Mercurial > repos > davidvanzessen > prisca
diff ALL.xml @ 0:ed6885c85660 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Wed, 31 Aug 2016 05:31:47 -0400 |
| parents | |
| children | 75853bceec00 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ALL.xml Wed Aug 31 05:31:47 2016 -0400 @@ -0,0 +1,46 @@ +<tool id="prisca" name="PRISCA" version="1.0"> + <description>PRecISe Clonal Analysis</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>