Mercurial > repos > davidvanzessen > clonal_sequences_in_paired_samples
comparison ALL.xml @ 12:eb5b569b44dd draft
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| author | davidvanzessen |
|---|---|
| date | Wed, 10 Dec 2014 09:49:16 -0500 |
| parents | |
| children | 5ab17bdf2530 |
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| 11:bc4612998d50 | 12:eb5b569b44dd |
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| 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> |