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comparison stampy_wrapper.xml @ 1:abe73a62b59a draft

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author subazini
date Wed, 17 Dec 2014 10:16:18 -0500
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0:10216882180b 1:abe73a62b59a
1 <tool id="Stampy" name="Stampy" version="1.0.21">
2 <description>is a package for mapping of short reads from illumina sequencing machines onto a reference genome</description>
3 <command interpreter="python"> stampy_wrapper.py
4
5 ## Indexing of the reference genome
6 --assembly=$Assembly
7 --species=$species
8 --genome_index=$G
9 --output=$output
10
11 ## Reference genome for creating index
12 --genome=$input
13 #if $refGenomeSource.genomeSource == "indexed":
14 --genome1="${refGenomeSource.index.fields.path}"
15 #end if
16 ## input file for single paired read
17 --input1=$input1
18
19 ## Second input only if input is paired-end.
20 #if $singlePaired.sPaired == "paired"
21 --input1=$singlePaired.input1
22 --input2=$singlePaired.input2
23 #end if
24 ## Parameters
25 --settings=$params.settingsType
26 #if $params.settingsType == "full":
27 --sd=${params.d}
28 --insert=${params.i}
29 --subrate=${params.r}
30 #end if
31 </command>
32 <inputs>
33 <param name="Assembly" type="text" value=""/>
34 <param name="species" type="text" value=""/>
35 <param name="G" type="text" value=""/>
36
37 <conditional name="refGenomeSource">
38 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
39 <option value="indexed">Use a built-in index</option>
40 <option value="history" selected="true">Use one from the history</option>
41 </param>
42 <when value="indexed">
43 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
44 <options from_file="stampy_indices.loc">
45 <column name ="value" index="0" />
46 <column name ="name" index="1" />
47 </options>
48 </param>
49 </when>
50 <when value="history">hg18_
51 <param name="input" type="data" format="fna" metadata_name="dbkey" label="Select the reference genome" />
52 </when>
53
54 </conditional>
55 <conditional name="singlePaired">
56 <param name="sPaired" type="select" label="Is this library mate-paired?">
57 <option value="single">Single-end</option>
58 <option value="paired">Paired-end</option>
59 </param>
60 <when value="single">
61 <param format="fna" name="input1" type="data" label="Input sequence" />
62 </when>
63 <when value="paired">
64 <param format="fna" name="input1" type="data" label="Input sequence" />
65 <param format="fna" name="input2" type="data" label="Input sequence" />
66 </when>
67 </conditional>
68 <conditional name="params">
69 <param name="settingsType" type="select" label="Parameter Settings" help="You can use the default settings or set custom values for the parameters.">
70 <option value="preSet">Use Defaults</option>
71 <option value="full">Full parameter list</option>
72 </param>
73 <when value="preSet" />
74 <!-- Full/advanced parameters. -->
75 <when value="full">
76 <param name="i" type="text" value="250" label="Insert size" />
77 <param name="d" type="text" value="50" label="standard deviation" />
78 <param name="r" type="text" value="0.001" label="substitutionrate" />
79 </when> <!-- full -->
80 </conditional> <!-- params -->
81
82 </inputs>
83
84 <outputs>
85 <data format="txt" name="output" label="outfile"/>
86 </outputs>
87 <help>
88 **Stampy**
89
90 Stampy is a package for the mapping of short reads from illumina sequencing machines onto a reference genome (http://www.well.ox.ac.uk/project-stampy). Selected options used here are given below
91
92 ------
93
94 **Indexing usage**
95
96 *Building index*
97
98 stampy.py --species=human --assembly=hg18_ncbi36 -G hg18 /data/genomes/hg18/*.fa.gz
99
100 *Building hash*
101
102 stampy.py -g hg18 -H hg18
103
104 ------
105
106
107 **Alignment usage**
108
109 stampy.py options -g hg18 -h hg18 -M reads_1.fastq reads_2.fastq
110
111
112 ------
113
114 **Options - Description**
115
116 --insertsize
117
118 Set the mean insert size for paired-end reads (default: 250)
119
120 --insertsd=N
121
122 Set the standard deviation of the insert size distribution (default: 60)
123
124 --substitutionrate=S
125
126 Introduce an expected fraction S of Poisson-distributed substitutions (default: 0.001)
127
128
129 </help>
130
131 </tool>
132