|
12
|
1 <tool id="vct_clonal_sequences" name="Clonal Sequences in paired samples" version="1.0">
|
|
|
2 <description>Comparison of clonal sequences in paired samples</description>
|
|
|
3 <command interpreter="bash">
|
|
|
4 wrapper.sh $in_file $out_file $out_file.files_path $min_freq $min_cells
|
|
|
5 </command>
|
|
|
6 <inputs>
|
|
|
7 <param name="in_file" format="tabular" type="data" label="Data to Process" />
|
|
|
8 <param name="min_freq" type="text" label="Minimum Frequency, between 0 and 100 in percentage" value='0'/>
|
|
|
9 <param name="min_cells" type="text" label="Minimum cell count" value='0'/>
|
|
|
10 </inputs>
|
|
|
11 <outputs>
|
|
|
12 <data format="html" name="out_file" />
|
|
|
13 </outputs>
|
|
|
14 <help>
|
|
|
15 Takes a tabular file as input, it needs to following columns:
|
|
|
16
|
|
|
17 +----------------------------------+----------------------------------------------+
|
|
|
18 | **Column name** | **Column contents** |
|
|
|
19 +----------------------------------+----------------------------------------------+
|
|
|
20 | Patient | The patient ID |
|
|
|
21 +----------------------------------+----------------------------------------------+
|
|
|
22 | Sample | The Sample ID, one, two or three per Patient |
|
|
|
23 +----------------------------------+----------------------------------------------+
|
|
|
24 | Cell_Count | The cell count within a sample/loci |
|
|
|
25 +----------------------------------+----------------------------------------------+
|
|
|
26 | Clone_Molocule_Count_From_Spikes | The count of a clone |
|
|
|
27 +----------------------------------+----------------------------------------------+
|
|
|
28 | Log10_Frequency | The frequency of a clone in log10 |
|
|
|
29 +----------------------------------+----------------------------------------------+
|
|
|
30 | J_Segment_Major_Gene | The J Gene of this clone |
|
|
|
31 +----------------------------------+----------------------------------------------+
|
|
|
32 | V_Segment_Major_Gene | The V Gene of this clone |
|
|
|
33 +----------------------------------+----------------------------------------------+
|
|
|
34 | Clone_Sequence | The entire sequence |
|
|
|
35 +----------------------------------+----------------------------------------------+
|
|
|
36 | CDR3_Sense_Sequence | The CDR3 sequence region. |
|
|
|
37 +----------------------------------+----------------------------------------------+
|
|
|
38
|
|
|
39
|
|
|
40 And generate a detailed HTML report on the sequences found in indiviual samples and in both samples.
|
|
|
41 </help>
|
|
|
42 </tool>
|
