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comparison cloudmap.xml @ 8:d79fe626c6fd

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upgrade to v0.1.7.1
author Wolfgang Maier
date Thu, 22 Oct 2015 15:34:23 +0200
parents 3619e85a5477
children 93db2f9bca12
comparison
equal deleted inserted replaced
7:3619e85a5477 8:d79fe626c6fd
1 <tool id="nacreousmap" name="NacreousMap" version="0.1.7.0"> 1 <tool id="nacreousmap" name="NacreousMap" version="0.1.7.1">
2 <description>Map causative mutations by multi-variant linkage analysis.</description> 2 <description>Map causative mutations by multi-variant linkage analysis.</description>
3 <expand macro="requirements"/> 3 <expand macro="requirements"/>
4 <version_command>mimodd version -q</version_command> 4 <version_command>mimodd version -q</version_command>
5 <command> 5 <command>
6 mimodd map ${opt.mode} "${opt.source.ifile}" 6 mimodd map ${opt.mode} "${opt.source.ifile}"
103 <param name="sylim" type="text" label="upper limit for the scatter plot y-axis (default: 1)" /> 103 <param name="sylim" type="text" label="upper limit for the scatter plot y-axis (default: 1)" />
104 <param name="xlim" type="select" label="x-axis scaling"> 104 <param name="xlim" type="select" label="x-axis scaling">
105 <option value="">preserve relative contig sizes</option> 105 <option value="">preserve relative contig sizes</option>
106 <option value="--fit-width">scale each contig to fit the plot width</option> 106 <option value="--fit-width">scale each contig to fit the plot width</option>
107 </param> 107 </param>
108 <param name="span" type="text" label="span value to be used in calculating the Loess regression line through the scatter data (default=0.1)" help="smaller values give a more responsive curve that often picks up local evidence for tight linkage better, but too small values lead to plotting failures (in that case just rerun the tool with a larger value)." /> 108 <param name="span" type="text" label="span value to be used in calculating the Loess regression line through the scatter data (default=0.1, specify 0 to prevent calculation)" help="smaller values give a more responsive curve that often picks up local evidence for tight linkage better, but too small values lead to plotting failures (in that case just rerun the tool with a larger value)." />
109 <expand macro="scatter_colors" /> 109 <expand macro="scatter_colors" />
110 </when> 110 </when>
111 <when value="-p"> 111 <when value="-p">
112 <expand macro="plot_all" /> 112 <expand macro="plot_all" />
113 </when> 113 </when>
154 <param name="sylim" type="text" label="upper limit for the scatter plot y-axis (default: 1)" /> 154 <param name="sylim" type="text" label="upper limit for the scatter plot y-axis (default: 1)" />
155 <param name="xlim" type="select" label="x-axis scaling"> 155 <param name="xlim" type="select" label="x-axis scaling">
156 <option value="">preserve relative contig sizes</option> 156 <option value="">preserve relative contig sizes</option>
157 <option value="--fit-width">scale each contig to fit the plot width</option> 157 <option value="--fit-width">scale each contig to fit the plot width</option>
158 </param> 158 </param>
159 <param name="span" type="text" label="span value to be used in calculating the Loess regression line through the scatter data (default=0.1)" help="smaller values give a more responsive curve that often picks up local evidence for tight linkage better, but too small values lead to plotting failures (in that case just rerun the tool with a larger value)." /> 159 <param name="span" type="text" label="span value to be used in calculating the Loess regression line through the scatter data (default=0.1, specify 0 to prevent calculation)" help="smaller values give a more responsive curve that often picks up local evidence for tight linkage better, but too small values lead to plotting failures (in that case just rerun the tool with a larger value)." />
160 <expand macro="hist_colors" /> 160 <expand macro="hist_colors" />
161 <expand macro="scatter_colors" /> 161 <expand macro="scatter_colors" />
162 </macro> 162 </macro>
163 <macro name="seqdict_param"> 163 <macro name="seqdict_param">
164 <conditional name="seqdict_required"> 164 <conditional name="seqdict_required">
211 <param name="ifile" type="data" format="vcf" label="input file with variants to analyze" /> 211 <param name="ifile" type="data" format="vcf" label="input file with variants to analyze" />
212 <expand macro="seqdict_param" /> 212 <expand macro="seqdict_param" />
213 <param name="sample" type="text" label="mapping sample name" help="the sample to perform mutation mapping for" /> 213 <param name="sample" type="text" label="mapping sample name" help="the sample to perform mutation mapping for" />
214 <param name="related_parent_sample" type="text" label="name of the related parent sample" help="the sample that provides variants present in your original mutant strain or in an ancestor (like the pre-mutagenesis strain); leave blank if not available" /> 214 <param name="related_parent_sample" type="text" label="name of the related parent sample" help="the sample that provides variants present in your original mutant strain or in an ancestor (like the pre-mutagenesis strain); leave blank if not available" />
215 <param name="unrelated_parent_sample" type="text" label="name of the unrelated parent sample" help="the sample that provides variants present in the unrelated mapping strain (or in an ancestor of it) used in the mapping cross; leave blank if not available" /> 215 <param name="unrelated_parent_sample" type="text" label="name of the unrelated parent sample" help="the sample that provides variants present in the unrelated mapping strain (or in an ancestor of it) used in the mapping cross; leave blank if not available" />
216 <param name="infer_missing" type="boolean" checked="false" truevalue="--infer-missing" falsevalue="" label="Infer alleles for missing parent" help="if variant data for either the related or the unrelated parent strain is not available, the tool can try to infer the alleles present in that parent from the allele spectrum found in the mapping sample. This is an EXPERIMENTAL option that will give a benefit only in certain situations. Enable at your own risk." /> 216 <param name="infer_missing" type="boolean" checked="false" truevalue="--infer-missing" falsevalue="" label="Infer alleles for missing parent" help="if variant data for either the related or the unrelated parent strain is not available, the tool can try to infer the alleles present in that parent from the allele spectrum found in the mapping sample. Use with caution on carefully filtered variant lists only!" />
217 <expand macro="vaf_unconditional" /> 217 <expand macro="vaf_unconditional" />
218 <param name="tabfile" type="select" label="additional per-variant output file" help="You can either choose to produce a tabular per-variant report, which is useful for fast replotting with different plot settings or a vcf-like CloudMap-compatibility file that can be used as input for the CloudMap Hawaiian Variant Mapping tool as an alternative plotting tool."> 218 <param name="tabfile" type="select" label="additional per-variant output file" help="You can either choose to produce a tabular per-variant report, which is useful for fast replotting with different plot settings or a vcf-like CloudMap-compatibility file that can be used as input for the CloudMap Hawaiian Variant Mapping tool as an alternative plotting tool.">
219 <option value="">Do not generate per-variant output</option> 219 <option value="">Do not generate per-variant output</option>
220 <option value="-t">Tabular per-variant report</option> 220 <option value="-t">Tabular per-variant report</option>
221 <option value="--cloudmap -t">CloudMap compatibility file</option> 221 <option value="--cloudmap -t">CloudMap compatibility file</option>