diff gemini_comp_hets.xml @ 0:d666cc4a37e7 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gemini_comp_hets.xml	Thu Feb 18 08:52:33 2016 -0500
@@ -0,0 +1,89 @@
+<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
+    <description>Identifying potential compound heterozygotes</description>
+    <macros>
+        <import>gemini_macros.xml</import>
+        <token name="@BINARY@">comp_hets</token>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version_command" />
+    <command>
+<![CDATA[
+        gemini @BINARY@
+
+            #if $report.report_selector != 'all':
+                --columns "${report.columns}"
+            #end if
+
+            @CMDLN_SQL_FILTER_FILTER_OPTION@
+
+            #if int($min_kindreds) > 0:
+                --min-kindreds $min_kindreds
+            #end if
+
+            #if str($families).strip():
+                --families "$families"
+            #end if
+
+            -d $d
+            $allow_unaffected
+
+            #if int($min_genotypequality) > 0:
+                --min-gq $min_genotypequality
+            #end if
+
+            #if int($gt_pl_max) != -1:
+                --gt_pl_max $gt_pl_max
+            #end if
+
+            $pattern_only
+            --max-priority $max_priority
+
+
+            "${ infile }"
+            > "${ outfile }"
+]]>
+    </command>
+    <inputs>
+        <expand macro="infile" />
+        <expand macro="column_filter" />
+        <expand macro="filter" />
+        <expand macro="min_kindreds" />
+        <expand macro="family" />
+        <expand macro="unaffected" />
+        <expand macro="min_sequence_depth" />
+        <param name="min_genotypequality" type="integer" value="0" min="0" label="The minimum genotype quality required for each sample in a family." help="default: 0 (--min-gq)" />
+        <param name="gt_pl_max" type="integer" value="-1" min="-1" label="The maximum phred-scaled genotype (PL) allowed for each sample in a family." help="default: -1 not set (--gt-pl-max)" />
+        <param name="pattern_only" type="boolean" truevalue="--pattern-only" falsevalue="" checked="False"
+            label="Find compound hets by inheritance pattern, without regard to affection" help="(--pattern-only)"/>
+        <param name="max_priority" type="integer" value="1" min="1" label="Default is to show only confident compound hets. Set to 2 or higher to include pairs that are less likely true comp-hets." help="default: 1 (--max-priority)" />
+    </inputs>
+    <outputs>
+        <data name="outfile" format="tabular" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" value="gemini_comphets_input.db" ftype="gemini.sqlite" />
+            <param name="report_selector" value="column_filter" />
+            <param name="columns" value="chrom,start,end,ref,alt,gene,impact" />
+            <param name="allow_unaffected" value="True" />
+            <param name="max_priority" value="3" />
+            <output name="outfile" file="gemini_comphets_result.tabular" />
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+Many recessive disorders are caused by compound heterozygotes. Unlike canonical recessive sites where the same recessive allele is
+inherited from both parents at the _same_ site in the gene, compound heterozygotes occur when the individual’s phenotype is caused
+by two heterozygous recessive alleles at _different_ sites in a particular gene.
+
+So basically, we are looking for two (typically loss-of-function (LoF)) heterozygous variants impacting the same gene at different loci.
+The complicating factor is that this is _recessive_ and as such, we must also require that the consequential alleles at each heterozygous
+site were inherited on different chromosomes (one from each parent). As such, in order to use this tool, we require that all variants are phased.
+Once this has been done, the comp_hets tool will provide a report of candidate compound heterozygotes for each sample/gene.
+
+
+    </help>
+    <expand macro="citations"/>
+</tool>