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annotate fastq_to_fasta.xml @ 4:5dbca5fbdc45 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
author iuc
date Thu, 30 Jan 2020 18:26:18 +0000
parents 4498e994e31b
children b8e3c0a52f33
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4498e994e31b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit 3953b65f6b1c0336e9cadbe0792a5d3b14b5643a
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1 <tool id="cshl_fastq_to_fasta" name="FASTQ to FASTA" version="1.0.2">
2
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2 <description>converter from FASTX-toolkit</description>
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3 <macros>
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iuc
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4 <import>macros.xml</import>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 @CATS@ fastq_to_fasta
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9 $SKIPN
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10 $RENAMESEQ
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11 -v @FQQUAL@
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5dbca5fbdc45 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
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12 @GZIP@ > '$output'
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13 ]]></command>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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14 <inputs>
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15 <expand macro="fastq_input" />
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16 <param name="SKIPN" type="select" label="Discard sequences with unknown (N) bases ">
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17 <option value="">yes</option>
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18 <option value="-n">no</option>
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19 </param>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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20 <param name="RENAMESEQ" type="select" label="Rename sequence names in output file (reduces file size)">
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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21 <option value="-r">yes</option>
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22 <option value="">no</option>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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23 </param>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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24 </inputs>
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25 <outputs>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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26 <data name="output" format="fasta" metadata_source="input" />
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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27 </outputs>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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28 <tests>
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29 <test>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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30 <!-- FASTQ-To-FASTA, keep N, don't rename -->
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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31 <param name="input" value="fastq_to_fasta1.fastq" ftype="fastqsolexa" />
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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32 <param name="SKIPN" value=""/>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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33 <param name="RENAMESEQ" value=""/>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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34 <output name="output" file="fastq_to_fasta1a.out" />
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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35 </test>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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36 <test>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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37 <!-- FASTQ-To-FASTA, discard N, rename -->
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38 <param name="input" value="fastq_to_fasta1.fastq" ftype="fastqsolexa" />
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39 <param name="SKIPN" value="no"/>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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40 <param name="RENAMESEQ" value="yes"/>
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41 <output name="output" file="fastq_to_fasta1b.out" />
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42 </test>
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43 <test>
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44 <!-- FASTQ-To-FASTA, discard N, rename -->
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45 <param name="input" value="fastq_to_fasta-in2.fastq" ftype="fastqsanger" />
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46 <param name="SKIPN" value="no"/>
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47 <param name="RENAMESEQ" value="yes"/>
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48 <output name="output" file="fastq_to_fasta-out2.out" />
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49 </test>
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50 </tests>
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51 <help><![CDATA[
0
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52 **What it does**
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53
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54 This tool converts data from Solexa format to FASTA format (scroll down for format description).
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55
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56 --------
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57
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58 **Example**
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59
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60 The following data in Solexa-FASTQ format::
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61
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62 @CSHL_4_FC042GAMMII_2_1_517_596
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63 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
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64 +CSHL_4_FC042GAMMII_2_1_517_596
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65 40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40
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66
0
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67 Will be converted to FASTA (with 'rename sequence names' = NO)::
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68
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69 >CSHL_4_FC042GAMMII_2_1_517_596
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70 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
1
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71
0
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72 Will be converted to FASTA (with 'rename sequence names' = YES)::
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73
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74 >1
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75 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
1
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76
0
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77 ------
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78
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79 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
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80
1
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81 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
2
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82 ]]></help>
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83 <expand macro="citations" />
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84 <!-- FASTQ-to-FASTA is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
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85 </tool>