is the deletion pseudocount. It must be larger than zero.</p>
      <div class="pop_close">[ <a href="javascript:help_popup()">close</a> ]</div>
    </div>

    <div class="pop_content" id="pop_pseudo_nodelete">
      <p>This is the no-deletion pseudocount. It must be larger than zero.</p>
      <div class="pop_close">[ <a href="javascript:help_popup()">close</a> ]</div>
    </div>

    <div class="pop_content" id="pop_pseudo_insert">
      <p>This is the insertion pseudocount. It must be larger than zero.</p>
      <div class="pop_close">[ <a href="javascript:help_popup()">close</a> ]</div>
    </div>

    <div class="pop_content" id="pop_pseudo_noinsert">
      <p>This is the no-insertion pseudocount. It must be larger than zero.</p>
      <div class="pop_close">[ <a href="javascript:help_popup()">close</a> ]</div>
    </div>

    <div class="pop_content" id="pop_replicates">
      <p>The number of alignment replicates performed.</p>
      <div class="pop_close">[ <a href="javascript:help_popup()">close</a> ]</div>
    </div>

    <div class="pop_content" id="pop_max_iter">
      <p>The maximum number of iterations without improvement that GLAM2 attempts.</p>
      <div class="pop_close">[ <a href="javascript:help_popup()">close</a> ]</div>
    </div>

    <div class="pop_content" id="pop_norc">
      <p>Checking this box instructs GLAM2 to <b>NOT</b> check the reverse
      complement of the input sequences for motif sites when reading sequences
      using the DNA or RNA alphabet.</p>
      <p><b>Note:</b> When your sequences are RNA, you should select this option
      to ensure that only the given strand is searched for motifs.</p>
      <div class="pop_close">[ <a href="javascript:help_popup()">close</a> ]</div>
    </div>

    <div class="pop_content" id="pop_shuffle">
      <p>Checking this box causes GLAM2 to shuffle each of the primary sequences
      individually. The sequences will still be the same length and have
      the same character frequencies but any existing patterns will be obliterated.</p>
      <p>Using this option repeatedly you can get an idea of the <i>E</i>-values of motifs
      discovered in "random" sequence datasets similar to your primary dataset.
      This can help you determine a reasonable <i>E</i>-value cutoff
      for motifs discovered in your unshuffled primary sequence dataset.</p>
      <div class="pop_close">[ <a href="javascript:help_popup()">close</a> ]</div>
    </div>

    <div class="pop_content" id="pop_embed">
      <p>Checking this box causes GLAM2 to include the input sequences in the
      output so that your query can be easily resubmitted and modified. This
      will increase the size of your output HTML file substantially if your
      sequence data is large!</p>
      <div class="pop_close">[ <a href="javascript:help_popup()">close</a> ]</div>
    </div>
    <!-- Page starts -->
    <div class="content_box">
    <!--{header}-->
    <p>
    <!--{title}-->GLAM2<!--{/title}--> - <!--{subtitle}-->Gapped Local Alignment of Motifs<!--{/subtitle}--><br>
    <!--{logo}-->../doc/images/glam2_icon.png<!--{/logo}-->: <!--{alt}-->GLAM2 Logo<!--{/alt}--><br>
    <!--{blurb}--><span class="blurb" data-id="glam2"></span><!--{/blurb}-->
    </p>
    <!--{/header}-->
      <form enctype="multipart/form-data" accept-charset="utf-8" 
      method="POST" action="glam2" id="glam2_form">
        <fieldset>
          <legend>Data Submission Form</legend>
          <p class="meme">Perform motif discovery for <b>gapped motifs</b> on 
          DNA or protein datasets.</p>
          <!--{sequences}-->
          <p style="border: 1px solid black">
          <!--{prefix}-->sequences<!--{/prefix}--><br>
          <!--{description}-->sequences<!--{/description}-->
          <!--{title}-->Input the sequences<!--{/title}--><br>
          <!--{subtitle}-->Enter sequences in which you want to find motifs.<!--{/subtitle}--><br>
          <!--{default}-->FILE<!--{/default}-->
          <!--{alph_type}-->DNA_OR_PROTEIN_ALPHABET<!--{/alph_type}-->
          <!--{min_seq_len}-->8<!--{/min_seq_len}-->
          <!--{min_seq_count}-->2<!--{/min_seq_count}-->
          <!--{max_seq_total}-->60000<!--{/max_seq_total}-->
          <!--{register}-->register_component<!--{/register}-->
          </p>
          <!--{/sequences}-->

