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1 <tool id="cshl_fastx_uncollapser" name="Uncollapse" version="1.0.0">
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2 <description>sequences</description>
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3 <command>
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4 cat '$input' |
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5 fastx_uncollapser -v -o '$output'
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6 </command>
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7 <inputs>
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8 <param format="fasta" name="input" type="data" label="Collapsed FASTA file" />
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9 </inputs>
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10
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11 <tests>
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12 <test>
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13 <param name="input" value="fasta_uncollapser1.fasta" />
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14 <output name="output" file="fasta_uncollapser1.out" />
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15 </test>
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16 </tests>
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17
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18 <outputs>
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19 <data format="fasta" name="output" metadata_source="input"
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20 />
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21 </outputs>
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22 <help>
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23
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24 **What it does**
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25
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26 This tool uncollapses a previously-collapsed FASTA file. It reads each collapsed sequence and generates multiple sequences based on the collapsed read count.
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27
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28 --------
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29
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30 **Example**
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31
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32 Example Input - a collapsed FASTA file (Sequence "ATAT" has four collapsed reads)::
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33
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34 >1-1
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35 TGCG
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36 >2-4
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37 ATAT
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38
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39 Example Output - uncollapsed FASTA file (Sequence "ATAT" now appears as 4 separate sequences)::
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40
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41 >1
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42 TGCG
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43 >2
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44 ATAT
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45 >3
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46 ATAT
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47 >4
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48 ATAT
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49 >5
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50 ATAT
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51
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52 .. class:: infomark
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53
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54 The original sequence id (with the read counts) are discarded, with the sequence given a numerical name.
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55
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56 -----
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57
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58 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
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59
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60 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
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61
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62 </help>
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63 </tool>
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64 <!-- FASTX-Uncollapser is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
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