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author devteam
date Tue, 20 Aug 2013 11:58:50 -0400
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1 <tool id="sam_pileup" name="Generate pileup" version="1.1.1">
2 <description>from BAM dataset</description>
3 <requirements>
4 <requirement type="package" version="0.1.16">samtools</requirement>
5 </requirements>
6 <command interpreter="python">
7 sam_pileup.py
8 --input1=$input1
9 --output=$output1
10 --ref=$refOrHistory.reference
11 #if $refOrHistory.reference == "history":
12 --ownFile=$refOrHistory.ownFile
13 #else:
14 --ownFile="None"
15 #end if
16 --dbkey=${input1.metadata.dbkey}
17 --indexDir=${GALAXY_DATA_INDEX_DIR}
18 --bamIndex=${input1.metadata.bam_index}
19 --lastCol=$lastCol
20 --indels=$indels
21 --mapCap=$mapCap
22 --consensus=$c.consensus
23 #if $c.consensus == "yes":
24 --theta=$c.theta
25 --hapNum=$c.hapNum
26 --fraction=$c.fraction
27 --phredProb=$c.phredProb
28 #else:
29 --theta="None"
30 --hapNum="None"
31 --fraction="None"
32 --phredProb="None"
33 #end if
34 </command>
35 <inputs>
36 <conditional name="refOrHistory">
37 <param name="reference" type="select" label="Will you select a reference genome from your history or use a built-in index?">
38 <option value="indexed">Use a built-in index</option>
39 <option value="history">Use one from the history</option>
40 </param>
41 <when value="indexed">
42 <param name="input1" type="data" format="bam" label="Select the BAM file to generate the pileup file for">
43 <validator type="unspecified_build" />
44 <validator type="dataset_metadata_in_file" filename="sam_fa_indices.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." line_startswith="index" />
45 </param>
46 </when>
47 <when value="history">
48 <param name="input1" type="data" format="bam" label="Select the BAM file to generate the pileup file for" />
49 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference genome" />
50 </when>
51 </conditional>
52 <param name="lastCol" type="select" label="Whether or not to print the mapping quality as the last column" help="Makes the output easier to parse, but is space inefficient">
53 <option value="no">Do not print the mapping quality as the last column</option>
54 <option value="yes">Print the mapping quality as the last column</option>
55 </param>
56 <param name="indels" type="select" label="Whether or not to print only output pileup lines containing indels">
57 <option value="no">Print all lines</option>
58 <option value="yes">Print only lines containing indels</option>
59 </param>
60 <param name="mapCap" type="integer" value="60" label="Where to cap mapping quality" />
61 <conditional name="c">
62 <param name="consensus" type="select" label="Call consensus according to MAQ model?">
63 <option selected="true" value="no">No</option>
64 <option value="yes">Yes</option>
65 </param>
66 <when value="no" />
67 <when value="yes">
68 <param name="theta" type="float" value="0.85" label="Theta parameter (error dependency coefficient) in the MAQ consensus calling model" />
69 <param name="hapNum" type="integer" value="2" label="Number of haplotypes in the sample" help="Greater than or equal to 2" />
70 <param name="fraction" type="float" value="0.001" label="Expected fraction of differences between a pair of haplotypes" />
71 <param name="phredProb" type="integer" value="40" label="Phred probability of an indel in sequencing/prep" />
72 </when>
73 </conditional>
74 </inputs>
75 <outputs>
76 <data format="tabular" name="output1" label="${tool.name} on ${on_string}: converted pileup" />
77 </outputs>
78 <tests>
79 <test>
80 <!--
81 Bam to pileup command:
82 samtools faidx chr_m.fasta
83 samtools pileup -M 60 -f chr_m.fasta test-data/sam_pileup_in1.bam > sam_pileup_out1.pileup
