Mercurial > repos > wolma > mimodd_annotate_variants
comparison annotate_variants.xml @ 1:840362af3e74 draft
version 0_1_5
| author | wolma |
|---|---|
| date | Tue, 09 Dec 2014 16:24:44 -0500 |
| parents | 995e258cc46c |
| children |
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| 0:995e258cc46c | 1:840362af3e74 |
|---|---|
| 1 <tool id="annotate_variants" name="Variant Annotation"> | 1 <tool id="annotate_variants" name="Variant Annotation"> |
| 2 <description>Predict the effects of SNPs and indels on known genes in the reference genome using SnpEff</description> | 2 <description>Predict the effects of SNPs and indels on known genes in the reference genome using SnpEff</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="0.1.3">mimodd</requirement> | 4 <requirement type="package" version="0.1.5">mimodd</requirement> |
| 5 </requirements> | 5 </requirements> |
| 6 <version_command>mimodd version -q</version_command> | |
| 6 <command> | 7 <command> |
| 7 mimodd annotate | 8 mimodd annotate |
| 8 | 9 |
| 9 $inputfile | 10 $inputfile |
| 10 | 11 |
| 11 #if $str($annotool.name)=='snpeff': | 12 #if $str($annotool.name)=='snpeff': |
| 12 --genome ${annotool.genomeVersion} | 13 --genome "${annotool.genomeVersion}" |
| 13 #if $annotool.ori_output: | 14 #if $annotool.ori_output: |
| 14 --snpeff_out $snpeff_file | 15 --snpeff-out $snpeff_file |
| 15 #end if | 16 #end if |
| 16 #if $annotool.stats: | 17 #if $annotool.stats: |
| 17 --stats $summary_file | 18 --stats $summary_file |
| 18 #end if | 19 #end if |
| 19 ${annotool.snpeff_settings.chr} ${annotool.snpeff_settings.no_us} ${annotool.snpeff_settings.no_ds} ${annotool.snpeff_settings.no_intron} ${annotool.snpeff_settings.no_intergenic} ${annotool.snpeff_settings.no_utr} | 20 ${annotool.snpeff_settings.chr} ${annotool.snpeff_settings.no_us} ${annotool.snpeff_settings.no_ds} ${annotool.snpeff_settings.no_intron} ${annotool.snpeff_settings.no_intergenic} ${annotool.snpeff_settings.no_utr} |
| 35 #if $str($formatting.oformat) == "html": | 36 #if $str($formatting.oformat) == "html": |
| 36 #if $formatting.formatter_file: | 37 #if $formatting.formatter_file: |
| 37 --link ${formatting.formatter_file} | 38 --link ${formatting.formatter_file} |
| 38 #end if | 39 #end if |
| 39 #if $formatting.species | 40 #if $formatting.species |
| 40 --species ${formatting.species} | 41 --species "${formatting.species}" |
| 41 #end if | 42 #end if |
| 42 #end if | 43 #end if |
| 43 | 44 |
| 44 #if $str($grouping): | 45 #if $str($grouping): |
| 45 --grouping $grouping | 46 --grouping $grouping |
| 99 </when> | 100 </when> |
| 100 <when value="change"> | 101 <when value="change"> |
| 101 <param name="chr" type="boolean" truevalue="-chr" falsevalue="" checked="false" label="prepend 'chr' to chromosome names, e.g., 'chr7' instead of '7'" /> | 102 <param name="chr" type="boolean" truevalue="-chr" falsevalue="" checked="false" label="prepend 'chr' to chromosome names, e.g., 'chr7' instead of '7'" /> |
| 102 <param name="min_cov" type="integer" optional="true" label="minimum coverage (default = not used)" help="do not include variants with a coverage lower than this value"/> | 103 <param name="min_cov" type="integer" optional="true" label="minimum coverage (default = not used)" help="do not include variants with a coverage lower than this value"/> |
| 103 <param name="min_qual" type="integer" optional="true" label="minimum quality (default = not used)" help="do not include variants with a quality lower than this value"/> | 104 <param name="min_qual" type="integer" optional="true" label="minimum quality (default = not used)" help="do not include variants with a quality lower than this value"/> |
| 104 <param name="no_ds" type="boolean" label="do not show downstream changes" truevalue="--no_downstream" falsevalue="" checked="false" help="annotation of effects on the downstream region of genes can be suppressed"/> | 105 <param name="no_ds" type="boolean" label="do not show downstream changes" truevalue="--no-downstream" falsevalue="" checked="false" help="annotation of effects on the downstream region of genes can be suppressed"/> |
| 105 <param name="no_us" type="boolean" label="do not show upstream changes" truevalue="--no_upstream" falsevalue="" checked="false" help="annotation of effects on the upstream region of genes can be suppressed"/> | 106 <param name="no_us" type="boolean" label="do not show upstream changes" truevalue="--no-upstream" falsevalue="" checked="false" help="annotation of effects on the upstream region of genes can be suppressed"/> |
| 106 <param name="no_intron" type="boolean" label="do not show intron changes" truevalue="--no_intron" falsevalue="" checked="false" help="annotation of effects on introns of genes can be suppressed"/> | 107 <param name="no_intron" type="boolean" label="do not show intron changes" truevalue="--no-intron" falsevalue="" checked="false" help="annotation of effects on introns of genes can be suppressed"/> |
