Mercurial > repos > xuef > vdm_plot
comparison my_VDM_tool.xml @ 2:dd74836c77ad draft
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author | xuef |
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date | Fri, 06 Nov 2020 16:38:33 +0000 |
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1:48e2fe881400 | 2:dd74836c77ad |
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1 <tool id="my_VDM_tool" name="VDM_tool" version="1.0.0"> | |
2 <!--A simple description of the tool that will appear in the tool panel in Galaxy.--> | |
3 <description>Map a mutation using in silico bulk segregant linkage analysis of pooled recombinant lines generated through backcrossing.</description> | |
4 <!-- Handles exit codes in Galaxy. --> | |
5 <stdio> | |
6 <exit_code range="1:"/> | |
7 </stdio> | |
8 <requirements> | |
9 <requirement type="package" version="3.2.1">R</requirement> | |
10 <requirement type="package" version="1.2.0">getopt</requirement> | |
11 </requirements> | |
12 | |
13 <command> | |
14 Rscript /home/fxue/galaxy/tools/my_VDM_tool/my_VDM_tool.R | |
15 --inf "$inf" | |
16 #if $species.species_select=="Celegans" | |
17 --itype "$species.ce" | |
18 #else if $species.species_select=="Zebrafish" | |
19 --itype "$species.ze" | |
20 #else if $species.species_select=="Brachypodium" | |
21 --itype "$species.br" | |
22 #else if $species.species_select=="Arabidopsis" | |
23 --itype "$species.ar" | |
24 #else if $species.species_select=="other" | |
25 --itype "$species.ot" | |
26 #end if | |
27 | |
28 --qual $qual | |
29 --thrup $thrup | |
30 --thrlow $thrlow | |
31 | |
32 #if $allfreq.allfreq_select=="AB" | |
33 --allr "$allfreq.ab" | |
34 #else if $allfreq.allfreq_select=="ratio" | |
35 --allr "$allfreq.ratio" | |
36 #end if | |
37 | |
38 #if $only_snp.only_snp_select=="TRUE" | |
39 --snp "$only_snp.true" | |
40 #else if $only_snp.only_snp_select=="FALSE" | |
41 --snp "$only_snp.false" | |
42 #end if | |
43 | |
44 --lsp $lsp | |
45 --pcol "$pcol" | |
46 --lcol "$lcol" | |
47 | |
48 #if $xaxis.xaxis_select=="TRUE" | |
49 --xstand $xaxis.true | |
50 #else if $xaxis.xaxis_select=="FALSE" | |
51 --xstand $xaxis.false | |
52 #end if | |
53 | |
54 --bsize $bsize | |
55 | |
56 #if $binnorm.binnorm_select=="TRUE" | |
57 --bnorm $binnorm.true | |
58 #else if $binnorm.binnorm_select=="FALSE" | |
59 --bnorm $binnorm.false | |
60 #end if | |
61 | |
62 #if $exclfiles.exclfiles_select=="FALSE" | |
63 --exclf $exclfiles.false | |
64 #else if $exclfiles.exclfiles_select=="TRUE" | |
65 --exclf $exclfiles.true | |
66 #end if | |
67 | |
68 | |
69 --exclthr $exclthr | |
70 --exclcol "$exclcol" | |
71 | |
72 --parn "$parn" | |
73 --outn "$outn" | |
74 --pdfn "$pdfn" | |
75 | |
76 </command> | |
77 <inputs> | |
78 <param type="data" name="inf" format="vcf" label="fastq file"/> | |
79 | |
80 <conditional name="species"> | |
81 <param name="species_select" type="select" label="Select the species"> | |
82 <option value="Celegans">C. elegans</option> | |
83 <option value="Zebrafish">Zebrafish</option> | |
84 <option value="Brachypodium">Brachypodium</option> | |
85 <option value="Arabidopsis">Arabidopsis</option> | |
86 <option value="other">other</option> | |
87 </param> | |
88 <when value="Celegans"> | |
89 <param name="ce" type="hidden" value="C.elegans" label="The C. elegans chromosome numbers and lengths (in Mb)" help="C.elegans help"/> | |
90 </when> | |
91 <when value="Zebrafish"> | |
92 <param name="ze" type="hidden" value="Zebrafish" label="The Zebrafish chromosome numbers and lengths (in Mb)" help="Zebrafish help"/> | |
93 </when> | |
94 <when value="Brachypodium"> | |
95 <param name="br" type="hidden" value="Brachypodium" label="The Brachypodium chromosome numbers and lengths (in Mb)" help="Brachypodium help"/> | |
96 </when> | |
97 <when value="Arabidopsis"> | |
98 <param name="ar" type="hidden" value="Arabidopsis" label="The Arabidopsis chromosome numbers and lengths (in Mb)" help="Arabidopsis help"/> | |
99 </when> | |
100 <when value="other"> | |
101 <param name="ot" type="data" format="tabular" label="Select file with chromosome numbers and lengths (in Mb) from your history" help="Table consisting of chromosome number in column 1 and length (in Mb) in column 2 (e.g. 'CHRI 16' or 'CHR1 16') with no column header names, tab-delimitation, and no quotation marks in a .txt file"/> | |
102 </when> | |
103 </conditional> | |
104 | |
105 <param type="float" name="qual" value="200" label="Filter by quality" help="Filter results based on quality value"/> | |
106 <param type="float" name="thrup" value="1" label="upper threshold for homozygosity" help="Allele frequency values greater than or equal to this will be considered as homozygous ALT for barplots of frequency homozygous variants along chromosomes"/> | |
