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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ commit bb83e01055cde8c766c630bec27afd3402ad6c88
author iuc
date Fri, 21 Feb 2025 21:22:34 +0000
parents 5aacd4eb027b
children
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1:5aacd4eb027b 2:0af381d1fbcf
1 <tool id="allegro" name="Allegro" version="@VER@.0" > 1 <tool id="allegro" name="Allegro" version="@TOOL_VERSION@.1" profile="21.05">
2 <description>Linkage and Haplotype analysis</description> 2 <description>Linkage and Haplotype analysis</description>
3 <xrefs>
4 <xref type="bio.tools">allegro</xref>
5 </xrefs>
6 <macros> 3 <macros>
7 <token name="@VER@">2</token> 4 <token name="@TOOL_VERSION@">2</token>
8 <xml name="macro_inputs" > 5 <xml name="macro_inputs" >
9 <param name="inp_ped" value="pedin.21" /> 6 <param name="inp_ped" value="pedin.21" />
10 <param name="inp_dat" value="datain.21" /> 7 <param name="inp_dat" value="datain.21" />
11 <param name="inp_map" value="map.21" /> 8 <param name="inp_map" value="map.21" />
12 </xml> 9 </xml>
13 </macros> 10 </macros>
11 <xrefs>
12 <xref type="bio.tools">allegro</xref>
13 </xrefs>
14 <requirements> 14 <requirements>
15 <requirement type="package" version="@VER@">allegro</requirement> 15 <requirement type="package" version="@TOOL_VERSION@">allegro</requirement>
16 </requirements> 16 </requirements>
17 <version_command><![CDATA[ 17 <version_command><![CDATA[
18 allegro 2>&1 | head -1 | awk -F' ' '{print $2}' 18 allegro 2>&1 | head -1 | awk -F' ' '{print $2}'
19 ]]> 19 ]]>
20 </version_command> 20 </version_command>
33 #if $cond_haplotypes.opt_crossover 33 #if $cond_haplotypes.opt_crossover
34 CROSSOVERRATE combined.out ${out_combined_cross} 34 CROSSOVERRATE combined.out ${out_combined_cross}
35 #end if 35 #end if
36 #elif $cond_haplotypes.opt_haplotypes.value == 'no' 36 #elif $cond_haplotypes.opt_haplotypes.value == 'no'
37 #if $cond_haplotypes.section_linkage.cond_linktype.extra_linkage_type.value == 'defaults' 37 #if $cond_haplotypes.section_linkage.cond_linktype.extra_linkage_type.value == 'defaults'
38 MODEL $cond_haplotypes.section_linkage.extra_linkage_mptspt.value par ${opt_xlinked} het param.mpt ${out_fparam} 38 MODEL $cond_haplotypes.section_linkage.extra_linkage_mptspt.value par $opt_xlinked het param.mpt ${out_fparam}
39 39
40 #elif $cond_haplotypes.section_linkage.cond_linktype.extra_linkage_type.value == 'allele_sharing' 40 #elif $cond_haplotypes.section_linkage.cond_linktype.extra_linkage_type.value == 'allele_sharing'
41 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} 41 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}
42 42
43 #elif $cond_haplotypes.section_linkage.cond_linktype.extra_linkage_type.value == 'classical' 43 #elif $cond_haplotypes.section_linkage.cond_linktype.extra_linkage_type.value == 'classical'
53 #elif $cond_haplotypes.section_linkage.cond_steps.extra_steps_type.value == 'MAXSTEPLENGTH' 53 #elif $cond_haplotypes.section_linkage.cond_steps.extra_steps_type.value == 'MAXSTEPLENGTH'
54 MAXSTEPLENGTH $cond_haplotypes.section_linkage.cond_steps.extra_maxstep 54 MAXSTEPLENGTH $cond_haplotypes.section_linkage.cond_steps.extra_maxstep
55 #end if 55 #end if
56 #end if 56 #end if
57 57
58 #if $opt_xlinked.value == 'X' 58 #if $opt_sexspecific
59 SEXSPECIFIC on 59 SEXSPECIFIC on
60 #end if 60 #end if
61 61
62 ENTROPY ${opt_entropy} 62 ENTROPY ${opt_entropy}
63 NPLEXACTP ${opt_nplexactp} 63 NPLEXACTP ${opt_nplexactp}
66 PAIRWISEIBD $cond_haplotypes.section_linkage.extra_linkage_mptspt.value $cond_pairwise.extra_pairwise_type.value 66 PAIRWISEIBD $cond_haplotypes.section_linkage.extra_linkage_mptspt.value $cond_pairwise.extra_pairwise_type.value
67 #end if 67 #end if
68 68
69 69
70 #if $cond_sim.opt_sim.value == 'yes' 70 #if $cond_sim.opt_sim.value == 'yes'
71 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 71 SIMULATE #slurp
