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1 <tool id="cshl_seqid_uncollapser" name="Uncollapse rows">
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2 <description>containing collapsed sequence IDs</description>
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3 <command>
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4 cat '$input' |
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5 fastx_uncollapser -c $idcol -v -o '$output'
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6 </command>
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7 <inputs>
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8 <param format="tabular,pslx" name="input" type="data" label="Library to uncollapse" />
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9 <param name="idcol" label="Column with collased sequence-identifier" type="data_column" data_ref="input" accept_default="false" >
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10 <help>This column contains the sequence id from a collapsed FASTA file in the form of "(seq number)-(read count)" (e.g. 15-4). Use 10 if you're analyzing BLAT output</help>
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11 </param>
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12 </inputs>
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13 <tests>
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14 <test>
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15 <param name="input" value="fastx_seqid_uncollapse1.psl" />
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16 <param name="idcol" value="10" />
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17 <param name="output" file="fastx_seqid_uncollapse1.out" />
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18 </test>
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19 </tests>
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20
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21 <outputs>
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22 <data format="input" name="output" metadata_source="input"
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23 />
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24 </outputs>
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25 <help>
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26
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27 **What it does**
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28
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29 This tool reads a row (in a table) containing a collapsed sequence ID, and duplicates the .
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30
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31 .. class:: warningmark
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32
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33 You must specify the column containing the collapsed sequence ID (e.g. 15-4).
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34
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35 --------
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36
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37 **Example Input File**
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38
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39 The following input file contains two collapsed sequence identifiers at column 10: *84-2* and *87-5*
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40
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41 (meaning the first has multiplicity-count of 2 and the second has multiplicity count of 5)::
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42
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43
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44 23 0 0 0 0 0 0 0 + 84-2 ...
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45 22 0 0 0 0 0 0 0 + 87-5 ...
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46
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47
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48 **Output Example**
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49
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50 After **uncollapsing** (on column 10), the line of the first sequence-identifier is repeated *twice*, and the line of the second sequence-identifier is repeated *five* times::
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51
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52 23 0 0 0 0 0 0 0 + 84-2 ...
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53 23 0 0 0 0 0 0 0 + 84-2 ...
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54 22 0 0 0 0 0 0 0 + 87-5 ...
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55 22 0 0 0 0 0 0 0 + 87-5 ...
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56 22 0 0 0 0 0 0 0 + 87-5 ...
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57 22 0 0 0 0 0 0 0 + 87-5 ...
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58 22 0 0 0 0 0 0 0 + 87-5 ...
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59
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60
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61 Uncollapsing a text file allows analsys of collapsed FASTA files to be used with any tool which doesn't 'understand' collapsed multiplicity counts.
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62
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63 .. class:: infomark
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64
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65 See the *Collapse* tool in the *FASTA Manipulation* category for more details about collapsing FASTA files.
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66
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67 -----
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68
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69 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
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70
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71 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
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72
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73 </help>
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74 </tool>
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75 <!-- FASTX-Uncollapser is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
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