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comparison tools/solid_tools/maq_cs_wrapper.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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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
74 This 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>