diff gemini_roh.xml @ 5:d65ca2fa673b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59

--- a/gemini_roh.xml	Fri Dec 14 13:04:54 2018 -0500
+++ b/gemini_roh.xml	Fri Jan 11 17:52:49 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1">
+<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@">
     <description>Identifying runs of homozygosity</description>
     <macros>
         <import>gemini_macros.xml</import>
@@ -17,39 +17,34 @@
             --max-hets $max_hets
             --max-unknowns $max_unknowns
             #if $samples.strip():
-                -s "${samples}"
+                #set $samples = ','.join([f.strip() for f in $samples.split(',')])
+                -s '$samples'
             #end if
-            "${ infile }"
-            > "${ outfile }"
+            '$infile'
+            > '$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)"/>
-
+        <param argument="--min-snps" name="min_snps" type="integer" value="25" min="0"
+        label="Minimum number of expected homozygous SNPs"
+        help="default: 25" />
+        <param argument="--min-total-depth" name="min_total_depth" type="integer" value="20" min="0"
+        label="The minimum overall sequencing depth required for a SNP to be considered"
+        help="default: 20" />
+        <param argument="--min-gt-depth" name="min_gt_depth" type="integer" value="0" min="0"
+        label="The minimum required sequencing depth underlying a given sample's genotype for a SNP to be considered"
+        help="default: 0" />
+        <param argument="--min-size" name="min_size" type="integer" value="100000" min="1"
+        label="Minimum run size in base pairs" help="default: 100000" />
+        <param argument="--max-hets" name="max_hets" type="integer" value="1" min="0"
+        label="Maximum number of allowed hets in the run" help="default: 1" />
+        <param argument="--max-unknowns" name="max_unknowns" type="integer" value="3" min="0"
+        label="Maximum number of allowed unknowns in the run"
+        help="default: 3" />
+        <param argument="-s" name="samples" type="text" value=""
+        label="Comma separated list of samples to screen for ROHs" help="e.g. S120,S450"/>
     </inputs>
-
     <outputs>
         <data name="outfile" format="tabular" />
     </outputs>
@@ -70,9 +65,6 @@
 
 **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