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annotate fastx_reverse_complement.xml @ 4:0c2907307ba4 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 3953b65f6b1c0336e9cadbe0792a5d3b14b5643a
author iuc
date Wed, 22 Aug 2018 11:05:48 -0400
parents 3f1017d3f785
children 6027ef51ef91
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0c2907307ba4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit 3953b65f6b1c0336e9cadbe0792a5d3b14b5643a
iuc
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1 <tool id="cshl_fastx_reverse_complement" version="1.0.2" name="Reverse-Complement">
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2 <description></description>
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iuc
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3 <macros>
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iuc
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4 <import>macros.xml</import>
3f1017d3f785 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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5 </macros>
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iuc
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6 <expand macro="requirements" />
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iuc
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7 <command detect_errors="exit_code"><![CDATA[
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8 @CATS@ fastx_reverse_complement -v
3f1017d3f785 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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9 -o '$output'
3f1017d3f785 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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10 @FQQUAL@
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0c2907307ba4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit 3953b65f6b1c0336e9cadbe0792a5d3b14b5643a
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11 @GZIP@
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iuc
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12 ]]></command>
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e246088b6e34 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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13 <inputs>
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14 <expand macro="fastx_input" />
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15 </inputs>
e246088b6e34 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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16 <outputs>
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iuc
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17 <data name="output" format_source="input" metadata_source="input" />
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18 </outputs>
e246088b6e34 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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19 <tests>
e246088b6e34 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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20 <test>
e246088b6e34 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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21 <!-- Reverse-complement a FASTA file -->
e246088b6e34 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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22 <param name="input" value="fastx_rev_comp1.fasta" />
e246088b6e34 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
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23 <output name="output" ftype="fasta" file="fastx_reverse_complement1.out" />
e246088b6e34 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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24 </test>
e246088b6e34 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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25 <test>
e246088b6e34 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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26 <!-- Reverse-complement a FASTQ file -->
e246088b6e34 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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27 <param name="input" value="fastx_rev_comp2.fastq" ftype="fastqsolexa"/>
e246088b6e34 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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28 <output name="output" ftype="fastqsolexa" file="fastx_reverse_complement2.out" />
e246088b6e34 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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29 </test>
e246088b6e34 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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30 </tests>
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3f1017d3f785 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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31 <help><![CDATA[
0
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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
0
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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 ]]></help>
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62 <expand macro="citations" />
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63 </tool>