comparison annotate_variants.xml @ 23:5db0545b9004 draft

update to v0.1.7.3

22:24154c580718

<tool id="annotate_variants" name="Variant Annotation" version="0.1.7.2">
  <description>Predict the effects of SNPs and indels on known genes in the reference genome using SnpEff</description>
  <macros>
    <import>toolshed_macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <version_command>python3 -m MiModD version -q</version_command>
  <command>
  	python3 -m MiModD annotate
	
	"$inputfile"

	#end if
	--verbose
  </command>

  <inputs>
    <param name="inputfile" type="data" format="vcf" label="vcf inputfile to be annotated" />
    <param name="grouping" type="select" label="Group variants by">
      <option value="">order in the input file</option>
      <option value="by_sample">sample</option>
      <option value="by_genes">most affected genes</option>
    </param>
    <conditional name="formatting">
      <param name="oformat" type="select" label="Format of the annotation output file">
	<option value="html">HTML</option>
	<option value="text">Tab-separated plain text</option>
      </param>
      <when value="html">
	<param name="formatter_file" type="data" format="txt" optional="true" label="Optional file with hyperlink formatting instructions" />
	<param name="species" type="text" label="Species" help="Overwrite the species guess from the SnpEff genome, often not necessary" />
      </when>
    </conditional>
    <conditional name="annotool">
      <param name="name" type="select" label="Use this tool to annotate the input file" help = "Select SnpEff here, if you want to have the vcf input annotated with genomic feature information. Select None if you do not want additional annotation, if you do not have SnpEff installed, or if you have no appropriate SnpEff annotation file for the input.">
	<option value="snpeff">SnpEff</option>
	<option value="None">None</option>
      </param>   
      <when value="snpeff">
          <param name="genome_list" type="data" format="tabular" label="genome list" /> 
          <param name="genomeVersion" type="select" label="Genome">
      	    <options from_dataset="genome_list">
              <column name="name" index="0"/>
              <column name="value" index="1"/>
            </options>
          </param>
          <param name="ori_output" type="boolean" checked="true" label="Keep the original SnpEff output" />
          <param name="stats" type="boolean" checked="true" label="Produce a summary file of results" />
          
	  <conditional name="snpeff_settings">
            <param name="detail_level" type="select" label="SnpEff-specific parameter settings" help="This section lets you specify the detailed parameter settings for the SnpEff tool.">
              <option value="default">default settings</option>
	      <option value="change">change settings</option>
            </param>   
            <when value="default">
	      ## default settings for SnpEff
	      <param name="chr" type="hidden" value=""/>
    	      <param name="min_cov" type="hidden" value=""/>
    	      <param name="min_qual" type="hidden" value=""/>
	      <param name="no_ds" type="hidden" value=""/>
    	      <param name="no_us" type="hidden" value=""/>
	      <param name="no_intron" type="hidden" value=""/>  
	      <param name="no_intergenic" type="hidden" value=""/>
	      <param name="no_utr" type="hidden" value=""/>
	      <param name="ud" type="hidden" value=""/>
            </when>
            <when value="change">
              <param name="chr" type="boolean" truevalue="-chr" falsevalue="" checked="false" label="prepend 'chr' to chromosome names, e.g., 'chr7' instead of '7'" />
              <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"/>
              <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"/>
              <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"/>
              <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"/>
              <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"/>
              <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"/>    
              <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"/>
              <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"/>
            </when>
	  </conditional>
      </when>
    </conditional>    
  </inputs>

  <outputs>
    <data name="outputfile" format="html" >
      <change_format>
	<when input="formatting.oformat" value="text" format="tabular"/>
      </change_format>
    </data>
    <data name="snpeff_file" format="vcf" >
      <filter>(annotool['name']=="snpeff" and annotool['ori_output'])</filter>
    </data>
    <data name="summary_file" format="html">
      <filter>(annotool['name']=="snpeff" and annotool['stats'])</filter>
    </data>
  </outputs>

  <help>

   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.
   
