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<tool id="vct_clonal_sequences" name="Clonal Sequences in paired samples" version="1.0">
	<description>Comparison of clonal sequences in paired samples</description>
	<command interpreter="bash">
		wrapper.sh $in_file $out_file $out_file.files_path $min_freq $min_cells $merge_on
	</command>
	<inputs>
		<param name="in_file" format="tabular" type="data" label="Data to Process" />
		<param name="min_freq" type="text" label="Minimum Frequency, between 0 and 100 in percentage" value='0'/>
		<param name="min_cells" type="text" label="Minimum cell count" value='0'/>
		<param name="merge_on" type="select" label="Merge On">
				<option value="Clone_Sequence">Clone_Sequence</option>
				<option value="V_J_CDR3">V+J+CDR3</option>
		</param>
	</inputs>
	<outputs>
		<data format="html" name="out_file" />
	</outputs>
	<help>
Takes a tabular file as input, it needs to following columns:

+----------------------------------+----------------------------------------------+
| **Column name**                  | **Column contents**                          |
+----------------------------------+----------------------------------------------+
| Patient                          | The patient ID                               |
+----------------------------------+----------------------------------------------+
| Sample                           | The Sample ID, one, two or three per Patient |
+----------------------------------+----------------------------------------------+
| Cell_Count                       | The cell count within a sample/loci          |
+----------------------------------+----------------------------------------------+
| Clone_Molocule_Count_From_Spikes | The count of a clone                         |
+----------------------------------+----------------------------------------------+
| Log10_Frequency                  | The frequency of a clone in log10            |
+----------------------------------+----------------------------------------------+
| J_Segment_Major_Gene             | The J Gene of this clone                     |
+----------------------------------+----------------------------------------------+
| V_Segment_Major_Gene             | The V Gene of this clone                     |
+----------------------------------+----------------------------------------------+
| Clone_Sequence                   | The entire sequence                          |
+----------------------------------+----------------------------------------------+
| CDR3_Sense_Sequence              | The CDR3 sequence region.                    |
+----------------------------------+----------------------------------------------+


And generate a detailed HTML report on the sequences found in indiviual samples and in both samples.
	</help>
</tool>