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annotate fastq_to_fasta.xml @ 1:3f358f73d45e draft
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
| author | devteam |
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| date | Tue, 13 Oct 2015 12:40:10 -0400 |
| parents | 9d253ab73d8b |
| children | 44ed3f74ea7a |
| rev | line source |
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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1 <tool id="cshl_fastq_to_fasta" name="FASTQ to FASTA" version="1.0.0"> |
| 0 | 2 <description>converter</description> |
| 3 <requirements> | |
| 4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement> | |
| 5 </requirements> | |
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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6 <command>gunzip -cf $input | fastq_to_fasta $SKIPN $RENAMESEQ -o $output -v |
| 0 | 7 #if $input.ext == "fastqsanger": |
| 8 -Q 33 | |
| 9 #end if | |
| 10 </command> | |
| 11 | |
| 12 <inputs> | |
| 13 <param format="fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="FASTQ Library to convert" /> | |
| 14 | |
| 15 <param name="SKIPN" type="select" label="Discard sequences with unknown (N) bases "> | |
| 16 <option value="">yes</option> | |
| 17 <option value="-n">no</option> | |
| 18 </param> | |
| 19 | |
| 20 <param name="RENAMESEQ" type="select" label="Rename sequence names in output file (reduces file size)"> | |
| 21 <option value="-r">yes</option> | |
| 22 <option value="">no</option> | |
| 23 </param> | |
| 24 | |
| 25 </inputs> | |
| 26 | |
| 27 <tests> | |
| 28 <test> | |
| 29 <!-- FASTQ-To-FASTA, keep N, don't rename --> | |
| 30 <param name="input" value="fastq_to_fasta1.fastq" ftype="fastqsolexa" /> | |
| 31 <param name="SKIPN" value=""/> | |
| 32 <param name="RENAMESEQ" value=""/> | |
| 33 <output name="output" file="fastq_to_fasta1a.out" /> | |
| 34 </test> | |
| 35 <test> | |
| 36 <!-- FASTQ-To-FASTA, discard N, rename --> | |
| 37 <param name="input" value="fastq_to_fasta1.fastq" ftype="fastqsolexa" /> | |
| 38 <param name="SKIPN" value="no"/> | |
| 39 <param name="RENAMESEQ" value="yes"/> | |
| 40 <output name="output" file="fastq_to_fasta1b.out" /> | |
| 41 </test> | |
| 42 </tests> | |
| 43 | |
| 44 <outputs> | |
| 45 <data format="fasta" name="output" metadata_source="input" /> | |
| 46 </outputs> | |
| 47 | |
| 48 <help> | |
| 49 | |
| 50 **What it does** | |
| 51 | |
| 52 This tool converts data from Solexa format to FASTA format (scroll down for format description). | |
| 53 | |
| 54 -------- | |
| 55 | |
| 56 **Example** | |
| 57 | |
| 58 The following data in Solexa-FASTQ format:: | |
| 59 | |
| 60 @CSHL_4_FC042GAMMII_2_1_517_596 | |
| 61 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT | |
| 62 +CSHL_4_FC042GAMMII_2_1_517_596 | |
| 63 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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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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64 |
| 0 | 65 Will be converted to FASTA (with 'rename sequence names' = NO):: |
| 66 | |
| 67 >CSHL_4_FC042GAMMII_2_1_517_596 | |
| 68 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT | |
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3f358f73d45e
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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69 |
| 0 | 70 Will be converted to FASTA (with 'rename sequence names' = YES):: |
| 71 | |
| 72 >1 | |
| 73 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT | |
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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74 |
| 0 | 75 ------ |
| 76 | |
| 77 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. | |
| 78 | |
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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79 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ |
| 0 | 80 </help> |
| 81 <!-- FASTQ-to-FASTA is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> | |
| 82 </tool> |