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comparison fastq_to_fasta.xml @ 1:3f358f73d45e draft

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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
author devteam
date Tue, 13 Oct 2015 12:40:10 -0400
parents 9d253ab73d8b
children 44ed3f74ea7a
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0:9d253ab73d8b 1:3f358f73d45e
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>