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comparison novocraft_wrapper.xml @ 0:10216882180b draft

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author subazini
date Wed, 17 Dec 2014 10:13:11 -0500
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1 <tool id="novocraft_wrapper" name="Novocraft" version="3.00.02">
2 <description>maps query reads onto the reference sequences</description>
3 <command interpreter="python">
4 novocraft_wrapper.py
5 ## Parameters
6 --settings=$params.settingsType
7 #if $params.settingsType == "full":
8 --align=${params.t}
9 --open=${params.g}
10 --extend=${params.x}
11 --trunc=${params.n}
12 --kmer=${params.k}
13 --step=${params.s}
14 --qual=${params.l}
15 --repe=${params.m}
16 --hclip=${params.H}
17 --pam=$params.pairedEnd
18 --sd=${params.d}
19 --insert=${params.i}
20 #end if
21
22 #if $genomeSource.refGenomeSource == "history":
23 ##build index on the fly
24 --refer="${genomeSource.refFile}"
25 ##--dbkey=$dbkey
26 #else:
27 ##use precomputed indexes
28 --ref1="${genomeSource.indices.fields.path}"
29 ##--do_not_build_index
30 #end if
31
32 ## input file(s)
33 --input1=$paired.input1
34 #if $paired.sPaired == "paired":
35 --input2=$paired.input2
36 #end if
37
38 ## Outputs.
39 --output=$output
40
41 </command>
42 <inputs>
43 <conditional name="genomeSource">
44 <param name="refGenomeSource" type="select" label="Select a reference genome from your history or use a built-in index?">
45 <option value="indexed">Use a built-in index</option>
46 <option value="history">Use one from the history</option>
47 </param>
48
49 <when value="indexed">
50 <param name="indices" type="select" label="Select a reference genome">
51 <options from_data_table="novocraft_indexes">
52 <filter type="sort_by" column="2" />
53 <validator type="no_options" message="No indexes are available" />
54 </options>
55 </param>
56 </when>
57
58 <when value="history">
59 <param name="refFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
60 </when>
61 </conditional>
62
63 <conditional name="paired">
64 <param name="sPaired" type="select" label="Is this library mate-paired?">
65 <option value="single">Single-end</option>
66 <option value="paired">Paired-end</option>
67 </param>
68
69 <when value="single">
70 <param name="input1" type="data" format="fastq" label="FASTQ file" help="FASTQ with Sanger-scaled quality values (fastqsanger)" />
71 </when>
72 <when value="paired">
73 <param name="input1" type="data" format="fastq" label="Forward FASTQ file" help="FASTQ with Sanger-scaled quality values (fastqsanger)" />
74 <param name="input2" type="data" format="fastq" label="Reverse FASTQ file" help="FASTQ with Sanger-scaled quality values (fastqsanger)" />
75 </when>
76 </conditional>
77 <conditional name="params">
78 <param name="settingsType" type="select" label="Parameter Settings" help="You can use the default settings or set custom values for the parameters.">
79 <option value="preSet">Use Defaults</option>
80 <option value="full">Full parameter list</option>
81 </param>
82 <when value="preSet" />
83 <!-- Full/advanced parameters. -->
84 <when value="full">
85 <!-- Indexing parameters -->
86 <param name="k" type="text" value="13" label="k-mer length for the index" />
87 <param name="s" type="text" value="2" label="step size for the index" />
88 <!-- Alignment Scoring -->
89 <param name="t" type="text" value="99" label="maximum alignment score" />
90 <param name="g" type="text" value="40" label="Gap opening penalty" />
91 <param name="x" type="text" value="6" label="Gap extending penalty" />
92 <!-- Read preprocessing -->
93 <param name="n" type="text" value="80" label="Truncate read to specified length" />
94 <!-- Quality control -->
95 <param name="l" type="text" value="50" label="minimum number of good quality bases" />
96 <param name="m" type="text" value="20" label="Repeat filter" />
97 <param name="H" type="text" value="2" label="Hard clip 3' bases" />
98 <param name="pairedEnd" type="select" label="Paired End" >
99 <option value="mp">MP</option>
100 <option value="pe">PE</option>
101 <option value="pp">++</option>
102 <option value="pn">+-</option>
103 <option value="np">-+</option>
104 </param>
105
106 <param name="i" type="text" value="200" label="Insert size" />
107 <param name="d" type="text" value="50" label="standard deviation" />
108
109 </when> <!-- full -->
110 </conditional> <!-- params -->
111
112
113 </inputs>
114 <outputs>
115 <data format="txt" name="output" label="${tool.name} on ${on_string}:"/>
116 </outputs>
117 <help>
118
119 **Novoalign**
120
121 Novoalign is highly accurate program for mapping next-generation sequencing reads to a reference database. (http://www.novocraft.com/). Selected parameters used here are listed here.
122
123 ------
124
125 **Indexing usage**
126
127 novoindex options indexfile sequencefiles
128
129 ------
130
131 **Options - Description**
132
133 -­k 99
134
135 k­mer length to be used for the index. Novoindex will select appropriate values if either of these is not specified. Default value is log4(N/20s) where N is genome size and s step size.
136
137 -s 9
138
139 step size for the index. Typical values are from 1 to 3, usually defaults to 1 or 2. Genomes larger than 4Gbp can be indexed using a stepsize > 1, the requirement is N/s less than 4G.
140
141 ------
142
143 **Alignment usage**
144
145 novoalign options
146
147 ------
148
149 **Options - Description**
150
151 -d dbname
152
153 Full pathname of indexed reference sequence from novoindex
154
155 -f read1 read2
156
157 Filenames for the read sequences for Side 1 and 2.
158
159 -­t 99
160
161 Sets absolute threshold or highest alignment score acceptable for the best alignment.
162
163 -g 99
164
165 Sets the gap opening penalty. Default 40
166
167 -­x 99
168
169 Sets the gap extend penalty. Default 6
170
171 -­l 99
172
173 Sets the minimum number of good quality bases for a read.
174
175 -­H [99]
176
177 Hard clips 3' bases with quality &lt;=[99] from reads before aligning them.
178
179
180
181 </help>
182
183 </tool>
184
185
186
187
188