Mercurial > repos > davidmurphy > codonlogo

view weblogolib/htdocs/create_html_template.html @ 9:f3462128e87c

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Minor alterations to the galaxy interface with some better examples and error messages added.
author davidmurphy
date Mon, 30 Jan 2012 08:17:57 -0500
parents c55bdc2fb9fa
children
line wrap: on
line source

<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN"
    "http://www.w3.org/TR/html4/transitional.dtd">
<html>
<head>
<link rel="stylesheet" type="text/css" href="logo.css" >


<title>CodonLogo 1.0- Create </title>
<meta name="author" content="Gavin E. Crooks" >


<style type="text/css">
td {
    border-left : white solid 4pt
}
.error { 
    color: #900;
    border-left: red solid +4pt;
}

.err_msg { 
    color: #900;
}

</style>
</head>

<body style="align:center">





<form method="post" action="create.cgi" enctype="multipart/form-data" >
<table width="80%" border = '0' cellspacing='0' cellpadding='1' align="center">
<tr><td >
<h1> Codonlogo 1.0 : Create</h1>

</td><td align = "right"> 
    &middot; 
  <a href="./">about</a>&nbsp;&middot;
  <a class="selected" href="create.cgi">create</a>&nbsp;&middot; 
  <a href="examples.html">examples</a>&nbsp;&middot; 
  <a href="manual.html">manual</a>&nbsp;&middot; 
<br>
<span style="font-size:small">$version</span>&nbsp;&nbsp;
</td></tr>

<tr><td >
Sequence data
</td><td > 
<input type="file" name="sequences_file"   > 
</td></tr>

<tr><td >
</td><td> 
<span style="font-size:small ">(or paste sequence data below)</span>
</td></tr>



<tr><td colspan='2' ${sequences_err} >
<textarea name="sequences" rows="12" cols ="100" style="width:100%">${sequences}</textarea>
</td></tr>



<tr><td>
</td><td align="right">
<input  style="font-size:large" type="submit" name="cmd_create" value="&nbsp;Create&nbsp;Logo&nbsp;&nbsp;&nbsp;&nbsp;"  > <br>
<span style="font-size:small"><input type="checkbox" name="download" value="false" >Download</span>
</td></tr>
     

<!-- Reset defaults must come after create_logo so that hitting enter creates a logo-->  
<!--
<tr><td>
<input type="submit" name="cmd_reset" value="Reset defaults" >
</td><td  class="err_msg" rowspan="2">
${error_message} &nbsp;
</td></tr>
<tr><td>&nbsp;</td></tr>
-->

<tr><td colspan='2' style="height:30pt;border-left-width:90pt;" class="err_msg">
${error_message}
</td></tr>

    
     
<tr><td ${format_err} >
Output format </td><td>
<select name="format">
<option ${png} value="png">PNG (low res.)</option>
<option ${png_print} value="png_print">PNG (high res.)</option>
<option ${jpeg} value="jpeg">JPEG (low res.)</option>
<option ${eps} value="eps">EPS (vector)</option>
<option ${pdf} value="pdf">PDF (vector)</option>
<option ${txt} value="txt">Data (plain text)</option> 
</select> 

</td></tr>

<tr><td ${size_err} >
Logo size 
</td><td >
<select name="size" >
<option ${small} >small</option>
<option ${medium}>medium</option>
<option ${large} >large</option>
</select> 
</td></tr>


<tr><td ${stacks_per_line_err}>
    Stacks per line
</td><td>
<input type="text" name="stacks_per_line" value="${stacks_per_line}" size="4" maxlength="4" >
</td></tr>

<tr><td ${alphabet_err}>
Sequence type </td><td>

<select name="alphabet">
<option ${alphabet_auto} value="alphabet_auto" >auto</option>
<option ${alphabet_protein} value="alphabet_protein">protein</option>
<option ${alphabet_dna} value="alphabet_dna">dna</option>
<option ${alphabet_rna} value="alphabet_rna">rna</option>
</select> 
</td></tr>

