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