diff prepare_population_structure.xml @ 24:248b06e86022

Added gd_genotype datatype. Modified tools to support new datatype.

--- a/prepare_population_structure.xml	Wed May 22 15:58:18 2013 -0400
+++ b/prepare_population_structure.xml	Tue May 28 16:24:19 2013 -0400
@@ -1,8 +1,14 @@
-<tool id="gd_prepare_population_structure" name="Prepare Input" version="1.0.0">
+<tool id="gd_prepare_population_structure" name="Prepare Input" version="1.1.0">
   <description>: Filter and convert to the format needed for these tools</description>
 
   <command interpreter="python">
-    prepare_population_structure.py "$input" "$min_reads" "$min_qual" "$min_spacing" "$output" "$output.files_path"
+    prepare_population_structure.py "$input"
+    #if $input_type.choice == '0'
+      "gd_snp" "$input_type.min_reads" "$input_type.min_qual"
+    #else if $input_type.choice == '1'
+      "gd_genotype" "0" "0"
+    #end if
+    "$min_spacing" "$output" "$output.files_path"
     #if $individuals.choice == '0'
         "all_individuals"
     #else if $individuals.choice == '1'
@@ -18,7 +24,21 @@
   </command>
 
   <inputs>
-    <param name="input" type="data" format="gd_snp" label="SNP dataset" />
+    <conditional name="input_type">
+      <param name="choice" type="select" format="integer" label="Input format">
+        <option value="0" selected="true">gd_snp</option>
+        <option value="1">gd_genotype</option>
+      </param>
+      <when value="0">
+        <param name="input" type="data" format="gd_snp" label="SNP dataset" />
+        <param name="min_reads" type="integer" min="0" value="0" label="Minimum SNP coverage" />
+        <param name="min_qual" type="integer" min="0" value="0" label="Minimum SNP quality" />
+      </when>
+      <when value="1">
+        <param name="input" type="data" format="gd_genotype" label="Genotype dataset" />
+      </when>
+    </conditional>
+
     <conditional name="individuals">
       <param name="choice" type="select" label="Individuals">
         <option value="0" selected="true">All individuals</option>
@@ -31,8 +51,7 @@
         </repeat>
       </when>
     </conditional>
-    <param name="min_reads" type="integer" min="0" value="0" label="Minimum SNP coverage" />
-    <param name="min_qual" type="integer" min="0" value="0" label="Minimum SNP quality" />
+
     <param name="min_spacing" type="integer" min="0" value="0" label="Minimum spacing between SNPs" />
   </inputs>
 
@@ -62,10 +81,11 @@
 
 **Dataset formats**
 
-The input datasets are in gd_snp_ and gd_indivs_ formats.
+The input datasets are in gd_snp_, gd_genotype_, and gd_indivs_ formats.
 The output dataset is in gd_ped_ format.  (`Dataset missing?`_)
 
 .. _gd_snp: ./static/formatHelp.html#gd_snp
+.. _gd_genotype: ./static/formatHelp.html#gd_genotype
 .. _gd_indivs: ./static/formatHelp.html#gd_indivs
 .. _gd_ped: ./static/formatHelp.html#gd_ped
 .. _Dataset missing?: ./static/formatHelp.html