# HG changeset patch
# User sanbi-uwc
# Date 1536744180 14400
# Node ID 50f56c93c1681c408cbe13fa6de91ca4ed33e923
# Parent  51f95fbef11205d302a133770cfad65212e82c57
planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/galaxy-tools/plink commit 5bc9005790b78aabb615f559f31ee71c714c7072

diff -r 51f95fbef112 -r 50f56c93c168 plink.xml
--- a/plink.xml	Mon Aug 27 09:35:06 2018 -0400
+++ b/plink.xml	Wed Sep 12 05:23:00 2018 -0400
@@ -1,4 +1,4 @@
-<?xml version="1.0"?> 
+<?xml version="1.0"?>
 <tool id="plink" name="PLINK" version="@TOOL_VERSION@+galaxy0">
   <description><![CDATA[
       PLINK is a free, open-source whole genome association analysis toolset, 
@@ -14,20 +14,27 @@
   </requirements>
         
   <command detect_errors="exit_code"><![CDATA[
-    for i in {1..${chr_num}}
+    ln -s '${input_bed_file}' input_file.bed &&
+    ln -s '${input_bim_file}' input_file.bim &&
+    ln -s '${input_fam_file}' input_file.fam &&
+    mkdir output &&
+    for i in {1..${chr_num}};
     do 
-      plink \
-      --noweb \
-      --bfile ${input_bed_file} \
-      --chr ${i} \
-      --make-bed \
-      --out ${input_bed_file}_chr${i};
-    done
+      plink 
+      --noweb 
+      --bfile input_file 
+      --chr \$i 
+      --make-bed 
+      --out output/input_file_chr\$i;
+    done;
+    
     ]]>                                                                                                                 
   </command>
         
   <inputs>
-    <param name="input_bed_file" type="data" format="bed" label="Select the bed file"/> 
+    <param name="input_bed_file" type="data" format="binary" label="Select the bed file"/> 
+    <param name="input_bim_file" type="data" format="bim" label="Select the bim file"/> 
+    <param name="input_fam_file" type="data" format="fam" label="Select the fam file"/> 
     <param name="chr_num" type="integer" value="22" label="Enter Chromosome Limit"/> 
     <!-- plink options -->
     <param name="noweb" argument="--noweb" type="boolean" truevalue="--noweb" falsevalue="" checked="false"                            
@@ -39,19 +46,24 @@
   </inputs>
         
   <outputs>
-    <data name="output_bed" format="bed" label="Bed Output file" />
-    <data name="output_bim" format="bim" label="Bim Output file" />
-    <data name="output_fam" format="fam" label="Fam Output file" />
-    <data name="output_log" format="log" label="Log Output file" />
-  </outputs>
+  	<collection type="list:list" label="Plink Chromosome(s) Collection List of List" name="output_plink_list_of_list">
+        <discover_datasets pattern="input_file_chr(?P&lt;identifier_0&gt;.+)\.(?P&lt;identifier_1&gt;.+)" directory="output"/>
+    </collection>
+   </outputs> 
         
   <tests>
     <test>
       <param name="input_bed_file" value="test.bed" />
-      <output name="output_bed" file="test_chr1.bed" lines_diff="4" />
-      <output name="output_bim" file="test_chr1.bim" lines_diff="4" />
-      <output name="output_fam" file="test_chr1.fam" lines_diff="4" />
-      <output name="output_log" file="test_chr1.log" lines_diff="4" />
+      <param name="input_bim_file" value="test.bim" />
+      <param name="input_fam_file" value="test.fam" />      
+      <output_collection name="pcoa" type="list:list">
+        <element name="1">  
+          <element name="bed" />
+          <element name="bim" />
+          <element name="fam" />
+          <element name="log" />                            
+        </element> 
+      </output_collection>                           
     </test>
   </tests>
   <help><![CDATA[
@@ -76,4 +88,4 @@
 'plink --help | more' describes all functions (warning: long)
 
   ]]></help>
-</tool>
\ No newline at end of file
+</tool>