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

リビジョン 2, 1.6 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="tabular_to_fastq" name="Tabular to FASTQ" version="1.0.0">
2  <description>converter</description>
3  <command interpreter="python">tabular_to_fastq.py '$input_file' '$output_file' '$identifier' '$sequence' '$quality'</command>
4  <inputs>
5    <param name="input_file" type="data" format="tabular" label="Tabular file to convert" />
6    <param name="identifier" label="Identifier column" type="data_column" data_ref="input_file" />
7    <param name="sequence" label="Sequence column" type="data_column" data_ref="input_file" />
8    <param name="quality" label="Quality column" type="data_column" data_ref="input_file" />
9  </inputs>
10  <outputs>
11    <data name="output_file" format="fastq" />
12  </outputs>
13  <tests>
14    <!-- basic test -->
15    <test>
16      <param name="input_file" value="fastq_to_tabular_out_1.tabular" ftype="tabular" />
17      <param name="identifier" value="1" />
18      <param name="sequence" value="2" />
19      <param name="quality" value="3" />
20      <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
21    </test>
22    <!-- color space test -->
23    <test>
24      <param name="input_file" value="fastq_to_tabular_out_2.tabular" ftype="tabular" />
25      <param name="identifier" value="1" />
26      <param name="sequence" value="2" />
27      <param name="quality" value="3" />
28      <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" />
29    </test>
30  </tests>
31  <help>
32**What it does**
33
34This tool attempts to convert a tabular file containing sequencing read data to a FASTQ formatted file. The FASTQ Groomer tool should always be used on the output of this tool.
35
36  </help>
37</tool>
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