Mercurial > repos > iuc > gemini_comp_hets

comparison gemini_comp_hets.xml @ 2:f52ad3dcee4e draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
author iuc
date Tue, 16 Feb 2016 05:52:05 -0500
parents a511fb5bd380
children ac78943ce161
comparison
equal deleted inserted replaced
1:4c4f5f89cda2 2:f52ad3dcee4e
20 #if int($min_kindreds) > 0: 20 #if int($min_kindreds) > 0:
21 --min-kindreds $min_kindreds 21 --min-kindreds $min_kindreds
22 #end if 22 #end if
23 23
24 #if str($families).strip(): 24 #if str($families).strip():
25 --families $families 25 --families "$families"
26 #end if 26 #end if
27 27
28 -d $d 28 -d $d
29 $allow_unaffected 29 $allow_unaffected
30 30
50 <expand macro="filter" /> 50 <expand macro="filter" />
51 <expand macro="min_kindreds" /> 51 <expand macro="min_kindreds" />
52 <expand macro="family" /> 52 <expand macro="family" />
53 <expand macro="unaffected" /> 53 <expand macro="unaffected" />
54 <expand macro="min_sequence_depth" /> 54 <expand macro="min_sequence_depth" />
55 <param name="min_genotypequality" type="integer" value="0" label="The minimum genotype quality required for each sample in a family." help="default: 0 (--min-gq)"> 55 <param name="min_genotypequality" type="integer" value="0" min="0" label="The minimum genotype quality required for each sample in a family." help="default: 0 (--min-gq)" />
56 <validator type="in_range" min="0"/> 56 <param name="gt_pl_max" type="integer" value="-1" min="-1" label="The maximum phred-scaled genotype (PL) allowed for each sample in a family." help="default: -1 not set (--gt-pl-max)" />
57 </param>
58 <param name="gt_pl_max" type="integer" value="-1" label="The maximum phred-scaled genotype (PL) allowed for each sample in a family." help="default: -1 not set (--gt-pl-max)">
59 <validator type="in_range" min="-1"/>
60 </param>
61 <param name="pattern_only" type="boolean" truevalue="--pattern-only" falsevalue="" checked="False" 57 <param name="pattern_only" type="boolean" truevalue="--pattern-only" falsevalue="" checked="False"
62 label="Find compound hets by inheritance pattern, without regard to affection" help="(--pattern-only)"/> 58 label="Find compound hets by inheritance pattern, without regard to affection" help="(--pattern-only)"/>
63 <param name="max_priority" type="integer" value="1" label="Default is to show only confident compound hets. Set to 2 or higher to include pairs that are less likely true comp-hets." help="default: 1 (--max-priority)"> 59 <param name="max_priority" type="integer" value="1" min="1" label="Default is to show only confident compound hets. Set to 2 or higher to include pairs that are less likely true comp-hets." help="default: 1 (--max-priority)" />
64 <validator type="in_range" min="1"/>
65 </param>
66
67 </inputs> 60 </inputs>
68 <outputs> 61 <outputs>
69 <data name="outfile" format="tabular" /> 62 <data name="outfile" format="tabular" />
70 </outputs> 63 </outputs>
71 <tests> 64 <tests>