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comparison cloudmap.xml @ 7:3619e85a5477

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v0.1.7.0 bug fixes
author Wolfgang Maier
date Tue, 22 Sep 2015 22:36:41 +0200
parents 85214e4428fd
children d79fe626c6fd
comparison
equal deleted inserted replaced
6:85214e4428fd 7:3619e85a5477
1 <tool id="nacreousmap" name="NacreousMap" version="0.1.7.0"> 1 <tool id="nacreousmap" name="NacreousMap" version="0.1.7.0">
2 <description>Map causative mutations by multi-variant linkage analysis.</description> 2 <description>Map causative mutations by multi-variant linkage analysis.</description>
3 <macros>
4 <import>toolshed_macros.xml</import>
5 </macros>
6 <expand macro="requirements"/> 3 <expand macro="requirements"/>
7 <version_command>mimodd version -q</version_command> 4 <version_command>mimodd version -q</version_command>
8 <command> 5 <command>
9 mimodd map "${opt.source.ifile}" ${opt.mode} 6 mimodd map ${opt.mode} "${opt.source.ifile}"
10 #if $str($opt.source.sample): 7 #if $str($opt.source.sample):
11 -m "${opt.source.sample}" 8 -m "${opt.source.sample}"
12 #end if 9 #end if
13 #if $str($opt.source.related_parent_sample): 10 #if $str($opt.source.related_parent_sample):
14 -r "${opt.source.related_parent_sample}" 11 -r "${opt.source.related_parent_sample}"
58 #end if 55 #end if
59 56
60 </command> 57 </command>
61 58
62 <macros> 59 <macros>
60 <import>toolshed_macros.xml</import>
63 <macro name="svd_unconditional"> 61 <macro name="svd_unconditional">
64 <expand macro="hidden_vaf_algo_params" /> 62 <expand macro="hidden_vaf_algo_params" />
65 <expand macro="seqdict_param" /> 63 <expand macro="seqdict_param" />
66 <expand macro="bins" /> 64 <expand macro="bins" />
67 <param name="norm" type="boolean" label="normalize variant counts to bin-width" truevalue="" falsevalue="--no-normalize" checked="true" help="without normalization the tool will just report the number of nucleotides per bin; with normalization the results for different bin-widths will be comparable." /> 65 <param name="norm" type="boolean" label="normalize variant counts to bin-width" truevalue="" falsevalue="--no-normalize" checked="true" help="without normalization the tool will just report the number of nucleotides per bin; with normalization the results for different bin-widths will be comparable." />
120 <param name="related_parent_sample" type="hidden" value="" /> 118 <param name="related_parent_sample" type="hidden" value="" />
121 <param name="unrelated_parent_sample" type="hidden" value="" /> 119 <param name="unrelated_parent_sample" type="hidden" value="" />
122 <param name="infer_missing" type="hidden" value="" /> 120 <param name="infer_missing" type="hidden" value="" />
123 </macro> 121 </macro>
124 <macro name="bins"> 122 <macro name="bins">
125 <repeat name="bin_sizes" title="bin sizes to analyze variants in (defaults to: 1Mb and 500Kb" default="0" min="0" help="Values can be entered in bases (e.g., 1000000), kilobases (e.g., 500Kb) or megabases (e.g., 1Mb), but must be integral, i.e. no decimal numbers are allowed."> 123 <repeat name="bin_sizes" title="bin sizes to analyze variants in (defaults to: 1Mb and 500Kb)" default="0" min="0" help="Values can be entered in bases (e.g., 1000000), kilobases (e.g., 500Kb) or megabases (e.g., 1Mb), but must be integral, i.e. no decimal numbers are allowed.">
126 <param name="bin_size" type="text" /> 124 <param name="bin_size" type="text" />
127 </repeat> 125 </repeat>
128 </macro> 126 </macro>
129 <macro name="scatter_default"> 127 <macro name="scatter_default">
130 <param name="sylim" type="hidden" value="" /> 128 <param name="sylim" type="hidden" value="" />