comparison snpindex.xml @ 7:561503a442f0

refactor
author Jim Johnson <jj@umn.edu>
date Tue, 08 Nov 2011 13:26:41 -0600
parents
children a89fec682254
comparison
equal deleted inserted replaced
6:3be0e0a858fe 7:561503a442f0
1 <tool id="gmap_snpindex" name="GMAP SNP Index" version="2.0.0">
2 <description>build index files for known SNPs</description>
3 <requirements>
4 <requirement type="binary">snpindex</requirement>
5 <!-- proposed tag for added datatype dependencies -->
6 <requirement type="datatype">gmapsnpindex</requirement>
7 <requirement type="datatype">gmapdb</requirement>
8 <requirement type="datatype">gmap_snps</requirement>
9 <requirement type="datatype">snps.iit</requirement>
10 </requirements>
11 <version_string>snpindex --version</version_string>
12 <command interpreter="command"> /bin/bash $shscript 2>1 1> $output </command>
13 <inputs>
14 <conditional name="refGenomeSource">
15 <param name="genomeSource" type="select" label="Will you map to a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
16 <option value="indexed">Use a built-in index</option>
17 <option value="gmapdb">Use gmapdb from the history</option>
18 </param>
19 <when value="indexed">
20 <param name="gmapindex" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team">
21 <options from_file="gmap_indices.loc">
22 <column name="uid" index="0" />
23 <column name="dbkey" index="1" />
24 <column name="name" index="2" />
25 <column name="kmers" index="3" />
26 <column name="maps" index="4" />
27 <column name="snps" index="5" />
28 <column name="value" index="6" />
29 </options>
30 </param>
31 </when>
32 <when value="gmapdb">
33 <param name="gmapdb" type="data" format="gmapdb" metadata_name="dbkey" label="Select a gmapdb"
34 help="A GMAP database built with GMAP Build"/>
35 </when>
36 </conditional>
37 <conditional name="dbsnp">
38 <param name="snp_source" type="select" label="Add SNP info from" >
39 <option value="snpTable">UCSC SNP Table</option>
40 <option value="snpFile">GMAP SNP File</option>
41 <option value="snpIIT">"GMAP SNPs map from GMAP iit store</option>
42 </param>
43 <when value="snpTable">
44 <param name="snps" type="data" format="tabular" label="UCSC SNPs table" help="Example: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/snp130.txt.gz" />
45 <param name="snpsex" type="data" format="tabular" optional="true" label="UCSC SNP Exceptions table" help="Example: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/snp130Exceptions.txt.gz" />
46 <param name="weight" type="select" label="Include SNPs with at least Confidence Level" help="">
47 <option value="1" selected="true">1 (High)</option>
48 <option value="2">2 (Medium)</option>
49 <option value="3">3 (All)</option>
50 </param>
51 </when>
52 <when value="snpFile">
53 <param name="snps" type="data" format="gmap_snps" label="GMAP SNPs file"
54 help="Format (3 columns):
55 &lt;br&gt;>rs62211261 21:14379270 CG
56 &lt;br&gt;>rs62211262 21:14379281 CG
57 &lt;br&gt;Each line must start with a &gt; character, then be followed by an
58 identifier (which may have duplicates). Then there should be the
59 chromosomal coordinate of the SNP. (Coordinates are all 1-based, so
60 the first character of a chromosome is number 1.) Finally, there
61 should be the two possible alleles: ( AC AG AT CG CT GT or AN CN GN TN)
62 &lt;br&gt;These alleles must correspond to the possible nucleotides on the plus strand of the genome.
63 If the one of these two letters does not match the allele in the reference
64 sequence, that SNP will be ignored in subsequent processing as a probable error.
65 The N stands for any other allele." />
66 </when>
67 <when value="snpIIT">
68 <param name="snpIIT" type="data" format="snps.iit" label="GMAP SNPs map" help="Created by: GMAP iit store" />
69 </when>
70 </conditional>
71 <param name="snps_name" type="text" value="snps" label="Name for this SNP index" help="no white space characters">
72 </param>
73 </inputs>
74 <outputs>
75 <!--
76 <data format="txt" name="log" label="${tool.name} on ${on_string}: log"/>
77 -->
78 <data format="gmapsnpindex" name="output" label="${tool.name} on ${on_string} snpindex" />
79 </outputs>
80 <configfiles>
81 <configfile name="shscript">
82 #!/bin/bash
83 #set $ds = chr(36)
84 #set $gt = chr(62)
85 #set $lt = chr(60)
86 #set $ad = chr(38)
87 #import os.path
88 #if $refGenomeSource.genomeSource == "gmapdb":
89 #set $gmapdb = $refGenomeSource.gmapdb.extra_files_path
90 #set $refname = $refGenomeSource.gmapdb.metadata.db_name
91 #else:
92 #set $gmapdb = $os.path.dirname($refGenomeSource.gmapindex.value)
93 $refname = $os.path.basename($refGenomeSource.gmapindex.value)
94 #end if
95 #set $gmapsnpdir = $output.extra_files_path
96 mkdir -p $gmapsnpdir
97 #set $snpsname = $snps_name.__str__
98 #set $snpsiit = '.'.join([$snpsname,'iit'])
99 #set $pathsnps = $os.path.join($gmapsnpdir,$snpsname)
100 #set $pathsnpsiit = $os.path.join($gmapsnpdir,$snpsiit)
101 #if $dbsnp.snp_source != 'none' and $dbsnp.snps.__str__ != 'None':
102 #if $dbsnp.snp_source == 'snpTable':
103 #if $dbsnp.snpsex.__str__ != 'None':
104 cat $dbsnp.snps | dbsnp_iit -w $dbsnp.weight -e $dbsnp.snpsex | iit_store -o $pathsnps
105 #else:
106 cat $dbsnp.snps | dbsnp_iit -w $dbsnp.weight | iit_store -o $pathsnps
107 #end if
108 #elif $dbsnp.snp_source == 'snpFile':
109 cat $dbsnp.snps | iit_store -o $pathsnps
110 #elif $dbsnp.snp_source == 'snpIIT':
111 cat $dbsnp.snps > $pathsnpsiit
112 #end if
113 snpindex -D $gmapdb -d $refname -V $output.extra_files_path -v $snpsname $pathsnpsiit
114 echo snpindex -D $gmapdb -d $refname -V $output.extra_files_path -v $snpsname $pathsnpsiit
115 #end if
116 </configfile>
117 </configfiles>
118
119 <tests>
120 </tests>
121
122 <help>
123
124
125 **GMAP SNP Index**
126
127 GMAP SNP Index (snpindex in the GMAP documentaion) creates an index for known SNPs allowing for SNP tolerant mapping and alignment when using GMAP_ (Genomic Mapping and Alignment Program for mRNA and EST sequences) and GSNAP_ (Genomic Short-read Nucleotide Alignment Program).
128
129 You will want to read the README_
130
131 Publication_ citation: Thomas D. Wu, Colin K. Watanabe Bioinformatics 2005 21(9):1859-1875; doi:10.1093/bioinformatics/bti310
132
133 .. _GMAP: http://research-pub.gene.com/gmap/
134 .. _GSNAP: http://research-pub.gene.com/gmap/
135 .. _README: http://research-pub.gene.com/gmap/src/README
136 .. _Publication: http://bioinformatics.oxfordjournals.org/cgi/content/full/21/9/1859
137
138
139 </help>
140 </tool>
141