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1 <tool id="cshl_fastx_reverse_complement" name="Reverse-Complement">
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2 <description></description>
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3 <command>
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4 cat '$input' |
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5 fastx_reverse_complement
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6 #if $input.ext == "fastqsanger":
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7 -Q 33
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8 #elif $input.ext == "fastq":
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9 -Q 64
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10 #end if
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11 -v -o '$output'
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12 </command>
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13 <inputs>
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14 <param format="fasta,fastq,fastqsanger" name="input" type="data" label="Library to reverse-complement" />
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15 </inputs>
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16
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17 <tests>
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18 <test>
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19 <!-- Reverse-complement a FASTA file -->
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20 <param name="input" value="fastx_rev_comp1.fasta" />
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21 <output name="output" file="fastx_reverse_complement1.out" />
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22 </test>
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23 <test>
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24 <!-- Reverse-complement a FASTQ file -->
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25 <param name="input" value="fastx_rev_comp2.fastq" />
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26 <output name="output" file="fastx_reverse_complement2.out" />
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27 </test>
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28 </tests>
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29
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30 <outputs>
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31 <data format="input" name="output" metadata_source="input"
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32 />
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33 </outputs>
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34
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35 <help>
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36 **What it does**
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37
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38 This tool reverse-complements each sequence in a library.
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39 If the library is a FASTQ, the quality-scores are also reversed.
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40
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41 --------
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42
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43 **Example**
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44
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45 Input FASTQ file::
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46
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47 @CSHL_1_FC42AGWWWXX:8:1:3:740
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48 TGTCTGTAGCCTCNTCCTTGTAATTCAAAGNNGGTA
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49 +CSHL_1_FC42AGWWWXX:8:1:3:740
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50 33 33 33 34 33 33 33 33 33 33 33 33 27 5 27 33 33 33 33 33 33 27 21 27 33 32 31 29 26 24 5 5 15 17 27 26
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51
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52
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53 Output FASTQ file::
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54
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55 @CSHL_1_FC42AGWWWXX:8:1:3:740
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56 TACCNNCTTTGAATTACAAGGANGAGGCTACAGACA
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57 +CSHL_1_FC42AGWWWXX:8:1:3:740
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58 26 27 17 15 5 5 24 26 29 31 32 33 27 21 27 33 33 33 33 33 33 27 5 27 33 33 33 33 33 33 33 33 34 33 33 33
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59
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60 ------
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61
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62 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
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63
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64 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
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65
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66 </help>
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67 </tool>
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68 <!-- FASTX-reverse-complement is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
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