root/galaxy-central/tools/solid_tools/maq_cs_wrapper.xml

リビジョン 2, 4.7 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="maq_cs_wrapper" name="MAQ for SOLiD" version="1.0.0">
2    <description> </description>
3    <command interpreter="python">
4    maq_cs_wrapper.py
5    $output1
6    $output2
7    $ref
8    $library_type.f3_reads
9    $library_type.f3_qual
10    $library_type.is_paired
11    #if $library_type.is_paired == "yes": 
12     $library_type.r3_reads
13     $library_type.r3_qual
14    #else:
15     "None"
16     "None"
17    #end if
18    $min_mapqual
19    $max_mismatch
20    $output3
21   
22    </command>
23
24    <inputs>
25        <param name="ref" type="data" format="fasta" label="Target Genome"/>
26        <conditional name="library_type">
27          <param name="is_paired" type="select" label="Is the library mate-paired?" multiple="false">
28             <option value="no">No</option>
29             <option value="yes">Yes</option>
30         </param>
31         <when value="no">
32           <param name="f3_reads" type="data" format="csfasta" label="F3 reads file"/>
33           <param format="qualsolid" name="f3_qual" type="data" label="F3 quality file" help="If your dataset doesn't show up in the menu, click the pencil icon next to your dataset and set the datatype to 'qualsolid'" />
34          </when>
35          <when value="yes">
36           <param name="f3_reads" type="data" format="csfasta" label="F3 reads file"/>
37           <param format="qualsolid" name="f3_qual" type="data" label="F3 quality file" help="If your dataset doesn't show up in the menu, click the pencil icon next to your dataset and set the datatype to 'qualsolid'" />
38           <param name="r3_reads" type="data" format="csfasta" label="R3 reads file"/>
39           <param format="qualsolid" name="r3_qual" type="data" label="R3 quality file" help="If your dataset doesn't show up in the menu, click the pencil icon next to your dataset and set the datatype to 'qualsolid'" />
40          </when>
41      </conditional>
42      <param name="min_mapqual" type="integer" size="3" value="0" label="Minimum mapping quality allowed for a read to be used" help="Reads below the specified mapping quality will not be considered in coverage and SNP analysis."/>
43      <param name="max_mismatch" type="integer" size="3" value="7" label="Maximum number of mismatches allowed for a read to be used" help="Reads above the specified threshold will not be considered in coverage and SNP analysis."/>
44    </inputs>
45    <outputs>
46        <data format="tabular" name="output1" metadata_source="ref" />
47        <data format="tabular" name="output2" metadata_source="ref" />
48        <data format="customtrack" name="output3" metadata_source="ref" />
49    </outputs>
50   
51    <!--  "ToolTestCase does not deal with multiple outputs properly yet."
52    <tests>
53       
54        <test>
55            <param name="ref" value="phiX_mod.fasta" />
56            <param name="is_paired" value="no" />
57            <param name="f3_reads" value="phiX_solid.csfasta" />
58            <param name="f3_qual" value="phiX_solid.qualsolid" />
59            <param name="min_mapqual" value="0" />
60            <param name="max_mismatch" value="7" />
61            <output name="output1" file="phiX_solid_maq.map" />
62            <output name="output2" file="phiX_solid_maq.pileup" />
63            <output name="output3" file="phiX_solid_maq.ctrack" />
64           
65        </test>
66    </tests>
67    -->
68<help>
69
70.. class:: infomark
71
72**What it does**
73
74This tool maps SOLiD color-space reads against the target genome using MAQ. It produces three output datasets:
75
76
77**ALIGNMENT INFO** : contains the read alignment information,
78
79**PILEUP** : contains the coverage and SNP statistics for every nucleotide of the target genome,
80
81**CUSTOM TRACK** : contains the coverage and SNP statistics as custom tracks displayable in the UCSC browser.
82
83-----
84
85**The ALIGNMENT INFO dataset will contain the following fields:**
86
87* column 1  = read name
88* column 2  = chromosome
89* column 3  = position
90* column 4  = strand
91* column 5  = insert size from the outer coorniates of a pair
92* column 6  = paired flag
93* column 7  = mapping quality
94* column 8  = single-end mapping quality
95* column 9  = alternative mapping quality
96* column 10 = number of mismatches of the best hit
97* column 11 = sum of qualities of mismatched bases of the best hit
98* column 12 = number of 0-mismatch hits of the first 24bp
99* column 13 = number of 1-mismatch hits of the first 24bp on the reference
100* column 14 = length of the read
101* column 15 = read sequence
102* column 16 = read quality
103
104
105**The PILEUP dataset will contain the following fields:**
106
107* column 1  = chromosome
108* column 2  = position
109* column 3  = reference nucleotide
110* column 4  = coverage (number of reads that cover this position)
111* column 5  = number of SNPs
112* column 6  = number of As
113* column 7  = number of Ts
114* column 8  = number of Gs
115* column 9  = number of Cs
116
117</help>
118<code file="maq_cs_wrapper_code.py"/>
119
120</tool>
Note: リポジトリブラウザについてのヘルプは TracBrowser を参照してください。