# HG changeset patch
# User iuc
# Date 1723653824 0
# Node ID bf06b66ab5c2ed91617dcb56a9b995b52e9d8ca2
# Parent  1001172b50896120c5d1fc505f9bb7a44190363c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 868f4386992de55d25da197660a43a913a09c8df

diff -r 1001172b5089 -r bf06b66ab5c2 bcftools_call.xml
--- a/bcftools_call.xml	Tue Jul 16 17:07:11 2024 +0000
+++ b/bcftools_call.xml	Wed Aug 14 16:43:44 2024 +0000
@@ -1,5 +1,5 @@
 <?xml version='1.0' encoding='utf-8'?>
-<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy4" profile="@PROFILE@">
     <description>SNP/indel variant calling from VCF/BCF</description>
     <macros>
         <token name="@EXECUTABLE@">call</token>
@@ -135,14 +135,19 @@
                             <option value="trio">trio - call genotypes given the father-mother-child constraint</option>
                         </param>
                         <when value="none">
-                            <expand macro="macro_restrict" type="target" label_type="Target" />
+                            <expand macro="macro_restrict" type="target" label_type="Target">
+                                <expand macro="macro_invert_targets"/>
+                            </expand>
                         </when>
                         <when value="alleles">
                             <expand macro="macro_restrictions_file" type="target" label_type="Target" />
+                            <expand macro="macro_invert_targets"/>
                             <param argument="--insert-missed" type="boolean" truevalue="--insert-missed" falsevalue="" label="Insert missed" help="Output also sites missed by mpileup but present in -T" />
                         </when>
                         <when value="trio">
-                            <expand macro="macro_restrict" type="target" label_type="Target" />
+                            <expand macro="macro_restrict" type="target" label_type="Target">
+                                <expand macro="macro_invert_targets"/>
+                            </expand>
                             <expand macro="macro_novel_rate" />
                         </when>
                     </conditional>
@@ -171,7 +176,9 @@
                             <expand macro="macro_novel_rate" />
                         </when>
                     </conditional>
-                    <expand macro="macro_restrict" type="target" label_type="Target" />
+                    <expand macro="macro_restrict" type="target" label_type="Target">
+                        <expand macro="macro_invert_targets" type="target" label_type="Target" />
+                    </expand>
                     <param argument="--pval-threshold" type="float" value="0.5" optional="true" label="Pval Threshold" help="Accept variant if P(ref|D)&lt;FLOAT" />
                 </when>
             </conditional>
@@ -312,6 +319,28 @@
                 </assert_contents>
             </output>
         </test>
+        <test>
+            <!-- Test targets-file option-->
+            <param name="input_file" ftype="vcf" value="mpileup.AD.vcf" />
+            <param name="method" value="multiallelic" />
+            <param name="output_type" value="v" />
+            <section name="sec_consensus_variant_calling">
+                <conditional name="variant_calling">
+                    <conditional name="genotypes">
+                        <conditional name="targets">
+                            <param name="targets_src" value="targets_file"/>
+                            <param name="targets_file" value="targets_file.tab"/>
+                        </conditional>
+                    </conditional>
+                </conditional>
+            </section>
+            <output name="output_file">
+                <assert_contents>
+                    <has_text text="--targets-file" />
+                    <not_has_text text="DP=1;ADF=1;ADR=0;DPR=1;MQ0F=0;AN=2;DP4=1,0,0,0;MQ=37" />
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help><![CDATA[
 ==================================
diff -r 1001172b5089 -r bf06b66ab5c2 test-data/targets_file.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/targets_file.tab	Wed Aug 14 16:43:44 2024 +0000
@@ -0,0 +1,1 @@
+1	1	1000