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comparison SNiPloid.xml @ 0:58111b3965b2 draft default tip

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author dereeper
date Thu, 01 Nov 2012 09:35:05 -0400
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1 <tool id="SNiPloid" name="SNiPloid">
2 <description>Comparison of SNP between a Tetraploid and its Parental Genomes</description>
3 <command interpreter="bash">./SNiPloid.sh
4 $Poly_Analysis.polyornot <!-- $1 -->
5 #if $Poly_Analysis.polyornot == "poly":
6
7 $Poly_Analysis.depthPolyploid1 $Poly_Analysis.depthPolyploid2 <!-- $4 $5 -->
8 $Poly_Analysis.VCFpolyploid1 $Poly_Analysis.DOCpolyploid1 <!-- $6 $7 -->
9 $Poly_Analysis.VCFpolyploid2 $Poly_Analysis.DOCpolyploid2 <!-- $8 $9 -->
10 #else:
11 $Poly_Analysis.Reference.ref <!-- $2 -->
12
13 #if $Poly_Analysis.Reference.ref == "1":
14 $Poly_Analysis.Reference.genome2Name
15 #end if
16
17 $Poly_Analysis.Reference.depthPolyploid1 $Poly_Analysis.Reference.depthGenome1 <!-- $6 $7 -->
18 $Poly_Analysis.Reference.VCFpolyploid1 $Poly_Analysis.Reference.DOCpolyploid1 <!-- $8 $9 -->
19 $Poly_Analysis.Reference.VCFgenome1 $Poly_Analysis.Reference.DOCgenome1 <!-- $10 $11 -->
20 #if $Poly_Analysis.Reference.ref == "0":
21 $Poly_Analysis.Reference.depthGenome2 <!-- $12 -->
22 $Poly_Analysis.Reference.VCFgenome2 $Poly_Analysis.Reference.DOCgenome2 <!-- $13 $14 -->
23 #end if
24 #end if
25 $SNP_csv $SNP_html $SNP_count $SNP_count_csv $enableLowQuality $log
26 #if $Poly_Analysis.polyornot == "poly":
27 $Poly_Analysis.value_filter_p1 $Poly_Analysis.value_filter_p2
28 #end if
29 #if $annotation.add_annot == "yes":
30 $annotation.add_annot $annotation.annotation_file $map
31 #end if
32 </command>
33
34 <inputs>
35
36 <conditional name="Poly_Analysis">
37
38 <param type="select" name="polyornot" label="Type of analysis">
39 <option value="poly" selected="True">POLYPLOID vs POLYPLOID</option>
40 <option value="notpoly">POLYPLOID vs PARENTAL DIPLOID GENOMES</option>
41 </param>
42
43 <when value="poly">
44 <param type="text" name="depthPolyploid1" label="Minimum read depth at a position to make a call (Polyploid 1)" value="20"/>
45 <param type="text" name="depthPolyploid2" label="Minimum read depth at a position to make a call (Polyploid 2)" value="20"/>
46 <param format="vcf" name="VCFpolyploid1" type="data" label="VCF file (Polyploid 1)"/>
47 <param format="vcf" name="VCFpolyploid2" type="data" label="VCF file (Polyploid 2)"/>
48 <param format="coverage" name="DOCpolyploid1" type="data" label="Depth of coverage information (Polyploid 1)"/>
49 <param format="coverage" name="DOCpolyploid2" type="data" label="Depth of coverage information (Polyploid 2)"/>
50 <param type="text" name="value_filter_p1" label="Minimum minor allele frequency (in %) (Polyploid 1)" value="10"/>
51 <param type="text" name="value_filter_p2" label="Minimum minor allele frequency (in %) (Polyploid 2)" value="10"/>
52 </when>
53
54 <when value="notpoly">
55 <conditional name="Reference">
56
57 <param type="select" name="ref" label="Reference" help="INTERN (Genome 2 as reference) or EXTERN">
58 <option value="1" selected="True">INTERN</option>
59 <option value="0">EXTERN</option>
60 </param>
61
62 <when value="0">
63 <param type="text" name="depthPolyploid1" label="Minimum read depth at a position to make a call (Polyploid)" value="20"/>
