diff vcfhethom.xml @ 0:1de250ea8c1a draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfhethom commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vcfhethom.xml	Mon Nov 09 12:33:06 2015 -0500
@@ -0,0 +1,62 @@
+<tool id="vcfhethom" name="VCFhetHomAlleles:" version="0.0.3">
+  <description>Count the number of heterozygotes and alleles, compute het/hom ratio</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"></expand>
+  <expand macro="stdio" />
+  <command>
+
+   #if str($analysis_type) == "count":
+       vcfhetcount "${vcf_input}" > "${out_file1}"
+   #elif str($analysis_type) == "ratio": 
+       vcfhethomratio "${vcf_input}" > "${out_file1}"
+   #elif str($analysis_type) == "allele_count":
+       vcfcountalleles "${vcf_input}" > "${out_file1}" 
+   #end if
+
+</command>
+
+  <inputs>
+    <param name="analysis_type" type="select" display="radio" label="Select type of calculation:">
+      <option value="count">Compute the number of heterozygotes</option>
+      <option value="ratio">Compute the ratio between heterozygotes and homozygotes</option>
+      <option value="allele_count">Compute the total number of alleles</option>
+    </param>
+    <param format="vcf" name="vcf_input" type="data" label="In this VCF dataset"/>
+  </inputs>
+  <outputs>
+    <data format="tabular" name="out_file1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="analysis_type" value="count"/>
+      <param name="vcf_input" value="vcflib.vcf"/>
+      <output name="out_file1" file="vcfhethom-test1.tab"/>
+    </test>
+    <test>
+      <param name="analysis_type" value="ratio"/>
+      <param name="vcf_input" value="vcflib.vcf"/>
+      <output name="out_file1" file="vcfhethom-test2.tab"/>
+    </test>
+    <test>
+      <param name="analysis_type" value="allele_count"/>
+      <param name="vcf_input" value="vcflib.vcf"/>
+      <output name="out_file1" file="vcfhethom-test3.tab"/>
+    </test>
+  </tests>
+  <help>
+
+This tool performs three basic calculations: 
+
+(1) Computes the number of heterozygotes
+(2) Computes the ratio between heterozygotes and homozygotes
+(3) Computes the total number of alleles in the input dataset
+
+----
+
+This tools is based on vcfhetcount, vcfhethomratio,and vcfcountalleles utilities from the VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).                                                                                                                                 
+
+</help>
+  <expand macro="citations" />
+</tool>