Mercurial > repos > devteam > fastx_reverse_complement

annotate fastx_reverse_complement.xml @ 5:6027ef51ef91 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
author iuc
date Thu, 30 Jan 2020 13:31:12 -0500
parents 0c2907307ba4
children 177f0621c266
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6027ef51ef91 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
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1 <tool id="cshl_fastx_reverse_complement" version="1.0.2+galaxy0" name="Reverse-Complement">
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2 <description></description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6027ef51ef91 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
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6 <expand macro="requirements">
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7 <requirement type="package" version="1.0.8">bzip2</requirement>
6027ef51ef91 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
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8 </expand>
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9 <command detect_errors="exit_code"><![CDATA[
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10 @CATS@ fastx_reverse_complement -v
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11 @FQQUAL@
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6027ef51ef91 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
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12 @GZIP@ > '$output'
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13 ]]></command>
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14 <inputs>
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15 <expand macro="fastx_input" />
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16 </inputs>
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17 <outputs>
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18 <data name="output" format_source="input" 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><![CDATA[
0
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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
0
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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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48
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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 <expand macro="citations" />
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64 </tool>