64 <param type="text" name="depthGenome1" label="Minimum read depth at a position to make a call (Genome 1)" value="20"/>
65 <param type="text" name="depthGenome2" label="Minimum read depth at a position to make a call (Genome 2)" value="20"/>
66 <param format="vcf" name="VCFpolyploid1" type="data" label="VCF file (Polyploid)"/>
67 <param format="vcf" name="VCFgenome1" type="data" label="VCF file (Genome 1)"/>
68 <param format="vcf" name="VCFgenome2" type="data" label="VCF file (Genome 2)"/>
69 <param format="coverage" name="DOCpolyploid1" type="data" label="Depth of coverage information (Polyploid)"/>
70 <param format="coverage" name="DOCgenome1" type="data" label="Depth of coverage information (Genome 1)"/>
71 <param format="coverage" name="DOCgenome2" type="data" label="Depth of coverage information (Genome2)"/>
72 </when>
73
74 <when value="1">
75 <param type="text" name="genome2Name" label="Genome 2 Name (Reference)" value="GenomeName"/>
76 <param type="text" name="depthPolyploid1" label="Minimum read depth at a position to make a call (Polyploid)" value="20"/>
77 <param type="text" name="depthGenome1" label="Minimum read depth at a position to make a call (Genome 1)" value="20"/>
78 <param format="vcf" name="VCFpolyploid1" type="data" label="VCF file (Polyploid)"/>
79 <param format="vcf" name="VCFgenome1" type="data" label="VCF file (Genome 1)" help="VCF file with [Genome 1] vs. [Genome 2] as Reference. /!\ Lost of heterozygosity for [Genome 2]"/>
80 <param format="coverage" name="DOCpolyploid1" type="data" label="Depth of coverage information (Polyploid)"/>
81 <param format="coverage" name="DOCgenome1" type="data" label="Depth of coverage information (Genome 1)"/>
82 </when>
83
84 </conditional>
85
86 </when>
87
88 </conditional>
89
90 <conditional name="annotation">
91 <param name="add_annot" type="select" label="Add a genome annotation file">
92 <option value="no" selected="True">No annotation available</option>
93 <option value="yes">Add a genome annotation</option>
94 </param>
95 <when value="yes">
96 <param format="gff3" name="annotation_file" type="data" label="Enter a genome annotation in GFF3 format"/>
97 </when>
98 <when value="no">
99 </when>
100 </conditional>
101
102 <param name="enableLowQuality" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Enable LowQual SNP ?" help="Default : only PASS SNP are considered" />
103
104
105 </inputs>
106
107 <outputs>
108
109 <data format="txt" name="SNP_csv" label="SNP output" />
110 <data format="html" name="SNP_html" label="SNP output (HTML)" />
111 <data format="html" name="SNP_count" label="Synthesis output (HTML)" />
112 <data format="txt" name="SNP_count_csv" label="Synthesis output" />
113 <data format="txt" name="log" label="log" />
114 <data format="png" name="map" label="map" />
115 </outputs>
116
117 <help>
118 .. class:: infomark
119
120 **Program encapsulated in Galaxy by Southgreen**
121
122 .. class:: infomark
123
124 **SNiPlay utilities**
125
126 -----
127
128 ==============
129 Authors:
130 ==============
131
132 **Marine Peralta, Alexis Dereeper**
133
134 -----
135
136 ==========
137 Overview
138 ==========
139
140 SNiPloid compares SNP between a tetraploid and its parental genomes, or between two polyploids.
141
142 -----
143
144 For further informations, please visite the website of the SNiPloid_ software.
145
146
147 .. _SNiPloid: http://sniplay.cirad.fr/cgi-bin/sniploid.cgi
148
149
150 </help>
151
152 </tool>