--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ALL.xml	Wed Dec 10 09:49:16 2014 -0500
@@ -0,0 +1,42 @@
+<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
+	</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'/>
+	</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>