root/galaxy-central/tools/fastq/fastq_to_fasta.xml

リビジョン 2, 1.3 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
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  </help>
33</tool>
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