<tr><td>
Ignore lower case
</td><td>
<input type="checkbox" name="ignore_lower_case" value="true" ${ignore_lower_case} > 
</td></tr>

<tr><td>
Use codons:
</td><td>
<input type="checkbox" name="altype" value="true" ${altype} > 
</td></tr>


<tr><td>
Units </td><td>
<select name="unit_name"  >
<option ${probability} >probability</option>
<option ${bits} >bits</option>
<option ${nats} >nats</option>
<option ${kT} >kT</option>
<option ${kJ_mol} >kJ/mol</option>
<option ${kcal_mol} >kcal/mol</option>
</select> 

</td></tr>

<tr><td ${first_index_err}>
First position number
</td><td>
<input  type="text" name="first_index" value="${first_index}" size="4" maxlength="80" >
</td></tr>

<tr><td ${logo_range_err} >
Logo range </td><td>
<input type="text" name="logo_start" value="${logo_start}" size="4" maxlength="80" > - <input type="text" name="logo_end"  value="${logo_end}" size="4" maxlength="80" >
</td></tr>



<tr><td ${composition_err}>
Composition
</td><td>
<select name="composition" >
<option ${comp_none} value = "comp_none" >No adjustment for composition</option>
<option ${comp_auto} value = "comp_auto" >auto</option>
<option ${comp_equiprobable} value = "comp_equiprobable"  >equiprobable</option>
<option ${comp_CG} value="comp_CG" >Percentage CG &#8658;</option>
<option ${comp_Celegans} value="comp_Celegans" >C. elegans (36%) </option>
<option ${comp_Dmelanogaster} value="comp_Dmelanogaster" >D. melanogaster (43%)</option>
<option ${comp_Ecoli} value="comp_Ecoli" >E. coli (50.5%) </option>
<option ${comp_Hsapiens} value="comp_Hsapiens" >H. sapiens (40%) </option>
<option ${comp_Mmusculus}  value="comp_Mmusculus" >M. musculus (42%)</option>
<option ${comp_Scerevisiae} value="comp_Scerevisiae" >S. cerevisiae (38%) </option>
</select>
or
<input type="text" name="percentCG" value="${percentCG}" size="4" maxlength="8"   >  % CG
</td></tr>

<tr><td>
Scale stack widths
</td><td>
<input type="checkbox" name="scale_width" value="true" ${scale_width} > 
</td></tr>

<tr><td>
Error bars
</td><td>
 <input type="checkbox" name="show_errorbars" value="true" ${show_errorbars}  >
</td></tr>
 





<tr    ><td ${logo_title_err}>
Title
</td><td >
<input   type="text"  name="logo_title"  size="52" maxlength="80" value="${logo_title}" > 
</td></tr>

<tr><td>
Figure label</td><td>
<input type="text" name="logo_label"  value="${logo_label}" size="4" maxlength="100" > 
</td></tr>


<tr><td>
X-axis
</td><td>
<input type="checkbox" name="show_xaxis" value="true" ${show_xaxis} >
Label: 
<input type="text" name="xaxis_label"  value="${xaxis_label}" size="20" maxlength="100" >  
</td></tr>


<tr><td>
Y-axis
</td><td>
<input type="checkbox" name="show_yaxis" value="true" ${show_yaxis} > 
Label: <input type="text" name="yaxis_label" value="${yaxis_label}" size="20" maxlength="32" >  

</td></tr>

<tr><td ${yaxis_scale_err} >
Y-axis scale:
</td><td>
<input type="text" name="yaxis_scale"  value="${yaxis_scale}" size="4" maxlength="100"  > 
</td></tr>

 <tr><td ${yaxis_tic_interval_err} >
Y-axis tic spacing:
</td><td>
<input type="text" name="yaxis_tic_interval" value="${yaxis_tic_interval}"  size="4" maxlength="100"  > 
</td></tr>



