--- a/gemini_roh.xml	Fri Oct 16 13:55:09 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,106 +0,0 @@
-<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
-    <description>Identifying runs of homozygosity</description>
-    <macros>
-        <import>gemini_macros.xml</import>
-        <token name="@BINARY@">roh</token>
-    </macros>
-    <expand macro="requirements" />
-    <expand macro="stdio" />
-    <expand macro="version_command" />
-    <command>
-<![CDATA[
-        gemini @BINARY@
-            --min-snps $min_snps
-            --min-total-depth $min_total_depth
-            --min-gt-depth $min_gt_depth
-            --min-size $min_size
-            --max-hets $max_hets
-            --max-unknowns $max_unknowns
-            #if $samples.strip() != '':
-                -s "${samples}"
-            #end if
-            "${ infile }"
-            > "${ outfile }"
-]]>
-    </command>
-    <inputs>
-        <expand macro="infile" />
-
-        <param name="min_snps" type="integer" value="25" label="Minimum number of expected homozygous SNPs" help="default: 25 (--min-snps)">
-            <validator type="in_range" min="0"/>
-        </param>
-        <param name="min_total_depth" type="integer" value="20" label="The minimum overall sequencing depth requiredfor a SNP to be considered" help="default: 20 (--min-total-depth)">
-            <validator type="in_range" min="0"/>
-        </param>
-        <param name="min_gt_depth" type="integer" value="0" label="The minimum required sequencing depth underlying a given sample's genotype for a SNP to be considered"
-            help="default: 0 (--min-gt-depth)">
-            <validator type="in_range" min="0"/>
-        </param>
-        <param name="min_size" type="integer" value="100000" label="Minimum run size in base pairs" help="default: 100000 (--min-size)">
-            <validator type="in_range" min="1"/>
-        </param>
-        <param name="max_hets" type="integer" value="1" label="Maximum number of allowed hets in the run" help="default: 1 (--max-hets)">
-            <validator type="in_range" min="1"/>
-        </param>
-        <param name="max_unknowns" type="integer" value="3" label="Maximum number of allowed unknowns in the run" help="default: 3 (-max-unknowns)">
-            <validator type="in_range" min="0"/>
-        </param>
-
-        <param name="samples" type="text" value="" label="Comma separated list of samples to screen for ROHs" help="e.g S120,S450 (-s)"/>
-
-    </inputs>
-
-    <outputs>
-        <data name="outfile" format="tabular" />
-    </outputs>
-    <tests>
-        <test>
-        </test>
-    </tests>
-    <help>
-
-**What it does**
-
-===========================================================================
-``ROH``: Identifying runs of homozygosity
-===========================================================================
-Runs of homozygosity are long stretches of homozygous genotypes that reflect
-segments shared identically by descent and are a result of consanguinity or
-natural selection. Consanguinity elevates the occurrence of rare recessive
-diseases (e.g. cystic fibrosis) that represent homozygotes for strongly deleterious
-mutations. Hence, the identification of these runs holds medical value.
-
-The 'roh' tool in GEMINI returns runs of homozygosity identified in whole genome data.
-The tool basically looks at every homozygous position on the chromosome as a possible
-start site for the run and looks for those that could give rise to a potentially long
-stretch of homozygous genotypes.
-
-For e.g. for the given example allowing ``1 HET`` genotype (h) and ``2 UKW`` genotypes (u)
-the possible roh runs (H) would be:
-
-
-::
-
-	genotype_run = H H H H h H H H H u H H H H H u H H H H H H H h H H H H H h H H H H H
-	roh_run1     = H H H H h H H H H u H H H H H u H H H H H H H
-	roh_run2     =           H H H H u H H H H H u H H H H H H H h H H H H H
-	roh_run3     =                     H H H H H u H H H H H H H h H H H H H
-	roh_run4     =                                 H H H H H H H h H H H H H
-
-roh returned for --min-snps = 20 would be:
-
-::
-
-	roh_run1     = H H H H h H H H H u H H H H H u H H H H H H H
-	roh_run2     =           H H H H u H H H H H u H H H H H H H h H H H H H
-
-
-As you can see, the immediate homozygous position right of a break (h or u) would be the possible
-start of a new roh run and genotypes to the left of a break are pruned since they cannot
-be part of a longer run than we have seen before.
-
-
-@CITATION@
-    </help>
-    <expand macro="citations"/>
-</tool>