.. _tell us about the problem: mailto:[e-mail]
  </help>
</tool>
	

23:5db0545b9004

<tool id="annotate_variants" name="Variant Annotation" version="0.1.7.3">
  <description>Predict the effects of SNPs and indels on known genes in the reference genome using SnpEff</description>
  <macros>
    <import>toolshed_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <version_command>python3 -m MiModD version -q</version_command>
  <command>
  	python3 -m MiModD annotate
	
	"$inputfile"

	#end if
	--verbose
  </command>

  <inputs>
    <param format="vcf" label="vcf inputfile to be annotated" name="inputfile" type="data" />
    <param label="Group variants by" name="grouping" type="select">
      <option value="">order in the input file</option>
      <option value="by_sample">sample</option>
      <option value="by_genes">most affected genes</option>
    </param>
    <conditional name="formatting">
      <param label="Format of the annotation output file" name="oformat" type="select">
	<option value="html">HTML</option>
	<option value="text">Tab-separated plain text</option>
      </param>
      <when value="html">
	<param format="txt" label="Optional file with hyperlink formatting instructions" name="formatter_file" optional="true" type="data" />
	<param help="Overwrite the species guess from the SnpEff genome, often not necessary" label="Species" name="species" type="text" />
      </when>
    </conditional>
    <conditional name="annotool">
      <param help="Select SnpEff here, if you want to have the vcf input annotated with genomic feature information. Select None if you do not want additional annotation, if you do not have SnpEff installed, or if you have no appropriate SnpEff annotation file for the input." label="Use this tool to annotate the input file" name="name" type="select">
	<option value="snpeff">SnpEff</option>
	<option value="None">None</option>
      </param>   
      <when value="snpeff">
          <param format="tabular" label="genome list" name="genome_list" type="data" /> 
          <param label="Genome" name="genomeVersion" type="select">
      	    <options from_dataset="genome_list">
              <column index="0" name="name" />
              <column index="1" name="value" />
            </options>
          </param>
          <param checked="true" label="Keep the original SnpEff output" name="ori_output" type="boolean" />
          <param checked="true" label="Produce a summary file of results" name="stats" type="boolean" />
          
	  <conditional name="snpeff_settings">
            <param help="This section lets you specify the detailed parameter settings for the SnpEff tool." label="SnpEff-specific parameter settings" name="detail_level" type="select">
              <option value="default">default settings</option>
	      <option value="change">change settings</option>
            </param>   
            <when value="default">
	      ## default settings for SnpEff
	      <param name="chr" type="hidden" value="" />
    	      <param name="min_cov" type="hidden" value="" />
    	      <param name="min_qual" type="hidden" value="" />
	      <param name="no_ds" type="hidden" value="" />
    	      <param name="no_us" type="hidden" value="" />
	      <param name="no_intron" type="hidden" value="" />  
	      <param name="no_intergenic" type="hidden" value="" />
	      <param name="no_utr" type="hidden" value="" />
	      <param name="ud" type="hidden" value="" />
            </when>
            <when value="change">
              <param checked="false" falsevalue="" label="prepend 'chr' to chromosome names, e.g., 'chr7' instead of '7'" name="chr" truevalue="-chr" type="boolean" />
              <param help="do not include variants with a coverage lower than this value" label="minimum coverage (default = not used)" name="min_cov" optional="true" type="integer" />
              <param help="do not include variants with a quality lower than this value" label="minimum quality (default = not used)" name="min_qual" optional="true" type="integer" />
              <param checked="false" falsevalue="" help="annotation of effects on the downstream region of genes can be suppressed" label="do not show downstream changes" name="no_ds" truevalue="--no-downstream" type="boolean" />
              <param checked="false" falsevalue="" help="annotation of effects on the upstream region of genes can be suppressed" label="do not show upstream changes" name="no_us" truevalue="--no-upstream" type="boolean" />
              <param checked="false" falsevalue="" help="annotation of effects on introns of genes can be suppressed" label="do not show intron changes" name="no_intron" truevalue="--no-intron" type="boolean" />
              <param checked="false" falsevalue="" help="annotation of effects on intergenic regions can be suppressed" label="do not show intergenic changes" name="no_intergenic" truevalue="--no-intergenic" type="boolean" />    
              <param checked="false" falsevalue="" help="annotation of effects on the untranslated regions of genes can be suppressed" label="do not show UTR changes" name="no_utr" truevalue="--no-utr" type="boolean" />
              <param help="specify the upstream/downstream interval length, i.e., variants more than INTERVAL nts from the next annotated gene are considered to be intergenic" label="upstream downstream interval length (default = 5000 bases)" name="ud" optional="true" type="integer" />
            </when>
	  </conditional>
      </when>
    </conditional>    
  </inputs>

  <outputs>
    <data format="html" name="outputfile">
      <change_format>
	<when format="tabular" input="formatting.oformat" value="text" />
      </change_format>
    </data>
    <data format="vcf" name="snpeff_file">
      <filter>(annotool['name']=="snpeff" and annotool['ori_output'])</filter>
    </data>
    <data format="html" name="summary_file">
      <filter>(annotool['name']=="snpeff" and annotool['stats'])</filter>
    </data>
  </outputs>

  <help>

   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.
   
.. _tell us about the problem: mailto:[e-mail]
  </help>
</tool>