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/tools/fastq/fastq_to_fasta.xml

https://bitbucket.org/cistrome/cistrome-harvard/
XML | 40 lines | 31 code | 6 blank | 3 comment | 0 complexity | 6573cdfc5a7163cdab95a4364ba5f771 MD5 | raw file
 1<tool id="fastq_to_fasta_python" name="FASTQ to FASTA" version="1.0.0">
 2  <description>converter</description>
 3  <command interpreter="python">fastq_to_fasta.py '$input_file' '$output_file' '${input_file.extension[len( 'fastq' ):]}'</command>
 4  <inputs>
 5    <param name="input_file" type="data" format="fastq" label="FASTQ file to convert" />
 6  </inputs>
 7  <outputs>
 8    <data name="output_file" format="fasta" />
 9  </outputs>
10  <tests>
11    <!-- basic test -->
12    <test>
13      <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
14      <output name="output_file" file="fastq_to_fasta_python_1.out" />
15    </test>
16    <!-- color space test -->
17    <test>
18      <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastqcssanger" />
19      <output name="output_file" file="fastq_to_fasta_python_2.out" />
20    </test>
21    <!-- test of ignoring invalid score values: this input has ascii characters falling outside of illumina range, but they should not matter -->
22    <test>
23      <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqillumina" />
24      <output name="output_file" file="fastq_to_fasta_python_1.out" />
25    </test>
26  </tests>
27  <help>
28**What it does**
29
30This tool converts FASTQ sequencing reads to FASTA sequences.
31
32------
33
34**Citation**
35
36If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. &lt;http://www.ncbi.nlm.nih.gov/pubmed/20562416&gt;`_
37
38
39  </help>
40</tool>