107 <param type="float" name="thrlow" value="0" label="lower threshold for homozygosity" help="Allele frequency values less than or equal to this will be considered as homozygous for barplots of frequency homozygous REF variants along chromosomes"/> | |
108 | |
109 | |
110 <conditional name="allfreq"> | |
111 <param name="allfreq_select" type="select" label="Select the source for allele frequency"> | |
112 <option value="AB">AB</option> | |
113 <option value="ratio">AO/(AO+RO)</option> | |
114 </param> | |
115 <when value="AB"> | |
116 <param name="ab" type="hidden" value="AB" label="Use AB field (from Freebayes) as the value for allele frequency" help=" "/> | |
117 </when> | |
118 <when value="ratio"> | |
119 <param name="ratio" type="hidden" value="ratio" label="Use AO/(AO+RO) calculation (from Freebayes) as the value for allele frequency" help=" "/> | |
120 </when> | |
121 </conditional> | |
122 | |
123 <conditional name="only_snp"> | |
124 <param name="only_snp_select" type="select" label="Select type of variants to use for plotting"> | |
125 <option value="TRUE">SNPs</option> | |
126 <option value="FALSE">all</option> | |
127 </param> | |
128 <when value="TRUE"> | |
129 <param name="true" type="hidden" value="TRUE" label="Use only SNP variants" help=" "/> | |
130 </when> | |
131 <when value="FALSE"> | |
132 <param name="false" type="hidden" value="FALSE" label="Use all types of variants" help=" "/> | |
133 </when> | |
134 </conditional> | |
135 | |
136 <param type="float" name="lsp" value="0.4" label="Loess span" help="Parameter that controls the smoothing of the Loess curve"/> | |
137 <param type="text" name="pcol" value="black" label="Colour of scatterplot points" help="See below for list of supported colors"/> | |
138 <param type="text" name="lcol" value="red" label="Colour of Loess curve" help="See below for list of supported colors"/> | |
139 | |
140 | |
141 <conditional name="xaxis"> | |
142 <param name="xaxis_select" type="select" label="Spacing of the x-axis in plots"> | |
143 <option value="TRUE">True</option> | |
144 <option value="FALSE">False</option> | |
145 </param> | |
146 <when value="TRUE"> | |
147 <param name="true" type="hidden" value="TRUE" label="Uniform spacing of the x-axis based on Mb" help="Scale of x-axis (in Mb) is fixed for the scatter plots and frequency plots across all chromosomes"/> | |
148 </when> | |
149 <when value="FALSE"> | |
150 <param name="false" type="hidden" value="FALSE" label="Variable spacing of the x-axis based on chromosome lengths" help="Scale of x-axis (in Mb) is dependent on chromosome length for the scatter plots and frequency plots for all chromosomes"/> | |
151 </when> | |
152 </conditional> | |
153 | |
154 <param type="integer" name="bsize" value="1000000" label="bin size" help="Size of the bins (in bp) for barplot of frequency of homozygous variants along chromosomes"/> | |
155 | |
156 <conditional name="binnorm"> | |
157 <param name="binnorm_select" type="select" label="Normalisation of y-axis in frequency barplots"> | |
158 <option value="TRUE">True</option> | |
159 <option value="FALSE">False</option> | |
160 </param> | |
161 <when value="TRUE"> | |
162 <param name="true" type="hidden" value="TRUE" label="Normalised y-axis frequency values based on formula" help="Normalisation formula as in cloudmap paper"/> | |
163 </when> | |
164 <when value="FALSE"> | |
165 <param name="false" type="hidden" value="FALSE" label="Original frequency y-axis values" help=" "/> | |
166 </when> | |
167 </conditional> | |
168 | |
169 <conditional name="exclfiles"> | |
170 <param name="exclfiles_select" type="select" label="Additional exclusion of variants by subtraction"> | |
171 <option value="FALSE">No</option> | |
172 <option value="TRUE">Yes</option> | |
173 </param> | |
174 <when value="FALSE"> | |
175 <param name="false" type="hidden" value="FALSE" label="No additional variant subtraction" help=""/> | |
176 </when> | |
177 <when value="TRUE"> | |
178 <param name="true" type="data" format="tabular" label="Select variant lists to subtract from your history" help="Requires CHR POS DEPTH REF ALT columns- recommend directly using the output table generated by this tool or refer to it for desired format"/> | |
179 | |
180 <param type="float" name="exclthr" value="0" label="Filter based on allelic ratio values" help="For filtering variant subtraction lists, only variants above this threshold value will be used for subtraction (e.g. 0 means all variants and 1 means only homozygous variants"/> | |
181 <param type="text" name="exclcol" value="green" label="Colour of original loess curve (before additional variant subtraction)" help="See below for list of supported colors"/> | |
182 </when> | |
183 </conditional> | |
184 | |
185 </inputs> | |
186 | |
187 <outputs> | |
188 <data name="parn" format="txt"/> | |
189 <data name="outn" format="txt"/> | |
190 <data name="pdfn" format="pdf"/> | |
191 </outputs> | |
192 | |
193 <tests> | |
194 </tests> | |
195 | |
196 <help> | |
197 </help> | |
198 </tool> |