annotate tabular2HTML.xml @ 0:a5814dd5a11a default tip

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<tool id="tabular2HTML" name="Tabular-to-HTML" version="1.0.0">
    <description>for easier table viewing</description>
    <command interpreter="perl">
        tabular2HTML.pl
			$tableHeader
			$input
			$output
			#if $headerSource.source == 'explicit':
	            #for $header in $headerSource.headers
    	            #if len($header.subheaders) > 0
        	            ${len($header.subheaders)}
            	    #else
                	    1
	                #end if
    	        #end for
			#end if
    </command>
    <inputs>
        <param name="input" type="data" format="tabular" label="Tabular data"/>
    	<conditional name="headerSource">
	    	<param name="source" type="select" label="Header">
	    		<option value="numbers">Column numbers</option>
	    		<option value="names">Column names (if available)</option>
	    		<option value="explicit">Specify headers and subheaders</option>
	    		<option value="none">None</option>
	    	</param>
	    	<when value="numbers">
	    	</when>
	    	<when value="names">
	 		</when>
	    	<when value="explicit">
    		    <repeat name="headers" title="Header">
        		    <param name="name" type="text" label="Name">
            		    <sanitizer>
                		    <valid initial="string.printable">
                    		    <remove value="&lt;"/>
                        		<remove value="&gt;"/>
		                    </valid>
							<mapping initial="none">
								<add source="&lt;" target="&amp;lt;"/>
								<add source="&gt;" target="&amp;gt;"/>
							</mapping>
						</sanitizer>
					</param>
					<repeat name="subheaders" title="Subheader">
						<param name="name" type="text" label="Name"/>
					</repeat>
				</repeat>
			</when>
			<when value="none">
			</when>
		</conditional>
	</inputs>
	<outputs>
		<data format="html" name="output"/>
	</outputs>
	<configfiles>
		<configfile name="tableHeader">
			&lt;html&gt;&lt;head&gt;&lt;style type="text/css"&gt;
			table,td,th
			{
				border: 1px solid #dddddd;
				border-collapse: collapse;
				padding: 4px;
				font-size: 10pt;
			}
			th{border-width:2px; background-color: #888888; color: #ffffff}
			tr.odd {background-color: #f2fff2}
			tr.even {background-color: #f2f2ff}
			td.darkRight {border-right: 2px solid #888888}
			&lt;/style&gt;&lt;/head&gt;&lt;body&gt;
			&lt;table style="border-collapse:collapse"&gt;
			#if $headerSource.source == 'numbers':
				&lt;tr&gt;
            	#for $i in range(int($input.metadata.columns)):
            		&lt;th&gt;${i + 1}&lt;/th&gt;
            	#end for
				&lt;/tr&gt;
			#elif $headerSource.source == 'names' and hasattr($input.datatype, 'column_names'):
				&lt;tr&gt;
				#for $columnName in $input.datatype.column_names:
					&lt;th&gt;$columnName&lt;/th&gt;
				#end for
				&lt;/tr&gt;
            #elif $headerSource.source == 'explicit':
				&lt;tr&gt;
				#for $header in $headerSource.headers:
					&lt;th
					#if len($header.subheaders) > 0:
						colspan="${len($header.subheaders)}"
					#else
						rowspan="2"
					#end if
					&gt;
					$header.name
					&lt;/th&gt;
				#end for
				&lt;tr&gt;
				#for $header in $headerSource.headers:
					#for $subheader in $header.subheaders:
						&lt;th&gt;
						${subheader.name}
						&lt;/th&gt;
					#end for
				#end for
				&lt;/tr&gt;
            #end if
        </configfile>
    </configfiles>
    <help>
**===What it does===**

Wraps tabular data in an HTML table for easier viewing.

------

**===Headers===**

**Column numbers** - The header will show the order of the columns.

**Column names** - The header will show column names if the data file is a
specific type of tabular file that has column names in
Galaxy (such as *sam* or *taxonomy*). Otherwise, no header will be shown.

**Specify headers and subheaders** - This allows custom headers, which can span
multiple columns if subheaders are included. For example, the tabular file::

  1      2    3      4
  read1  100  12345  50
  read2  150  56789  60

...with the headers and subheaders::

  Query
    ID
    length
  Hit
    gi
    score

...would create an html table with the format:

+----------------+---------------+
|     Query      |      Hit      |
+-------+--------+-------+-------+
|  ID   | length |   gi  | score |
+=======+========+=======+=======+
| read1 |  100   | 12345 |  50   |
+-------+--------+-------+-------+
| read2 |  150   | 56789 |  60   |
+-------+--------+-------+-------+

    </help>
</tool>