/tools/metag_tools/fastqsolexa_to_fasta_qual.xml
https://bitbucket.org/ialbert/galaxy-genetrack · XML · 91 lines · 69 code · 21 blank · 1 comment · 0 complexity · c74a453bc2e777e0b69e8231800e5db4 MD5 · raw file
- <tool id="fastqsolexa_to_fasta_qual" name="FASTQSOLEXA-to-FASTA-QUAL" version="1.0.0">
- <description>extracts sequences and quality scores from FASTQSOLEXA data</description>
- <command interpreter="python">fastqsolexa_to_fasta_qual.py $input1 $output1 $output2 $input1.extension</command>
- <inputs>
- <param name="input1" type="data" format="fastqsolexa" label="Fastqsolexa file"/>
- </inputs>
- <outputs>
- <data name="output1" format="fasta"/>
- <data name="output2" format="qualsolexa"/>
- </outputs>
- <tests>
- <!-- NOTE: this tool generates 2 output files, but our functional tests currently only handle the last one generated -->
- <test>
- <param name="input1" value="1.fastqsolexa" ftype="fastqsolexa" />
- <output name="output1" file="fastqsolexa_to_fasta_qual_out4.fasta" />
- </test>
- <test>
- <param name="input1" value="2.fastqsolexa" ftype="fastqsolexa" />
- <output name="output1" file="fastqsolexa_to_fasta_qual_out2.fasta" />
- </test>
- </tests>
- <help>
- .. class:: warningmark
- IMPORTANT: This tool currently only supports data where the quality scores are integers or ASCII quality scores with base 64.
- -----
- **What it does**
- This tool extracts sequences and quality scores from FASTQ data ( Solexa variant ), producing a FASTA dataset and a QUAL dataset.
- -----
- **Example1**
- - Converting the following Solexa fastq data::
- @seq1
- GACAGCTTGGTTTTTAGTGAGTTGTTCCTTTCTTT
- +seq1
- hhhhhhhhhhhhhhhhhhhhhhhhhhPW@hhhhhh
- @seq2
- GCAATGACGGCAGCAATAAACTCAACAGGTGCTGG
- +seq2
- hhhhhhhhhhhhhhYhhahhhhWhAhFhSIJGChO
- - will extract the following sequences::
- >seq1
- GACAGCTTGGTTTTTAGTGAGTTGTTCCTTTCTTT
- >seq2
- GCAATGACGGCAGCAATAAACTCAACAGGTGCTGG
-
- - and quality scores::
- >seq1
- 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 16 23 0 40 40 40 40 40 40
- >seq2
- 40 40 40 40 40 40 40 40 40 40 40 40 40 40 25 40 40 33 40 40 40 40 23 40 1 40 6 40 19 9 10 7 3 40 15
- **Example2**
- - Converting the following Solexa fastq data::
- @HANNIBAL_1_FC302VTAAXX:2:1:228:167
- GAATTGATCAGGACATAGGACAACTGTAGGCACCAT
- +HANNIBAL_1_FC302VTAAXX:2:1:228:167
- 40 40 40 40 35 40 40 40 25 40 40 26 40 9 33 11 40 35 17 40 40 33 40 7 9 15 3 22 15 30 11 17 9 4 9 4
- @HANNIBAL_1_FC302VTAAXX:2:1:156:340
- GAGTTCTCGTCGCCTGTAGGCACCATCAATCGTATG
- +HANNIBAL_1_FC302VTAAXX:2:1:156:340
- 40 15 40 17 6 36 40 40 40 25 40 9 35 33 40 14 14 18 15 17 19 28 31 4 24 18 27 14 15 18 2 8 12 8 11 9
- - will extract the following sequences::
- >HANNIBAL_1_FC302VTAAXX:2:1:228:167
- GAATTGATCAGGACATAGGACAACTGTAGGCACCAT
- >HANNIBAL_1_FC302VTAAXX:2:1:156:340
- GAGTTCTCGTCGCCTGTAGGCACCATCAATCGTATG
- - and quality scores::
- >HANNIBAL_1_FC302VTAAXX:2:1:228:167
- 40 40 40 40 35 40 40 40 25 40 40 26 40 9 33 11 40 35 17 40 40 33 40 7 9 15 3 22 15 30 11 17 9 4 9 4
- >HANNIBAL_1_FC302VTAAXX:2:1:156:340
- 40 15 40 17 6 36 40 40 40 25 40 9 35 33 40 14 14 18 15 17 19 28 31 4 24 18 27 14 15 18 2 8 12 8 11 9
- </help>
- </tool>