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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 <requirements><requirement type="package">fastx_toolkit</requirement></requirements>
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4 <command>zcat -f '$input' | fastx_reverse_complement -v -o $output
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5 #if $input.ext == "fastqsanger":
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6 -Q 33
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7 #end if
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8 </command>
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9 <inputs>
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10 <param format="fasta,fastqsolexa,fastqsanger" name="input" type="data" label="Library to reverse-complement" />
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11 </inputs>
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12
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13 <tests>
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14 <test>
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15 <!-- Reverse-complement a FASTA file -->
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16 <param name="input" value="fastx_rev_comp1.fasta" />
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17 <output name="output" file="fastx_reverse_complement1.out" />
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18 </test>
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19 <test>
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20 <!-- Reverse-complement a FASTQ file -->
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21 <param name="input" value="fastx_rev_comp2.fastq" ftype="fastqsolexa"/>
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22 <output name="output" file="fastx_reverse_complement2.out" />
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23 </test>
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24 </tests>
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25
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26
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27 <outputs>
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28 <data format="input" name="output" metadata_source="input" />
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29 </outputs>
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30
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31 <help>
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32 **What it does**
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33
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34 This tool reverse-complements each sequence in a library.
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35 If the library is a FASTQ, the quality-scores are also reversed.
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36
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37 --------
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38
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39 **Example**
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40
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41 Input FASTQ file::
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42
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43 @CSHL_1_FC42AGWWWXX:8:1:3:740
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44 TGTCTGTAGCCTCNTCCTTGTAATTCAAAGNNGGTA
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45 +CSHL_1_FC42AGWWWXX:8:1:3:740
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46 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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47
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48
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49 Output FASTQ file::
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50
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51 @CSHL_1_FC42AGWWWXX:8:1:3:740
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52 TACCNNCTTTGAATTACAAGGANGAGGCTACAGACA
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53 +CSHL_1_FC42AGWWWXX:8:1:3:740
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54 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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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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