/tools/next_gen_conversion/fastq_conversions.xml
https://bitbucket.org/h_morita_dbcls/galaxy-central · XML · 133 lines · 126 code · 7 blank · 0 comment · 0 complexity · d5fbdc397c5d3cd0e122eeb5d72e6d13 MD5 · raw file
- <tool id="fastq_conversions" name="FASTQ Conversions" version="1.0.0">
- <description>converts between FASTQ data and other data formats</description>
- <command interpreter="python">
- fastq_conversions.py
- --command=$conversionType.type
- --input=$input
- #if $conversionType.type == "sol2std":
- --outputFastqsanger=$outputFastqsanger
- #else:
- --outputFastqsanger="None"
- #end if
- #if $conversionType.type == "std2sol":
- --outputFastqsolexa=$outputFastqsolexa
- #else:
- --outputFastqsolexa="None"
- #end if
- #if $conversionType.type == "fq2fa":
- --outputFasta=$outputFasta
- #else:
- --outputFasta="None"
- #end if
- </command>
- <inputs>
- <conditional name="conversionType">
- <param name="type" type="select" label="What type of conversion do you want to do?">
- <option value="sol2std">Solexa/Illumina FASTQ to standard Sanger FASTQ</option>
- <option value="std2sol">Standard Sanger FASTQ to Solexa/Illumina FASTQ</option>
- <option value="fq2fa">Various FASTQ to FASTA</option>
- </param>
- <when value="sol2std">
- <param name="input" type="data" format="fastqsolexa" label="File to convert" />
- </when>
- <when value="std2sol">
- <param name="input" type="data" format="fastqsanger" label="File to convert" />
- </when>
- <when value="fq2fa">
- <param name="input" type="data" format="fastqsolexa, fastqsanger" label="File to convert" />
- </when>
- </conditional>
- </inputs>
- <outputs>
- <data name="outputFastqsanger" format="fastqsanger">
- <filter>conversionType['type'] == 'sol2std'</filter>
- </data>
- <data name="outputFastqsolexa" format="fastqsolexa">
- <filter>conversionType['type'] == 'std2sol'</filter>
- </data>
- <data name="outputFasta" format="fasta">
- <filter>conversionType['type'] == 'fq2fa'</filter>
- </data>
- </outputs>
- <tests>
- <test>
- <param name="type" value="sol2std" />
- <param name="input" value="fastq_conv_in1.fastq" ftype="fastqsolexa" />
- <output name="outputFastqsanger" file="fastq_conv_out1.fastqsanger" />
- </test>
- <test>
- <param name="type" value="std2sol" />
- <param name="input" value="1.fastqsanger" ftype="fastqsanger" />
- <output name="outputFastqsolexa" file="fastq_conv_out2.fastqsolexa" />
- </test>
- <test>
- <param name="type" value="fq2fa" />
- <param name="input" value="1.fastqsanger" ftype="fastqsanger" />
- <output name="outputFasta" file="fastq_conv_out4.fasta" />
- </test>
- </tests>
- <help>
- **What it does**
- This tool offers several conversions options relating to the FASTQ format.
- -----
- **Examples**
- - Converting the Solexa/Illumina FASTQ data::
- @081017-and-081020:1:1:1715:1759
- GGACTCAGATAGTAATCCACGCTCCTTTAAAATATC
- +
- II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B
- - will produce the following Sanger FASTQ data::
- @081017-and-081020:1:1:1715:1759
- GGACTCAGATAGTAATCCACGCTCCTTTAAAATATC
- +
- ++!+++++++!!!!!"+++++++!!!!)!%!!+!!%!
-
- - Converting standard Sanger FASTQ::
-
- @1831_573_1004/1
- AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG
- +
- ><C&&9952+C>5<.?<79,=42<292:<(9/-7
- @1831_573_1050/1
- TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT
- +
- ;@@17?@=>7??@A8?==@4A?A4)&+.'&+'1,
- - will produce the following Solexa/Illumina FASTQ data::
- @1831_573_1004/1
- AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG
- +
- ][bEEXXTQJb]T[M^[VXK\SQ[QXQY[GXNLV
- @1831_573_1050/1
- TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT
- +
- Z__PV^_\]V^^_`W^\\_S`^`SHEJMFEJFPK
- - Converting the Sanger FASTQ data::
- @1831_573_1004/1
- AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG
- +
- ><C&&9952+C>5<.?<79,=42<292:<(9/-7
- @1831_573_1050/1
- TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT
- +
- ;@@17?@=>7??@A8?==@4A?A4)&+.'&+'1,
-
- - will produce the following FASTA data::
- >1831_573_1004/1
- AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG
- >1831_573_1050/1
- TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT
- </help>
- </tool>