72 #if $cond_sim.extra_sim_dloc != ""
73 dloc:$cond_sim.extra_sim_dloc #slurp
74 #end if
75 npre:$cond_sim.extra_sim_npre rep:$cond_sim.extra_sim_rep err:$cond_sim.extra_sim_err yield:$cond_sim.extra_sim_yield het:$cond_sim.extra_sim_het
72 #end if 76 #end if
73 77
74 MAXMEMORY 102400 78 MAXMEMORY 102400
75 UNIT $opt_unit 79 UNIT $opt_unit
76 80
141 <when value="yes" > 145 <when value="yes" >
142 <param name="extra_linkage_par_freq" type="float" value="0" min="0" max="1" label="Frequency" /> 146 <param name="extra_linkage_par_freq" type="float" value="0" min="0" max="1" label="Frequency" />
143 <param name="extra_linkage_par_pen" type="text" value="p0/p1/p2" label="Penetrance" /> 147 <param name="extra_linkage_par_pen" type="text" value="p0/p1/p2" label="Penetrance" />
144 </when> 148 </when>
145 </conditional> 149 </conditional>
146 <param name="extra_linkage_par_het" type="float" value="" label="HET Frequency (leave blank for dynamic)" /> 150 <param name="extra_linkage_par_het" type="float" value="" optional="true" label="HET Frequency (leave blank for dynamic)" />
147 </when> 151 </when>
148 </conditional> 152 </conditional>
149 153
150 <conditional name="cond_steps" > 154 <conditional name="cond_steps" >
151 <param name="extra_steps_type" type="select" label="Step Type" > 155 <param name="extra_steps_type" type="select" label="Step Type" >
197 <option value="yes" >Yes</option> 201 <option value="yes" >Yes</option>
198 <option value="no" selected="true" >No</option> 202 <option value="no" selected="true" >No</option>
199 </param> 203 </param>
200 <when value="no" /> 204 <when value="no" />
201 <when value="yes" > 205 <when value="yes" >
202 <param name="extra_sim_dloc" type="float" value="" min="0" label="Disease Locus (cM). Leave blank for unlinked disease locus." /> 206 <param name="extra_sim_dloc" type="float" value="" optional="true" min="0" label="Disease Locus (cM). Leave blank for unlinked disease locus." />
203 <param name="extra_sim_npre" type="integer" value="1" label="Number of prefiles to generate" /> 207 <param name="extra_sim_npre" type="integer" value="1" label="Number of prefiles to generate" />
204 <param name="extra_sim_rep" type="integer" value="1" label="How many times to repeat family pattern" /> 208 <param name="extra_sim_rep" type="integer" value="1" label="How many times to repeat family pattern" />
205 <param name="extra_sim_err" type="float" value="0" min="0" label="Error Rate" /> 209 <param name="extra_sim_err" type="float" value="0" min="0" label="Error Rate" />
206 <param name="extra_sim_yield" type="float" value="1" label="Genotype Yield" /> 210 <param name="extra_sim_yield" type="float" value="1" label="Genotype Yield" />
207 <param name="extra_sim_het" type="float" value="0" label="HET probability" /> 211 <param name="extra_sim_het" type="float" value="0" label="HET probability" />
210 <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." /> 214 <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." />
211 <param name="opt_unit" type="boolean" truevalue="centimorgan" falsevalue="recombination" value="false" label="Datafile uses centimorgan distances instead of recombination frequencies" /> 215 <param name="opt_unit" type="boolean" truevalue="centimorgan" falsevalue="recombination" value="false" label="Datafile uses centimorgan distances instead of recombination frequencies" />
212 </inputs> 216 </inputs>
213 217
214 <outputs> 218 <outputs>
215 <data name="out_ihaplo" format="allegro_haplo" label="${tool.name} on ${on_string}: Haplotypes" /> 219 <data name="out_ihaplo" format="allegro_ihaplo" label="${tool.name} on ${on_string}: Haplotypes" />
216 <data name="out_fparam" format="allegro_linkage" label="${tool.name} on ${on_string}: Linkage" /> 220 <data name="out_fparam" format="allegro_fparam" label="${tool.name} on ${on_string}: Linkage" />
