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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/swiftlink/ commit 2d4c604c2e76baaf744748be3d56e5504a0184b7
author iuc
date Sat, 09 Dec 2017 17:37:03 -0500
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-1:000000000000 0:0802a40af216
1 <tool id="swiftlink" name="Swiftlink" version="@VERSION@.0" >
2 <description>Parallel MCMC Linkage Analysis</description>
3 <macros>
4 <token name="@VERSION@">1.0</token>
5 <xml name="test_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="@VERSION@">swiftlink</requirement>
13 <requirement type="package" version="2017.3">linkage2allegro</requirement>
14 </requirements>
15 <!-- <version_command></version_command> Note: a version is never output by the program... -->
16 <command detect_errors='exit_code'><![CDATA[
17 swiftlink
18 -p '${inp_ped}'
19 -m '${inp_map}'
20 -d '${inp_dat}'
21 ${misc.X}
22 ${misc.a}
23 -q ${misc.q}
24 -c \${GALAXY_SLOTS:-3}
25 -i ${mcmc.i}
26 -b ${mcmc.b}
27 -s ${mcmc.s}
28 -x ${mcmc.x}
29 -l ${mcmc.l}
30 -n ${mcmc.n}
31 -R ${mcmc.R}
32
33 #if $misc.r
34 -r '${misc.r}'
35 #end if
36
37 #if $elod_opts.e == 'yes': ## 'true' / 'false' as opt values parse badly
38 -e
39 -f $elod_opts.f
40 -w $elod_opts.w
41 -k '$elod_opts.k'
42 -u $elod_opts.u 2> ${out_elod} ## stderr and stdout switched for some reason...
43 #else
44 -o swiftlink.out
45 && linkage2allegro '${inp_ped}' '${inp_map}' swiftlink -l swiftlink.out
46 && mv linkage.allegro_lod '${out_fparam}'
47 #end if
48
49 ]]>
50 </command>
51
52 <inputs>
53 <param name="inp_ped" type="data" format="linkage_pedin" label="Pedigree" />
54 <param name="inp_dat" type="data" format="linkage_recomb" label="Recombination Freqs." />
55 <param name="inp_map" type="data" format="linkage_map" label="Marker Positions" />
56
57 <conditional name="elod_opts" >
58 <param argument="-e" type="select" label="Calculate Expected LOD scores from pedigree only.">
59 <option value="yes">Yes</option>
60 <option value="no" selected="true">No</option>
61 </param>
62 <when value="yes" >
63 <param name="f" argument="-f" type="float" min="0" max="0.99" value="0.0001" label="Frequency" />
64 <param name="w" argument="-w" type="float" min="0" max="1" value="0.5" label="Seperation" />
65 <param name="k" argument="-k" type="text" value="0.00,0.00,1.00" label="Penetrance List" />
66 <param name="u" argument="-u" type="integer" min="1" value="1000000" label="Replicates" />
67 </when>
68 <when value="no" ></when>
69 </conditional>
70
71 <section name="mcmc" title="Marko Chain Monte Carlo (MCMC) Options" expanded="false" >
72 <param argument="-i" type="integer" min="1" value="50000" label="Iterations" />
73 <param argument="-b" type="integer" min="1" value="50000" label="Burn-ins" />
74 <param argument="-s" type="integer" min="1" value="1000" label="Sequential Imputation" />
75 <param argument="-x" type="integer" min="1" value="10" label="Scoring Period" />
76 <param argument="-n" type="integer" min="1" value="5" label="Lod Scores" />
77 <param argument="-R" type="integer" min="1" value="1" label="Runs" />
78 <param argument="-l" type="float" min="0" max="1" value="0.5" label="L-Sampler Probability" />
79 </section>
80
81 <section name="misc" title="Miscellaneous" expanded="true" >
82 <param argument="-X" type="boolean" truevalue="-X" falsevalue="" value="false" label="X-linked"/>
83 <param argument="-a" type="boolean" truevalue="-a" falsevalue="" value="false" label="Affecteds only"/>
84 <param argument="-q" type="integer" min="1" value="1000000" label="Peel-sequence Iterator"/>
85 <param argument="-r" type="data" format="txt" label="Random seeds (single-column)" optional="true" />
86 </section>
87 </inputs>
88
89 <outputs>
90 <data name="out_fparam" format="allegro_fparam" label="${tool.name} on ${on_string}: MPT Linkage File" >
91 <filter>elod_opts['e'] == "no"</filter>
92 </data>
93 <data name="out_elod" format="txt" label="${tool.name} on ${on_string}: Elod score" >
94 <filter>elod_opts['e'] == "yes"</filter>
95 </data>
96 </outputs>
97
98 <tests>
99 <test>
100 <expand macro="test_inputs" />
101
102 <param name="b" value="1000" />
103 <param name="i" value="2000" />
104 <param name="x" value="150" />
105 <param name="e" value="yes" />
106 <param name="u" value="1000" />
107
108 <output name="out_elod" >
109 <assert_contents>
110 <has_text_matching expression='sex-linked = false' />
111 <has_text_matching expression='Total\s+\|\s+\d+\.\d+\s*' />
112 </assert_contents>
113 </output>
114 </test>
115 <test>
116 <expand macro="test_inputs" />
117
118 <param name="b" value="5000" />
119 <param name="i" value="100" />
120 <param name="x" value="100" />
121
122 <output name="out_fparam" >
123 <assert_contents>
124 <has_text_matching expression="(\s+-?\d+\.\d+){4}\s+rs468601" />
125 </assert_contents>
126 </output>
127 </test>
128 </tests>
129 <help>
130 SwiftLink performs multipoint parametric linkage analysis on large consanguineous pedigrees and is primarily targeted at pedigrees that cannot be analysed by a Lander-Green algorithm based program, i.e. many markers, but larger pedigrees. The current version of SwiftLink only supports SNP markers.
131 </help>
132 <citations>
133 <citation type="doi">10.1093/bioinformatics/bts704</citation>
134 </citations>
135 </tool>