84 chr_m.fasta is the prefix of the index
85 -->
86 <param name="reference" value="history" />
87 <param name="input1" value="sam_pileup_in1.bam" ftype="bam" />
88 <param name="ownFile" value="chr_m.fasta" ftype="fasta" dbkey="equCab2" />
89 <param name="lastCol" value="no" />
90 <param name="indels" value="no" />
91 <param name="mapCap" value="60" />
92 <param name="consensus" value="no" />
93 <output name="output1" file="sam_pileup_out1.pileup" />
94 </test>
95 <test>
96 <!--
97 Bam to pileup command:
98 samtools pileup -M 60 -c -T 0.85 -N 2 -r 0.001 -I 40 -f chr_m.fasta test-data/sam_pileup_in1.bam > sam_pileup_out2.pileup
99 chr_m.fasta is the prefix of the index
100 -->
101 <param name="reference" value="indexed" />
102 <param name="input1" value="sam_pileup_in1.bam" ftype="bam" dbkey="equCab2" />
103 <param name="lastCol" value="no" />
104 <param name="indels" value="no" />
105 <param name="mapCap" value="60" />
106 <param name="consensus" value="yes" />
107 <param name="theta" value="0.85" />
108 <param name="hapNum" value="2" />
109 <param name="fraction" value="0.001" />
110 <param name="phredProb" value="40" />
111 <output name="output1" file="sam_pileup_out2.pileup" />
112 </test>
113 </tests>
114 <help>
115
116 **What it does**
117
118 Uses SAMTools_' pileup command to produce a pileup dataset from a provided BAM dataset. It generates two types of pileup datasets depending on the specified options. If *Call consensus according to MAQ model?* option is set to **No**, the tool produces simple pileup. If the option is set to **Yes**, a ten column pileup dataset with consensus is generated. Both types of datasets are briefly summarized below.
119
120 .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
121
122 ------
123
124 **Types of pileup datasets**
125
126 The description of pileup format below is largely based on information that can be found on SAMTools Pileup_ documentation page. The 6- and 10-column variants are described below.
127
128 .. _Pileup: http://samtools.sourceforge.net/pileup.shtml
129
130 **Six column pileup**::
131
132 1 2 3 4 5 6
133 ---------------------------------
134 chrM 412 A 2 ., II
135 chrM 413 G 4 ..t, IIIH
136 chrM 414 C 4 ...a III2
137 chrM 415 C 4 TTTt III7
138
139 where::
140
141 Column Definition
142 ------- ----------------------------
143 1 Chromosome
144 2 Position (1-based)
145 3 Reference base at that position
146 4 Coverage (# reads aligning over that position)
147 5 Bases within reads where (see Galaxy wiki for more info)
148 6 Quality values (phred33 scale, see Galaxy wiki for more)
149
150 **Ten column pileup**
151
152 The `ten-column` (consensus_) pileup incorporates additional consensus information generated with *-c* option of *samtools pileup* command::
153
154
155 1 2 3 4 5 6 7 8 9 10
156 ------------------------------------------------
157 chrM 412 A A 75 0 25 2 ., II
158 chrM 413 G G 72 0 25 4 ..t, IIIH
159 chrM 414 C C 75 0 25 4 ...a III2
160 chrM 415 C T 75 75 25 4 TTTt III7
161
162 where::
163
164 Column Definition
165 ------- --------------------------------------------------------
166 1 Chromosome
167 2 Position (1-based)
168 3 Reference base at that position
169 4 Consensus bases
170 5 Consensus quality
171 6 SNP quality
172 7 Maximum mapping quality
173 8 Coverage (# reads aligning over that position)
174 9 Bases within reads where (see Galaxy wiki for more info)
175 10 Quality values (phred33 scale, see Galaxy wiki for more)
176
177
178 .. _consensus: http://samtools.sourceforge.net/cns0.shtml
179
180 ------
181
182 **Citation**
183
184 For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. &lt;http://www.ncbi.nlm.nih.gov/pubmed/19505943&gt;`_
185
186
187 </help>
188 </tool>
189
190