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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ commit 458d9276671695befc9ca85c4d355725ef36b831
author iuc
date Sat, 09 Dec 2017 06:39:42 -0500
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-1:000000000000 0:8c29e3621475
1 <tool id="allegro" name="Allegro" version="@VER@.0" >
2 <description>Linkage and Haplotype analysis</description>
3 <macros>
4 <token name="@VER@">2</token>
5 <xml name="macro_inputs" >
6 <param name="inp_ped" value="pedin.21" />
7 <param name="inp_dat" value="datain.21" />
8 <param name="inp_map" value="map.21" />
9 </xml>
10 </macros>
11 <requirements>
12 <requirement type="package" version="@VER@">allegro</requirement>
13 </requirements>
14 <version_command><![CDATA[
15 allegro 2>&1 | head -1 | awk -F' ' '{print $2}'
16 ]]>
17 </version_command>
18 <command detect_errors='exit_code'>allegro $allegro_conf</command>
19
20 <configfiles>
21 <configfile name="allegro_conf" ><![CDATA[
22 PREFILE $inp_ped
23 DATFILE $inp_dat
24 #if $inp_map
25 MAPFILE $inp_map
26 #end if
27
28 #if $cond_haplotypes.opt_haplotypes == 'yes'
29 HAPLOTYPE haplo.out ${out_ihaplo} ${out_founder} inher.out
30 #if $cond_haplotypes.opt_crossover
31 CROSSOVERRATE combined.out ${out_combined_cross}
32 #end if
33 #elif $cond_haplotypes.opt_haplotypes.value == 'no'
34 #if $cond_haplotypes.section_linkage.cond_linktype.extra_linkage_type.value == 'defaults'
35 MODEL $cond_haplotypes.section_linkage.extra_linkage_mptspt.value par ${opt_xlinked} het param.mpt ${out_fparam}
36
37 #elif $cond_haplotypes.section_linkage.cond_linktype.extra_linkage_type.value == 'allele_sharing'
38 MODEL $cond_haplotypes.section_linkage.extra_linkage_mptspt.value $cond_haplotypes.section_linkage.cond_linktype.extra_linkage_linexp.value $cond_haplotypes.section_linkage.cond_linktype.extra_linkage_scoring.value $cond_haplotypes.section_linkage.cond_linktype.extra_weighting.value param.mpt ${out_linexp}
39
40 #elif $cond_haplotypes.section_linkage.cond_linktype.extra_linkage_type.value == 'classical'
41 #if $cond_haplotypes.section_linkage.cond_linktype.cond_customfreqs.opt_custom_freqs.value == 'yes'
42 MODEL $cond_haplotypes.section_linkage.extra_linkage_mptspt.value par $opt_xlinked} freq:$cond_haplotypes.section_linkage.cond_linktype.cond_customfreqs.extra_linkage_par_freq pen:$cond_haplotypes.section_linkage.cond_linktype.cond_customfreqs.extra_linkage_par_pen $cond_haplotypes.section_linkage.cond_linktype.extra_linkage_par_het param.mpt ${out_fparam}
43 #end if
44 #end if
45
46 #if $cond_haplotypes.section_linkage.cond_steps.extra_steps_type.value == 'STEPS'
47 STEPS $cond_haplotypes.section_linkage.cond_steps.extra_steps
48 #elif $cond_haplotypes.section_linkage.cond_steps.extra_steps_type.value == 'STEPFILE'
49 STEPFILE $cond_haplotypes.section_linkage.cond_steps.inp_stepfile
50 #elif $cond_haplotypes.section_linkage.cond_steps.extra_steps_type.value == 'MAXSTEPLENGTH'
51 MAXSTEPLENGTH $cond_haplotypes.section_linkage.cond_steps.extra_maxstep
52 #end if
53 #end if
54
55 #if $opt_xlinked.value == 'X'
56 SEXSPECIFIC on
57 #end if
58
59 ENTROPY ${opt_entropy}
60 NPLEXACTP ${opt_nplexactp}
61
62 #if $cond_pairwise.opt_pairwise.value == 'yes'
63 PAIRWISEIBD $cond_haplotypes.section_linkage.extra_linkage_mptspt.value $cond_pairwise.extra_pairwise_type.value
64 #end if
65
66
67 #if $cond_sim.opt_sim.value == 'yes'
68 SIMULATE $cond_sim.extra_sim_dloc $cond_sim.extra_sim_npre $cond_sim.extra_sim_rep $cond_sim.extra_sim_err $cond_sim.extra_sim_yield $cond_sim.extra_sim_het
69 #end if
70
71 MAXMEMORY 102400
72 UNIT $opt_unit
73
74 UNINFORMATIVE
75
76
77 ]]>
78 </configfile>
79 </configfiles>
80
81 <inputs>
82 <param name="inp_ped" type="data" format="linkage_pedin" label="Pedigree" />
83 <param name="inp_dat" type="data" format="linkage_recomb" label="Recombination Freqs." />
84 <param name="inp_map" type="data" format="linkage_map" label="Marker Positions" optional="true" />
85
86 <conditional name="cond_haplotypes" >
87 <param name="opt_haplotypes" type="select" label="Use Haplotypes?" >
88 <option value="yes" >Yes</option>
89 <option value="no" selected="true" >No</option>
