# HG changeset patch
# User sanbi-uwc
# Date 1537274932 14400
# Node ID 1a00583b6b2c28831d52ea0e3cb604cc60d5571a
# Parent  201d098d6d67b42dbef0ce56ba26d87654008c36
planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 40d1319d78fae41b53fe3511db41ee5479c58db8-dirty

diff -r 201d098d6d67 -r 1a00583b6b2c shapeit_phase.xml
--- a/shapeit_phase.xml	Tue Sep 18 06:39:22 2018 -0400
+++ b/shapeit_phase.xml	Tue Sep 18 08:48:52 2018 -0400
@@ -1,6 +1,5 @@
-<tool id="shapeit_phase" name="shapeit_phase" version="0.14.0">
+<tool id="shapeit_phase" name="shapeit_phase" version="0.15.0">
     <description>genomic data with or without reference panel</description>
-
     <requirements>
         <requirement type="package" version="2.r837">shapeit</requirement>
     </requirements>
@@ -62,6 +61,10 @@
 
         shapeit
 
+        #if $check_mode != "":
+          -check
+        #end if
+
         #if $input_files.input_type_select == "vcf":
           --input-vcf ${input_files.vcf_file}
         #else if $input_files.input_type_select == "plink_ped_map":
@@ -172,12 +175,21 @@
             --seed $use_advanced_parameters.rng_seed
           #end if
         #end if
-        --output-max $out_haps $out_sample
-        --output-graph $out_graph
-        --output-log $out_log
+
+        #if $check_mode == "":
+          --output-max $out_haps $out_sample
+          --output-graph $out_graph
+          --output-log $out_log
+        #else
+          --output-log output
+          && mv output.mendel.log $out_log
+          && mv output.mendel.snp.strand $out_strand
+          && mv output.mendel.snp.strand.exclude $out_exclude
+        #end if
     ]]></command>
 
     <inputs>
+      <param name="check_mode" type="boolean" truevalue="-check" falsevalue="" label="Run in -check mode (check data)" />
       <conditional name="input_files">
         <param name="input_type_select" type="select" label="Please specify your input files.">
           <option value="vcf" selected="True">VCF Variant Call Format</option>
@@ -430,9 +442,21 @@
 
     </inputs>
     <outputs>
-      <data name="out_haps" format="tabular" label="${tool.name} on ${on_string} haplotypes (.haps)"/>
-      <data name="out_sample" format="tabular" label="${tool.name} on ${on_string} additional information (.sample)"/>
-      <data name="out_graph" format="txt" label="${tool.name} on ${on_string} haplotype graphs (.hgraph)"/>
+      <data name="out_haps" format="tabular" label="${tool.name} on ${on_string} haplotypes (.haps)">
+        <filter>not check_mode</filter>
+      </data>
+      <data name="out_sample" format="tabular" label="${tool.name} on ${on_string} additional information (.sample)">
+        <filter>not check_mode</filter>
+      </data>
+      <data name="out_graph" format="txt" label="${tool.name} on ${on_string} haplotype graphs (.hgraph)">
+        <filter>not check_mode</filter>
+      </data>
+      <data name="out_strand" format="tabular" label="${tool.name} on ${on_string} problematic SNP report (.strand)">
+        <filter>check_mode</filter>
+      </data>
+      <data name="out_exclude" format="txt" label="${tool.name} on ${on_string} problematic SNPs to exclude (.exclude)">
+        <filter>check_mode</filter>
+      </data>
       <data name="out_log" format="txt" label="${tool.name} on ${on_string} logfile (.log)"/>
     </outputs>
     <help><![CDATA[