|
0
|
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>
|
