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annotate fastx_reverse_complement.xml @ 2:43540312cb76 draft

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author devteam
date Tue, 13 Oct 2015 12:41:59 -0400
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1 <tool id="cshl_fastx_reverse_complement" version="1.0.0" name="Reverse-Complement">
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2 <description></description>
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3 <requirements>
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4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
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5 </requirements>
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6 <command>
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7 <![CDATA[
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8 zcat -f < '$input' | fastx_reverse_complement -v -o '$output'
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9 #if $input.ext == "fastqsanger":
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10 -Q 33
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11 #end if
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12 ]]>
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13 </command>
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14 <inputs>
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15 <param format="fasta,fastqsolexa,fastqsanger" name="input" type="data" label="Library to reverse-complement" />
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16 </inputs>
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17 <outputs>
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18 <data format_source="input" name="output" metadata_source="input" />
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19 </outputs>
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20 <tests>
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21 <test>
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22 <!-- Reverse-complement a FASTA file -->
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23 <param name="input" value="fastx_rev_comp1.fasta" />
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24 <output name="output" ftype="fasta" file="fastx_reverse_complement1.out" />
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25 </test>
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26 <test>
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27 <!-- Reverse-complement a FASTQ file -->
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28 <param name="input" value="fastx_rev_comp2.fastq" ftype="fastqsolexa"/>
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29 <output name="output" ftype="fastqsolexa" file="fastx_reverse_complement2.out" />
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30 </test>
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31 </tests>
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32 <help>
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33 **What it does**
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34
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35 This tool reverse-complements each sequence in a library.
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36 If the library is a FASTQ, the quality-scores are also reversed.
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37
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38 --------
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39
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40 **Example**
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41
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42 Input FASTQ file::
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43
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44 @CSHL_1_FC42AGWWWXX:8:1:3:740
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45 TGTCTGTAGCCTCNTCCTTGTAATTCAAAGNNGGTA
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46 +CSHL_1_FC42AGWWWXX:8:1:3:740
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47 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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49
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50 Output FASTQ file::
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51
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52 @CSHL_1_FC42AGWWWXX:8:1:3:740
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53 TACCNNCTTTGAATTACAAGGANGAGGCTACAGACA
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54 +CSHL_1_FC42AGWWWXX:8:1:3:740
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55 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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56
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57 ------
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58
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59 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
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60
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61 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
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62 </help>
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63 </tool>