Mercurial > repos > dereeper > sniploid
comparison SNiPloid.xml @ 0:58111b3965b2 draft default tip
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author | dereeper |
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date | Thu, 01 Nov 2012 09:35:05 -0400 |
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-1:000000000000 | 0:58111b3965b2 |
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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> |