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

リビジョン 2, 3.5 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="fastq_combiner" name="Combine FASTA and QUAL" version="1.0.1">
2  <description>into FASTQ</description>
3  <command interpreter="python">fastq_combiner.py '$fasta_file' '${fasta_file.extension}' '$qual_file' '${qual_file.extension}' '$output_file' '$force_quality_encoding'</command>
4  <inputs>
5    <param name="fasta_file" type="data" format="fasta,csfasta" label="FASTA File" />
6    <param name="qual_file" type="data" format="qual" label="Quality Score File" optional="True" />
7    <param name="force_quality_encoding" type="select" label="Force Quality Score encoding">
8      <option value="None">Use Source Encoding</option>
9      <option value="ascii" selected="True">ASCII</option>
10      <option value="decimal">Decimal</option>
11    </param>
12  </inputs>
13  <outputs>
14    <data name="output_file" format="fastqsanger">
15      <change_format>
16        <when input_dataset="fasta_file" attribute="extension" value="csfasta" format="fastqcssanger" />
17        <when input_dataset="qual_file" attribute="extension" value="qualsolid" format="fastqcssanger" />
18        <when input_dataset="qual_file" attribute="extension" value="qualsolexa" format="fastqsolexa" />
19        <when input_dataset="qual_file" attribute="extension" value="qualillumina" format="fastqillumina" />
20      </change_format>
21    </data>
22  </outputs>
23  <tests>
24    <test>
25      <param name="fasta_file" value="s2fq_phiX.csfasta" ftype="csfasta" />
26      <param name="qual_file" value="s2fq_phiX.qualsolid" ftype="qualsolid" />
27      <param name="force_quality_encoding" value="None" />
28      <output name="output_file" file="combine_phiX_out_1.fastqcssanger" />
29    </test>
30    <test>
31      <param name="fasta_file" value="s2fq_phiX.csfasta" ftype="csfasta" />
32      <param name="qual_file" value="s2fq_phiX.qualsolid" ftype="qualsolid" />
33      <param name="force_quality_encoding" value="ascii" />
34      <output name="output_file" file="combine_phiX_out_2.fastqcssanger" />
35    </test>
36    <test>
37      <param name="fasta_file" value="fastq_combiner_in_1.fasta" ftype="fasta" />
38      <param name="qual_file" value="fastq_combiner_in_1.qual454" ftype="qual454" />
39      <param name="force_quality_encoding" value="None" />
40      <output name="output_file" file="wrapping_as_sanger.fastqsanger" />
41    </test>
42    <test>
43      <param name="fasta_file" value="fastq_combiner_in_1.fasta" ftype="fasta" />
44      <param name="qual_file" value="fastq_combiner_in_1.qual454" ftype="qual454" />
45      <param name="force_quality_encoding" value="decimal" />
46      <output name="output_file" file="wrapping_as_sanger_decimal.fastqsanger" />
47    </test>
48    <test>
49      <param name="fasta_file" value="fastq_combiner_in_1.fasta" ftype="fasta" />
50      <param name="qual_file" />
51      <param name="force_quality_encoding" value="decimal" />
52      <output name="output_file" file="fastq_combiner_no_qual_decimal_out_1.fastqsanger" />
53    </test>
54    <test>
55      <param name="fasta_file" value="s2fq_phiX.csfasta" ftype="csfasta" />
56      <param name="qual_file" />
57      <param name="force_quality_encoding" value="ascii" />
58      <output name="output_file" file="fastq_combiner_no_qual_ascii_out_1.fastqcssanger" />
59    </test>
60  </tests>
61  <help>
62**What it does**
63
64This tool joins a FASTA file to a Quality Score file, creating a single FASTQ block for each read.
65
66Specifying a set of quality scores is optional; when not provided, the output will be fastqsanger or fastqcssanger (when a csfasta is provided) with each quality score being the maximal allowed value (93).
67
68Use this tool, for example, to convert 454-type output to FASTQ.
69  </help>
70</tool>
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