90 </param>
91
92 <when value="yes" >
93 <param name="opt_crossover" type="boolean" value="false" label="Show crossover rate" />
94 </when>
95 <when value="no" >
96 <section name="section_linkage" title="Linkage" expanded="true" >
97 <param name="extra_linkage_mptspt" type="select" label="Use multipoint IBD sharing probabilities, instead of single point" >
98 <option value="mpt" selected="true" >mpt</option>
99 <option value="spt" >spt</option>
100 </param>
101
102 <conditional name="cond_linktype" >
103 <param name="extra_linkage_type" type="select" label="Type of analysis" >
104 <option value="defaults" selected="true" >Defaults</option>
105 <option value="allele_sharing" >Allele Sharing</option>
106 <option value="classical" >Classical</option>
107 </param>
108
109 <when value="defaults" />
110
111 <when value="allele_sharing">
112 <param name="extra_linkage_linexp" type="select" label="Linear or Exponential" >
113 <option value="lin" >Linear</option>
114 <option value="exp" >Exponential</option>
115 </param>
116 <param name="extra_linkage_scoring" type="select" label="Scoring function" >
117 <option value="pairs">Pairs</option>
118 <option value="all">All</option>
119 <option value="homoz">Homozygous</option>
120 <option value="mnallele">MNAllele</option>
121 <option value="robdom">RobDom</option>
122 <option value="ps:mm/mf/ff">PS:MM/MF/FF</option>
123 </param>
124
125 <param name="extra_weighting" type="select" label="Weighting function" >
126 <option value="equal">Equal</option>
127 <option value="power:0.5">Power</option>
128 </param>
129 </when>
130
131 <when value="classical" >
132 <conditional name="cond_customfreqs" >
133 <param name="opt_custom_freqs" type="select" label="Use custom frequencies instead of datafile" >
134 <option value="yes" >Yes</option>
135 <option value="no" selected="true" >No</option>
136 </param>
137 <when value="no" />
138 <when value="yes" >
139 <param name="extra_linkage_par_freq" type="float" value="0" min="0" max="1" label="Frequency" />
140 <param name="extra_linkage_par_pen" type="text" value="p0/p1/p2" label="Penetrance" />
141 </when>
142 </conditional>
143 <param name="extra_linkage_par_het" type="float" value="" label="HET Frequency (leave blank for dynamic)" />
144 </when>
145 </conditional>
146
147 <conditional name="cond_steps" >
148 <param name="extra_steps_type" type="select" label="Step Type" >
149 <option value="STEPS">Calculations between adjacent markers</option>
150 <option value="STEPFILE">Calculations at positions set in file</option>
151 <option value="MAXSTEPLENGTH">Calculations at periodic (cM) intervals</option>
152 </param>
153 <when value="STEPS">
154 <param name="extra_steps" type="integer" min="1" value="2" label="# Steps" />
155 </when>
156 <when value="STEPFILE">
157 <param name="inp_stepfile" type="data" format="txt" label="Step file" />
158 </when>
159 <when value="MAXSTEPLENGTH">
160 <param name="extra_maxstep" type="float" min="1" value="2" label="cM" />
161 </when>
162 </conditional>
163 </section>
164 </when>
165 </conditional>
166
167 <param name="opt_xlinked" type="select" label="Disease model" >
168 <option value="">Autosomal</option>
169 <option value="X">X-Linked</option>
170 </param>
171
172 <param name="opt_entropy" type="boolean" truevalue="on" falsevalue="off" checked="false" label="Entropy" />
173 <param name="opt_nplexactp" type="boolean" truevalue="on" falsevalue="off" checked="false" label="Use exact P-values" />
174
175 <conditional name="cond_pairwise" >
176 <param name="opt_pairwise" type="select" label="Perform Pairwise Analysis?" >
177 <option value="yes" >Yes</option>
178 <option value="no" selected="true" >No</option>
179 </param>
180
181 <when value="no"/>
182 <when value="yes" >
183 <param name="extra_pairwise_type" type="select" label="Weighting" >
184 <option value="all">All</option>
185 <option value="genotype">Genotype</option>
186 <option value="affected">Affected</option>
187 <option value="informative">Informative</option>
188 </param>
189 </when>
190 </conditional>
191
192 <conditional name="cond_sim" >
193 <param name="opt_sim" type="select" label="Simulate multipoint data?" >
194 <option value="yes" >Yes</option>
