Please specify a plate results file to upload for analysis:<br>
<div class="field">
<%= f.file_field :input_file %>
</div>
<div class="actions" style="margin-top:30px;">
<%= link_to "Single-Plate Example File","/resources/YPDAFEXglucoseTests_2-25-10.csv" %><br>
<%= link_to "Multi-Plate Example File","/resources/test_YYYY_MM_DD_HH_MM_SS.csv" %><br>
</div>
</li>
<li>
<h3><span data-tooltip="Optionally upload a companion .csv file containing identifying information for all wells in the experiments(s) to be analyzed, including strain identifiers and growth media (or growth environment) definitions, which are used for graphic output.">Plate Layout File</span></h3>
Optionally upload a plate layout file:<br>
<div class="field">
<%= f.file_field :layout_file %>
</div>
<div class="actions" style="margin-top:30px;">
<%= link_to "Single-Plate Layout Example File","/resources/YPDAFEXglucoseTests_2-25-10_Layout.csv" %><br>
<%= link_to "Multi-Plate Layout Example File","/resources/MultiPlateLayout_plateID.csv" %>
</div>
</li>
<li>
<h3><span data-tooltip="OD value for blank well read. As the default option <NULL>, GCAT will automatically take the first OD reading of each well to be the blank.">Media background</span></h3>
<%= f.text_field :blank_value_input, :placeholder => 'Enter your OD blank value here' %>
</div>
</li>
<li>
<h3><span data-tooltip="GCAT transforms optical density (OD) to log(x+δ). x = OD – Media background. Specify a value for n or choose from the defaults. Note: 0 is not recommended unless all wells contain many repeated measurements for initial density that can be used to accurately estimate the baseline density. See the user manual for more details.">OD Transform</span></h3>
<h3><span data-tooltip="Enter a threshold to determine the presence of a growing culture. GCAT rejects curves where the density measurements never reach this value above the specified inoculation timepoint." >Growth Threshold</span></h3>
<div class="field">
<%= f.label :growth_threshold, "Enter the growth threshold. The default value is 0.05. " %><br />
<h3><span data-tooltip="Enter indices (as a comma-separated list) of any erroneous reads that should be removed across the entire experiment. " >Points to ignore</span></h3>
<div class="field">
<%= f.label :remove_points,"Enter a comma-separated list of points. Example: 2,3,4,5 (positive integers only). The default is an empty list." %><br />
<!--<h3><span data-tooltip="GCAT automatically detects sudden changes in OD ('jumps'). Check this box if these instances should be removed when possible. If only one or two jumps are present GCAT will attempt to remove only the affected region." >Remove Jumps</span></h3>-->
<%#= f.check_box(:remove_jumps) %>
<%#= f.label(:remove_jumps, "Employ the jump detection algorithm to attempt to remove problematic points.") %>
<%
=begin %>
<h3><span data-tooltip="Enter the number of rows (letters) and columns (numbers) of wells on each of the plates of this experiment." >Plate Dimensions</span></h3>
<h3><span data-tooltip="Select a correctly formatted timestamp (see user manual for details). The timestamp will be used to convert the time entries into the number of hours." >Timestamp format</span></h3>
<%= mail_to "gcat.help@glbrc.wisc.edu","Please Send Any Questions To The GLBRC Help Desk And Be Sure To Include 'GCAT' In Your Subject Title", :subject => "GCAT" %>