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1 <tool id="vct_clonal_sequences" name="Clonal Sequences in paired samples" version="1.0">
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2 <description>Comparison of clonal sequences in paired samples</description>
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3 <command interpreter="bash">
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29
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4 wrapper.sh $in_file $out_file $out_file.files_path $min_freq $min_cells $merge_on
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5 </command>
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6 <inputs>
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7 <param name="in_file" format="tabular" type="data" label="Data to Process" />
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8 <param name="min_freq" type="text" label="Minimum Frequency, between 0 and 100 in percentage" value='0'/>
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9 <param name="min_cells" type="text" label="Minimum cell count" value='0'/>
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10 <param name="merge_on" type="select" label="Merge On">
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11 <option value="Clone_Sequence">Clone_Sequence</option>
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12 <option value="V_J_CDR3">V+J+CDR3</option>
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13 </param>
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12
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14 </inputs>
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15 <outputs>
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16 <data format="html" name="out_file" />
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17 </outputs>
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18 <help>
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19 Takes a tabular file as input, it needs to following columns:
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20
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21 +----------------------------------+----------------------------------------------+
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22 | **Column name** | **Column contents** |
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23 +----------------------------------+----------------------------------------------+
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24 | Patient | The patient ID |
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25 +----------------------------------+----------------------------------------------+
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26 | Sample | The Sample ID, one, two or three per Patient |
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27 +----------------------------------+----------------------------------------------+
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28 | Cell_Count | The cell count within a sample/loci |
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29 +----------------------------------+----------------------------------------------+
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30 | Clone_Molocule_Count_From_Spikes | The count of a clone |
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31 +----------------------------------+----------------------------------------------+
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32 | Log10_Frequency | The frequency of a clone in log10 |
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33 +----------------------------------+----------------------------------------------+
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34 | J_Segment_Major_Gene | The J Gene of this clone |
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35 +----------------------------------+----------------------------------------------+
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36 | V_Segment_Major_Gene | The V Gene of this clone |
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37 +----------------------------------+----------------------------------------------+
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38 | Clone_Sequence | The entire sequence |
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39 +----------------------------------+----------------------------------------------+
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40 | CDR3_Sense_Sequence | The CDR3 sequence region. |
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41 +----------------------------------+----------------------------------------------+
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42
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43
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44 And generate a detailed HTML report on the sequences found in indiviual samples and in both samples.
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45 </help>
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46 </tool>
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