217 <data name="out_founder" format="allegro_descent" label="${tool.name} on ${on_string}: Descent" /> 221 <data name="out_founder" format="allegro_descent" label="${tool.name} on ${on_string}: Descent" />
218 <data name="out_linexp" format="txt" label="${tool.name} on ${on_string}: Linear Expression" /> 222 <data name="out_linexp" format="txt" label="${tool.name} on ${on_string}: Linear Expression" />
219 <data name="out_combined_cross" format="txt" label="${tool.name} on ${on_string}: Combined Crossovers" /> 223 <data name="out_combined_cross" format="txt" label="${tool.name} on ${on_string}: Combined Crossovers" />
220 </outputs> 224 </outputs>
221 225
222 <tests> 226 <tests>
223 <test><!-- Default Haplotypes --> 227 <!-- Default Haplotypes -->
228 <test>
224 <expand macro="macro_inputs" /> 229 <expand macro="macro_inputs" />
225 230 <conditional name="cond_haplotypes">
226 <param name="extra_linkage_type" value="classical" /> 231 <param name="opt_haplotypes" value="yes" />
227 <param name="extra_linkage_mptspt" value="mpt" /> 232 </conditional>
228 <param name="opt_haplotypes" value="yes" />
229
230 <output name="out_ihaplo" > 233 <output name="out_ihaplo" >
231 <assert_contents> 234 <assert_contents>
232 <has_text_matching expression="1\s+206003\s+111\s+112(\s+[012])+" /> 235 <has_text_matching expression="1\s+206003\s+111\s+112(\s+[012])+" />
233 </assert_contents> 236 </assert_contents>
234 </output> 237 </output>
235 </test> 238 </test>
236 <test><!-- Linkage with custom steps--> 239 <!-- Linkage with custom steps-->
240 <test>
237 <expand macro="macro_inputs" /> 241 <expand macro="macro_inputs" />
238 242 <conditional name="cond_haplotypes">
239 <param name="extra_linkage_type" value="classical" /> 243 <section name="section_linkage">
240 <param name="extra_linkage_mptspt" value="mpt" /> 244 <param name="extra_linkage_mptspt" value="mpt" />
241 <param name="extra_linkage_mptspt" value="mpt" /> 245 <conditional name="cond_linktype" >
242 <param name="extra_steps" value="3" /> 246 <param name="extra_linkage_type" value="classical" />
243 <param name="extra_maxstep" value="30" /> 247 </conditional>
244 248 <conditional name="cond_steps" >
245 249 <param name="extra_steps" value="3" />
250 </conditional>
251 </section>
252 </conditional>
246 <output name="out_fparam" > 253 <output name="out_fparam" >
247 <assert_contents> 254 <assert_contents>
248 <has_text_matching expression="1(\s+[-0-9.]+){2}\s+rs2822572" /> 255 <has_text_matching expression="1(\s+[-0-9.]+){2}\s+rs2822572" />
249 </assert_contents> 256 </assert_contents>
250 </output> 257 </output>
251 </test> 258 </test>
252 <test><!-- Single-point linear expression test with power weights --> 259 <!-- Single-point linear expression test with power weights -->
260 <test>
253 <expand macro="macro_inputs" /> 261 <expand macro="macro_inputs" />
254 262 <conditional name="cond_haplotypes">
255 <param name="extra_linkage_type" value="allele_sharing" /> 263 <section name="section_linkage">
256 <param name="extra_linkage_mptspt" value="spt" /> 264 <param name="extra_linkage_mptspt" value="spt" />
257 <param name="extra_linkage_linexp" value="lin" /> 265 <conditional name="cond_linktype" >
258 <param name="extra_linkage_scoring" value="homoz" /> 266 <param name="extra_linkage_type" value="allele_sharing" />
259 <param name="extra_weighting" value="power:50" /> 267 <param name="extra_linkage_linexp" value="lin" />
260 268 <param name="extra_linkage_scoring" value="homoz" />
269 <param name="extra_weighting" value="power:0.5" />
270 </conditional>
271 </section>
272 </conditional>
261 <output name="out_fparam" > 273 <output name="out_fparam" >
262 <assert_contents> 274 <assert_contents>
263 <has_text_matching expression='(\-\d+\.\d+\s+)+rs2822696' /> 275 <has_text_matching expression='(\-\d+\.\d+\s+)+rs2822696' />
264 </assert_contents> 276 </assert_contents>
265 </output> 277 </output>