Mercurial > repos > iuc > gemini
diff gemini_annotate.xml @ 0:720cbfb4190d draft
Imported from capsule None
author | iuc |
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date | Mon, 25 Aug 2014 17:15:54 -0400 |
parents | |
children | 93bb0cfacefb |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gemini_annotate.xml Mon Aug 25 17:15:54 2014 -0400 @@ -0,0 +1,96 @@ +<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> + <description>adding your own custom annotations</description> + <expand macro="requirements" /> + <expand macro="version_command" /> + <macros> + <import>gemini_macros.xml</import> + <token name="@BINARY@">annotate</token> + </macros> + <command> +<![CDATA[ + +bgzip -c $annotate_source > tabixed.gz; +tabix -p bed tabixed.gz; + + gemini @BINARY@ + -f tabixed.gz + -c $column_name + -a $a.a_selector + #if $a.a_selector == 'extract': + -t $a.column_type + -e $a.column_extracts + -o $a.operation + #end if + + "${ infile }" + > "${ outfile }" +]]> + + </command> + <expand macro="stdio" /> + <inputs> + <param name="infile" type="data" format="sqlite" label="GEMINI database" /> + <param name="annotate_source" type="data" format="bed" label="File containing the annotations in BED format" help="(-f)"/> + + <param name="column_name" size="20" type="text" value="" + label="The name of the column to be added to the variant table" help="(-c)"> + <sanitizer invalid_char=" "> + <valid initial="string.letters,string.digits"> + <add value="_" /> + </valid> + </sanitizer> + </param> + <conditional name="a"> + <param name="a_selector" type="select" label="How should the annotation file be used?" help="(-a)"> + <option value="boolean">Did a variant overlap a region or not? (boolean)</option> + <option value="count">How many regions did a variant overlap? (count)</option> + <option value="extract" selected="True">Extract specific values from a BED file. (extract)</option> + </param> + <when value="extract"> + + <param name="column_extracts" label="Column to extract information from for list annotations" + type="data_column" data_ref="annotate_source" force_select="true" help="(-e)"/> + + + <param name="column_type" type="select" label="What data type(s) should be used to represent the new values in the database?" + help="(-t)"> + <option value="float">Decimal precision number (float)</option> + <option value="integer">Integer number (integer)</option> + <option value="text">Text columns such as “valid”, “yes” (text)</option> + </param> + + <param name="operation" type="select" label="Operation to apply to the extract column values ..." + help="in the event that a variant overlaps multiple annotations in your annotation file. (-o)"> + <option value="mean">Compute the average of the (numeric) values</option> + <option value="median">Compute the median of the (numeric) values</option> + <option value="mix">Compute the minimum of the (numeric) values</option> + <option value="max">Compute the maximum of the (numeric) values</option> + <option value="mode">Compute the maximum of the (numeric) values</option> + <option value="first">Use the value from the first record in the annotation file</option> + <option value="last">Use the value from the last record in the annotation file</option> + <option value="list">Create a comma-separated list of the observed (text) values</option> + <option value="uniq_list">Create a comma-separated list of non-redundant observed (text) values</option> + </param> + + </when> + <when value="boolean"/> + <when value="count"/> + </conditional> + + </inputs> + <outputs> + <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" /> + </outputs> + <tests> + <test> + </test> + </tests> + <help> +**What it does** + +It is inevitable that researchers will want to enhance the gemini framework with their own, custom annotations. gemini provides a sub-command called annotate for exactly this purpose. + +@CITATION@ + </help> + <expand macro="citations"/> +</tool>