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1 <tool id="rgttable" name="Read Group Tracking Table" version="1.0">
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2 <description>Generate FPKM tables from cuffdiff read_group_tracking files.</description>
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3 <command interpreter="perl">
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4 rgttable.pl
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5 #if $column.selcol == 'yes':
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6 -c $column.colnum
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7 #end if
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8 $rgt_in $rgt_out
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9 </command>
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10 <inputs>
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11 <param name="rgt_in" type="data" format="tabular" label="Input file" />
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12 <conditional name="column">
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13 <param name="selcol" type="select" label="FPKM column" >
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14 <option value="no" selected="true">Use column 7 for the value (default for FPKM)</option>
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15 <option value="yes" >Select the column to use for the value</option>
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16 </param>
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17 <when value="no"/>
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18 <when value="yes">
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19 <param name="colnum" type="data_column" data_ref="rgt_in" numerical="true" optional="true" label="column" />
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20 </when>
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21 </conditional>
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22 <!--
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23 <param name="column" type="integer" value="7" label="Data column to keep (default 7)" />
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24 -->
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25 </inputs>
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26 <stdio>
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27 </stdio>
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28 <outputs>
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29 <data name="rgt_out" format="tabular" />
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30 </outputs>
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31 <tests>
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32 <test>
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33 <param name="rgt_in" ftype="tabular" value="genes.read_group_tracking" />
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34 <param name="selcol" value="no" />
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35 <output name="rgt_out" file="genes.rgt.tsv" />
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36 </test>
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37 </tests>
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38 <help>
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39 This script converts read group tracking files produced by Cuffdiff into a format useful
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40 for importing into other programs.
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41 The output has a row for each tracking_id, with a column for tracking_id, and additional columns for each unique combination of condition and replicate.
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42
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43 This works with the isoforms, genes, cds, and tss_groups
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44 read group tracking files generated by cuffdiff.
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45
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46 INPUT
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47 A cuffdiff read_group_tracking file
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48
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49 ============= =========== =========== =========== ===================== ===================== ========= ================ ========
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50 tracking_id condition replicate raw_frags internal_scaled_frags external_scaled_frags FPKM effective_length status
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51 ============= =========== =========== =========== ===================== ===================== ========= ================ ========
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52 AES heart 0 1 1.15043 1.15043 18.1912 = OK
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53 AES heart 1 1 0.800708 0.800708 18.5033 = OK
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54 AES heart 2 4 2.96393 2.96393 68.5644 = OK
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55 AES skeletal 0 0 0 0 0 = OK
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56 AES skeletal 1 1 1.05362 1.05362 25.0567 = OK
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57 AES skeletal 2 0 0 0 0 = OK
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58 ============= =========== =========== =========== ===================== ===================== ========= ================ ========
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59
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60 OUTPUT
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61
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62 ============= ========= ========= ========= ============ ============ ============
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63 tracking_id heart-0 heart-1 heart-2 skeletal-0 skeletal-1 skeletal-2
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64 ============= ========= ========= ========= ============ ============ ============
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65 AES 18.1912 18.5033 68.5644 0 25.0567 0
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66 ============= ========= ========= ========= ============ ============ ============
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67
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68
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69
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70 </help>
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71 </tool>
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