Mercurial > repos > devteam > fastq_to_fasta
comparison fastq_to_fasta.xml @ 1:186b8d913e6c draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit a1517c9d22029095120643bbe2c8fa53754dd2b7
author | devteam |
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date | Wed, 11 Nov 2015 12:38:08 -0500 |
parents | 04614cf6ed39 |
children | ce309f4ff17f |
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0:04614cf6ed39 | 1:186b8d913e6c |
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1 <tool id="cshl_fastq_to_fasta" name="FASTQ to FASTA"> | 1 <tool id="cshl_fastq_to_fasta" name="FASTQ to FASTA" version="1.0.0"> |
2 <description>converter</description> | 2 <description>converter</description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement> | 4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement> |
5 </requirements> | 5 </requirements> |
6 <command>gunzip -cf $input | fastq_to_fasta $SKIPN $RENAMESEQ -o $output -v | 6 <command>gunzip -cf $input | fastq_to_fasta $SKIPN $RENAMESEQ -o $output -v |
7 #if $input.ext == "fastqsanger": | 7 #if $input.ext == "fastqsanger": |
8 -Q 33 | 8 -Q 33 |
9 #end if | 9 #end if |
10 </command> | 10 </command> |
11 | 11 |
59 | 59 |
60 @CSHL_4_FC042GAMMII_2_1_517_596 | 60 @CSHL_4_FC042GAMMII_2_1_517_596 |
61 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT | 61 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT |
62 +CSHL_4_FC042GAMMII_2_1_517_596 | 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 | 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 |
64 | 64 |
65 Will be converted to FASTA (with 'rename sequence names' = NO):: | 65 Will be converted to FASTA (with 'rename sequence names' = NO):: |
66 | 66 |
67 >CSHL_4_FC042GAMMII_2_1_517_596 | 67 >CSHL_4_FC042GAMMII_2_1_517_596 |
68 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT | 68 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT |
69 | 69 |
70 Will be converted to FASTA (with 'rename sequence names' = YES):: | 70 Will be converted to FASTA (with 'rename sequence names' = YES):: |
71 | 71 |
72 >1 | 72 >1 |
73 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT | 73 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT |
74 | 74 |
75 ------ | 75 ------ |
76 | 76 |
77 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. | 77 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. |
78 | 78 |
79 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ | 79 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ |
80 </help> | 80 </help> |
81 <!-- FASTQ-to-FASTA is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> | 81 <!-- FASTQ-to-FASTA is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> |
82 </tool> | 82 </tool> |