Mercurial > repos > iuc > bcftools_view

changeset 13:98d5499ead46 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8f0dacb44516206751262495e6a6de22ae312572"
author iuc
date Tue, 13 Apr 2021 15:19:30 +0000
parents 23680a42e149
children 1d1762860d7e
files bcftools_view.xml
diffstat 1 files changed, 27 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/bcftools_view.xml	Fri Feb 05 19:46:48 2021 +0000
+++ b/bcftools_view.xml	Tue Apr 13 15:19:30 2021 +0000
@@ -38,7 +38,7 @@
 #if str($section.max_ac)
   --max-ac ${section.max_ac}
 #end if
-#if str($section.select_genotype) != "__none__":
+#if str($section.select_genotype) != "None":
   --genotype "${section.select_genotype}"
 #end if
 ## known or novel
@@ -121,13 +121,20 @@
                    help="(-c --min-ac) Minimum count for non-reference (nref), 1st alternate (alt1), least frequent (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles" />
             <param name="max_ac" type="integer" label="Max Ac" optional="True"
                    help="(-C --max-ac) Maximum count for non-reference (nref), 1st alternate (alt1), least frequent (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles" />
-            <param name="select_genotype" type="select">
-                <option value="__none__" selected="True">No selection</option>
-                <option value="require one or more hom/het/missing genotype or" />
-                <option value="if prefixed with &quot;^&quot;" />
-                <option value="exclude sites with hom/het/missing genotypes" />
+            <param name="select_genotype" type="select" label="Select Genotype" optional="True">
+                <help>
+                Include only sites with one or more homozygous (hom), heterozygous (het) or missing (miss) genotypes.
+                When prefixed with ^, the logic is reversed.
+                Please notice that if the input file doesn't have any genotype columns,
+                then this option is ignored altogether.
+                </help>
+                <option value="hom">hom</option>
+                <option value="het">het</option>
+                <option value="miss">miss</option>
+                <option value="^hom">^hom</option>
+                <option value="^het">^het</option>
+                <option value="^miss">^miss</option>
             </param>
-
             <param name="types" type="select" label="Select Types"  multiple="true" optional="True">
                 <help>
                  List of variant types to select. Site is selected if any of the ALT alleles is of the type requested.
@@ -345,6 +352,19 @@
                 </assert_contents>
             </output>
         </test>
+        <test>
+            <param name="input_file" ftype="vcf" value="view.vcf" />
+            <param name="phased" value="--phased" />
+            <param name="output_type" value="v" />
+            <param name="select_genotype" value="^het" />
+            <output name="output_file">
+                <assert_contents>
+                    <has_text text="--genotype ^het" />
+                    <has_text text="rs78249411" />
+                    <not_has_text text="3048719" />
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help><![CDATA[
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