          <!--{job_details/}-->

          <!-- Advanced Options -->
          <div style="margin-top:5px; margin-bottom: 5px; width:90%;">
            <!--{advanced_options/}-->
          <div>
            <!-- min seqs -->
            <h3 class="meme">How many sequences are needed in each alignment?</h3>
            <label for="min_seqs">minimum sequences:</label>
            <input class="meme intonly sz2" type="number" id="min_seqs"
            name="min_seqs" value="${min_seqs}" step="1" min="2" size="4">
            <div class="help" data-topic="pop_min_seqs"></div>
            <!-- /min seqs -->
            <!-- aligned columns -->
            <h3 class="meme">How many columns should be aligned?</h3>
            <span class="pad1">
            <!-- initial columns -->
            <label for="initial_cols">initial:</label>
            <input class="meme intonly sz2" type="number" id="initial_cols"
            name="initial_cols" value="${initial_cols}" step="1" min="2" max="300" size="3">
            <!-- /initial columns -->
            </span>
            <span class="pad1">
            <!-- minimum columns -->
            <label for="min_cols">minimum:&nbsp;</label>
            <input class="meme intonly sz2" type="number" id="min_cols"
            name="min_cols" value="${min_cols}" step="1" min="2" max="300" size="3">
            <!-- /minimum columns -->
            </span>
            <!-- maximum columns -->
            <label for="max_cols">maximum:&nbsp;</label>
            <input class="meme intonly sz3" type="number" id="max_cols"
            name="max_cols" value="${max_cols}" step="1" min="2" max="300" size="3">
            <!-- /maximum columns -->
            <div class="help" data-topic="pop_aligned_cols"></div>
            <!-- /aligned columns -->
            <!-- pseudocounts -->
            <h3 class="meme">What should the pseudocounts be?</h3>
            <span class="minw11">
            <!-- delete pseudo-->
            <label for="pseudo_del">for delete:&nbsp;</label>
            <input class="meme numonly sz4" type="text" id="pseudo_del"
            name="pseudo_del" value="${pseudo_del}" step="any" min="0" size="4">
            <div class="help" data-topic="pop_pseudo_delete"></div>
            <!-- /delete pseudo-->
            </span>
            <!-- no-delete pseudo -->
            <label for="pseudo_nodel">for no-delete:&nbsp;</label>
            <input class="meme numonly sz4" type="text" id="pseudo_nodel"
            name="pseudo_nodel" value="${pseudo_nodel}" step="any" min="0" size="4">
            <div class="help" data-topic="pop_pseudo_nodelete"></div>
            <!-- /no-delete pseudo -->
            <br>
            <span class="minw11">
            <!-- insert pseudo -->
            <label for="pseudo_ins">for insert:&nbsp;</label>
            <input class="meme numonly sz4" type="text" id="pseudo_ins"
            name="pseudo_ins" value="${pseudo_ins}" step="any" min="0" size="4">
            <div class="help" data-topic="pop_pseudo_insert"></div>
            <!-- /insert pseudo -->
            </span>
            <!-- no-insert pseudo -->
            <label for="pseudo_noins">for no-insert:&nbsp;</label>
            <input class="meme numonly sz4" type="text" id="pseudo_noins"
            name="pseudo_noins" value="${pseudo_noins}" step="any" min="0" size="4">
            <div class="help" data-topic="pop_pseudo_noinsert"></div>
            <!-- /no-insert pseudo -->
            <!-- /pseudocounts -->
            <!-- replicates -->
            <h3 class="meme">How many alignment replicates?</h3>
            <label for="replicates">replicates:</label>
            <input class="meme intonly sz4" type="number" id="replicates" 
            name="replicates" value="${replicates}" step="1" min="0" max="100" size="4">
            <div class="help" data-topic="pop_replicates"></div>
            <!-- /replicates -->
            <!-- min seqs -->
            <h3 class="meme">How many iterations without improvement needed to give up?</h3>
            <label for="max_iter">iterations:</label>
            <input class="meme intonly sz7" type="number" id="max_iter" 
            name="max_iter" value="${max_iter}" step="1" min="1" max="1000000" size="7">
            <div class="help" data-topic="pop_max_iter"></div>
            <!-- /min seqs -->
            <!-- norc -->
            <h3 class="meme top">Can motif sites be on both strands? (DNA/RNA only)</h3>
            <input class="meme" type="checkbox" id="norc" name="norc" value="1" XXXXnorc_checkedXXXX>
            <label for="norc">search given strand only</label>
            <div class="help" data-topic="pop_norc"></div>
            <!-- /norc -->
            <!-- shuffle -->
            <h3 class="meme">Should GLAM2 shuffle the sequences?</h3>
            <input class="meme" type="checkbox" id="shuffle" name="shuffle" value="1">
            <label for="shuffle">Shuffle the sequences</label>
            <div class="help" data-topic="pop_shuffle"></div>
            <!-- /shuffle -->
            <!-- embed -->
            <h3 class="meme">Should GLAM2 embed the sequences?</h3>
            <input class="meme" type="checkbox" id="embed" name="embed" value="1" checked>
            <label for="embed">Embed the sequences</label>
            <div class="help" data-topic="pop_embed"></div>
            <!-- /embed -->
          </div>
          </div>
          <!-- /Advanced Options -->
          <!-- Search and clear buttons -->
          <!--{submit_reset/}-->
        </fieldset>
      </form>
      <!--{footer/}-->
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