<tr><td>
Sequence end labels
</td><td>
<input type="checkbox" name="show_ends" value="true" ${show_ends} > 
</td></tr>
  
<tr><td>
Version fineprint 
  </td><td>
<input type="checkbox" name="show_fineprint" value="true" ${show_fineprint} >
</td></tr>




<tr><td  ${color_scheme_err}>Color scheme
</td><td>
<select name="color_scheme"  >
<option ${color_auto} value="color_auto">Auto</option>
<option ${color_monochrome} value="color_monochrome" >Monochrome</option>
<option ${color_base_pairing} value="color_base_pairing">Base pairing (NA default)</option>
<option ${color_classic} value="color_classic">Classic (NA)</option>
<option ${color_hydrophobicity} value="color_hydrophobicity">Hydrophobicity (AA default)</option>
<option ${color_chemistry} value="color_chemistry">Chemistry (AA)</option>
<option ${color_charge} value="color_charge">Charge (AA)</option>
<option ${color_custom} value="color_custom">Custom (Specify below)</option>
</select> 
<!--&nbsp; Color key:
<input type="checkbox" name="show_color_key" value="true" ${show_color_key} disabled >
-->
</td></tr>

<tr><td></td><td>
<table cellpadding="0" cellspacing="0"  style="font-size:small">
<tr>
<td>Symbols</td><td>Color</td> <!--<td>Description</td>-->
</tr>

<tr >
<td ${color0_err}><input name="symbols0" type="text"  size="16" maxlength="64" value="${symbols0}"></td>
<td><input name="color0" type="text"  size="16" maxlength="64"  value="${color0}"></td>
<!--<td><input name="desc0"  size="16" maxlength="64"  value="${desc0}"></td> -->
</tr>

<tr >
<td ${color1_err}><input name="symbols1" type="text"  size="16" maxlength="64" value="${symbols1}"></td>
<td><input name="color1" type="text"  size="16" maxlength="64"  value="${color1}"></td>
<!--<td><input name="desc1"  size="16" maxlength="64"  value="${desc1}"></td>-->
</tr>

<tr>
<td ${color2_err}><input name="symbols2" type="text"  size="16" maxlength="64" value="${symbols2}"></td>
<td><input name="color2" type="text"  size="16" maxlength="64"  value="${color2}"></td>
<!--<td><input name="desc2"  size="16" maxlength="64"  value="${desc2}"></td>-->
</tr>

<tr>
<td ${color3_err}><input name="symbols3" type="text"  size="16" maxlength="64" value="${symbols3}"></td>
<td><input name="color3" type="text"  size="16" maxlength="64"  value="${color3}"></td>
<!--<td><input name="desc3"  size="16" maxlength="64"  value="${desc3}"></td>-->
</tr>

<tr>
<td ${color4_err}><input name="symbols4" type="text"  size="16" maxlength="64" value="${symbols4}"></td>
<td><input name="color4" type="text"  size="16" maxlength="64"  value="${color4}"></td>
<!--<td><input name="desc4"  size="16" maxlength="64"  value="${desc4}"></td>-->
</tr>



</table>
</td></tr>

 <tr><td>
&nbsp; 
</td><td>
&nbsp;
</td></tr>
      
<tr><td>
<input type="submit" name="cmd_reset" value="Reset defaults" >
</td><td align="right">
<input  style="font-size:large" type="submit" name="cmd_create" value="&nbsp;Create&nbsp;Logo&nbsp;&nbsp;&nbsp;&nbsp;"  >
</td></tr>
     
     


</table>
</form>

<script type="text/javascript">
var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." : "http://www.");
document.write(unescape("%3Cscript src='" + gaJsHost + "google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));
</script>
<script type="text/javascript">
var pageTracker = _gat._getTracker("UA-5951066-1");
pageTracker._trackPageview();
</script>
</body>
</html>