195 <option value="no" selected="true" >No</option>
196 </param>
197 <when value="no" />
198 <when value="yes" >
199 <param name="extra_sim_dloc" type="float" value="" min="0" label="Disease Locus (cM). Leave blank for unlinked disease locus." />
200 <param name="extra_sim_npre" type="integer" value="1" label="Number of prefiles to generate" />
201 <param name="extra_sim_rep" type="integer" value="1" label="How many times to repeat family pattern" />
202 <param name="extra_sim_err" type="float" value="0" min="0" label="Error Rate" />
203 <param name="extra_sim_yield" type="float" value="1" label="Genotype Yield" />
204 <param name="extra_sim_het" type="float" value="0" label="HET probability" />
205 </when>
206 </conditional>
207 <param name="opt_sexspecific" type="boolean" truevalue="on" falsevalue="off" value="false" label="Use Sex-Specific Penetrances (specified in data file)" help="Note that you will need to include sex-specific penetrances in your data input file for this to work." />
208 <param name="opt_unit" type="boolean" truevalue="centimorgan" falsevalue="recombination" value="false" label="Datafile uses centimorgan distances instead of recombination frequencies" />
209 </inputs>
210
211 <outputs>
212 <data name="out_ihaplo" format="allegro_haplo" label="${tool.name} on ${on_string}: Haplotypes" />
213 <data name="out_fparam" format="allegro_linkage" label="${tool.name} on ${on_string}: Linkage" />
214 <data name="out_founder" format="allegro_descent" label="${tool.name} on ${on_string}: Descent" />
215 <data name="out_linexp" format="txt" label="${tool.name} on ${on_string}: Linear Expression" />
216 <data name="out_combined_cross" format="txt" label="${tool.name} on ${on_string}: Combined Crossovers" />
217 </outputs>
218
219 <tests>
220 <test><!-- Default Haplotypes -->
221 <expand macro="macro_inputs" />
222
223 <param name="extra_linkage_type" value="classical" />
224 <param name="extra_linkage_mptspt" value="mpt" />
225 <param name="opt_haplotypes" value="yes" />
226
227 <output name="out_ihaplo" >
228 <assert_contents>
229 <has_text_matching expression="1\s+206003\s+111\s+112(\s+[012])+" />
230 </assert_contents>
231 </output>
232 </test>
233 <test><!-- Linkage with custom steps-->
234 <expand macro="macro_inputs" />
235
236 <param name="extra_linkage_type" value="classical" />
237 <param name="extra_linkage_mptspt" value="mpt" />
238 <param name="extra_linkage_mptspt" value="mpt" />
239 <param name="extra_steps" value="3" />
240 <param name="extra_maxstep" value="30" />
241
242
243 <output name="out_fparam" >
244 <assert_contents>
245 <has_text_matching expression="1(\s+[-0-9.]+){2}\s+rs2822572" />
246 </assert_contents>
247 </output>
248 </test>
249 <test><!-- Single-point linear expression test with power weights -->
250 <expand macro="macro_inputs" />
251
252 <param name="extra_linkage_type" value="allele_sharing" />
253 <param name="extra_linkage_mptspt" value="spt" />
254 <param name="extra_linkage_linexp" value="lin" />
255 <param name="extra_linkage_scoring" value="homoz" />
256 <param name="extra_weighting" value="power:50" />
257
258 <output name="out_fparam" >
259 <assert_contents>
260 <has_text_matching expression='(\-\d+\.\d+\s+)+rs2822696' />
261 </assert_contents>
262 </output>
263 </test>
264 </tests>
265 <help>
266 Allegro is a computer program for multipoint genetic linkage analysis and related calculations. Allegro can do both classical parametric linkage analysis and analysis based on allele sharing models. In addition, Allegro estimates total number of recombinations between markers, computes posterior IBD sharing probabilities, re-constructs haplotypes and does two types of simulation. Thus Allegro includes the basic functionality of the well known Genehunter program (Kruglyak et al. 1996). It can analyse pedigrees of moderate size,and it can handle many markers. The biggest advantages of Allegro over Genehunterar the allele sharing models that it provides and a much shorter execution time.
267 </help>
268 <citations>
269 <citation type="doi">10.1038/ng1005-1015</citation>
270 <citation type="doi">10.1038/75514</citation>
271 </citations>
272 </tool>