| 107 <param name="no_intergenic" type="boolean" label="do not show intergenic changes" truevalue="--no_intergenic" falsevalue="" checked="false" help="annotation of effects on intergenic regions can be suppressed"/> | 108 <param name="no_intergenic" type="boolean" label="do not show intergenic changes" truevalue="--no-intergenic" falsevalue="" checked="false" help="annotation of effects on intergenic regions can be suppressed"/> |
| 108 <param name="no_utr" type="boolean" label="do not show UTR changes" truevalue="--no_utr" falsevalue="" checked="false" help="annotation of effects on the untranslated regions of genes can be suppressed"/> | 109 <param name="no_utr" type="boolean" label="do not show UTR changes" truevalue="--no-utr" falsevalue="" checked="false" help="annotation of effects on the untranslated regions of genes can be suppressed"/> |
| 109 <param name="ud" type="integer" optional="true" label="upstream downstream interval length (default = 5000 bases)" help="specify the upstream/downstream interval length, i.e., variants more than INTERVAL nts from the next annotated gene are considered to be intergenic"/> | 110 <param name="ud" type="integer" optional="true" label="upstream downstream interval length (default = 5000 bases)" help="specify the upstream/downstream interval length, i.e., variants more than INTERVAL nts from the next annotated gene are considered to be intergenic"/> |
| 110 </when> | 111 </when> |
| 111 </conditional> | 112 </conditional> |
| 112 </when> | 113 </when> |
| 113 </conditional> | 114 </conditional> |
| 138 | 139 |
| 139 Use of this feature requires that you have an appropriate SnpEff genome file installed on the host machine. You can use the *List installed SnpEff genomes* tool to generate a list of all available SnpEff genomes. | 140 Use of this feature requires that you have an appropriate SnpEff genome file installed on the host machine. You can use the *List installed SnpEff genomes* tool to generate a list of all available SnpEff genomes. |
| 140 This list can then be used (by selecting the dataset as the *genome list*) to populate the *genome* dropdown menu, from which you can select the SnpEff genome file to be used for the annotation. | 141 This list can then be used (by selecting the dataset as the *genome list*) to populate the *genome* dropdown menu, from which you can select the SnpEff genome file to be used for the annotation. |
| 141 | 142 |
| 142 As output file formats HTML or plain text are supported. | 143 As output file formats HTML or plain text are supported. |
| 143 In HTML mode, variant positions and/or affected genomic features can be turned into hyperlinks to corresponding views in web-based genome browsers. | 144 In HTML mode, variant positions and/or affected genomic features can be turned into hyperlinks to corresponding views in web-based genome browsers and databases. |
| 144 | 145 |
| 145 The behavior of this feature depends on: | 146 The behavior of this feature depends on: |
| 146 | 147 |
| 147 1) Recognition of the species that is analyzed | 148 1) Recognition of the species that is analyzed |
| 148 | 149 |
| 157 If no matching entry is found in the file, an error will be raised. | 158 If no matching entry is found in the file, an error will be raised. |
| 158 | 159 |
| 159 If you did not supply a hyperlink formatting instruction file, the tool will consult an internal lookup table to see if it finds default rules for the construction of the hyperlinks for the species. | 160 If you did not supply a hyperlink formatting instruction file, the tool will consult an internal lookup table to see if it finds default rules for the construction of the hyperlinks for the species. |
| 160 If not, no hyperlinks will be generated and the html output will look essentially like plain text. | 161 If not, no hyperlinks will be generated and the html output will look essentially like plain text. |
| 161 | 162 |
| 163 **TIP:** | |
| 164 MiModD's internal hyperlink formatting lookup tables are maintained and growing with every new version, but since weblinks are changing frequently as well, it is possible that you will encounter broken hyperlinks for your species of interest. In such a case, you can resort to two things: `tell us about the problem`_ to make sure it gets fixed in the next release and, in the meantime, use a custom file with hyperlink formatting instructions to overwrite the default entry for your species. | |
| 165 | |
| 166 .. _tell us about the problem: mailto:mimodd@googlegroups.com | |
| 162 </help> | 167 </help> |
| 163 </tool> | 168 </tool> |
| 164 | 169 |