root/galaxy-central/tools/next_gen_conversion/solid_to_fastq.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="solid_to_fastq" name="SOLiD-to-FASTQ" version="1.0.0">
2  <description>converts SOLiD data to FASTQ data</description>
3  <command interpreter="python">
4    solid_to_fastq.py
5    --input1=$input1
6    --input2=$input2
7    #if $paired.pairedSingle == "single":
8     --input3="None"
9     --input4="None"
10    #else:
11     --input3=$input3
12     --input4=$input4
13    #end if
14    --output1=$output1
15    #if $paired.pairedSingle == "single":
16     --output2="None"
17    #else:
18     --output2=$output2
19    #end if
20  </command>
21  <inputs>
22    <conditional name="paired">
23      <param name="pairedSingle" type="select" label="Is this library mate-paired?">
24        <option value="single">Single</option>
25        <option value="paired">Paired</option>
26      </param>
27      <when value="single">
28        <param name="input1" type="data" format="csfasta" label="F3 read file" />
29        <param name="input2" type="data" format="qualsolid" label="F3 qual file" />
30      </when>
31      <when value="paired">
32        <param name="input1" type="data" format="csfasta" label="F3 read file" />
33        <param name="input2" type="data" format="qualsolid" label="F3 qual file" />
34        <param name="input3" type="data" format="csfasta" label="R3 read file" />
35        <param name="input4" type="data" format="qualsolid" label="R3 qual file" />     
36      </when>
37    </conditional>
38  </inputs>
39  <outputs>
40    <!-- Variable number of outputs. Either one (for single-end) or two (for paired-end) -->
41    <data name="output1" format="fastqsanger"/>
42    <data name="output2" format="fastqsanger">
43      <filter>paired['pairedSingle'] == 'paired'</filter>
44    </data>   
45  </outputs>
46  <tests>
47    <test>
48      <param name="pairedSingle" value="single" />
49      <param name="input1" value="s2fq_phiX.csfasta" ftype="csfasta" />
50      <param name="input2" value="s2fq_phiX.qualsolid" ftype="qualsolid" />
51      <output name="output1" file="s2fq_out1.fastqsanger" />
52    </test>
53    <test>
54      <param name="pairedSingle" value="paired" />
55      <param name="input1" value="s2fq_paired_F3.csfasta" ftype="csfasta" />
56      <param name="input2" value="s2fq_paired_F3_QV.qualsolid" ftype="qualsolid" />
57      <param name="input3" value="s2fq_paired_R3.csfasta" ftype="csfasta" />
58      <param name="input4" value="s2fq_paired_R3_QV.qualsolid" ftype="qualsolid" />
59      <output name="output1" file="s2fq_out2.fastqsanger" />
60      <!-- testing framework does not deal with multiple outputs yet
61      <output name="output2" file="s2fq_out3.fastqsanger" />
62      -->
63    </test>
64  </tests>
65  <help>
66
67**What it does**
68
69This tool takes reads and quality files and converts them to FASTQ data ( Sanger variant ). Any -1 qualities are converted to 1 before being converted to FASTQ. Note that it also converts sequences to base pairs.
70
71-----
72
73**Example**
74
75- Converting the following sequences::
76
77    >1831_573_1004_F3
78    T00030133312212111300011021310132222
79    >1831_573_1567_F3
80    T03330322230322112131010221102122113
81
82- and quality scores::
83
84    >1831_573_1004_F3
85    4 29 34 34 32 32 24 24 20 17 10 34 29 20 34 13 30 34 22 24 11 28 19 17 34 17 24 17 25 34 7 24 14 12 22
86    >1831_573_1567_F3
87    8 26 31 31 16 22 30 31 28 29 22 30 30 31 32 23 30 28 28 31 19 32 30 32 19 8 32 10 13 6 32 10 6 16 11
88
89- will produce the following Sanger FASTQ data::
90
91    @1831_573_1004/1
92    AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG
93    +
94    >CCAA9952+C>5C.?C79,=42C292:C(9/-7
95    @1831_573_1567/1
96    TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT
97    +
98    ;@@17?@=>7??@A8?==@4A?A4)A+.'A+'1,
99
100    </help>
101</tool>
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