diff bcftools_plugin_setgt.xml @ 25:a5669238dbcc draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc

--- a/bcftools_plugin_setgt.xml	Sun Aug 18 09:51:36 2024 +0000
+++ b/bcftools_plugin_setgt.xml	Tue Dec 02 07:44:36 2025 +0000
@@ -9,7 +9,6 @@
     <expand macro="requirements" />
     <expand macro="version_command" />
     <command detect_errors="aggressive"><![CDATA[
-@PREPARE_ENV@
 @PREPARE_INPUT_FILE@
 #set $section = $sec_restrict
 @PREPARE_TARGETS_FILE@
@@ -42,8 +41,8 @@
     <inputs>
         <expand macro="macro_input" />
         <section name="sec_restrict" title="Restrict to">
-            <expand macro="macro_restrict" />
-            <expand macro="macro_restrict" type="target" label_type="Target" />
+            <expand macro="macro_region_restrict" />
+            <expand macro="macro_target_restrict" />
             <expand macro="macro_include" />
             <expand macro="macro_exclude" />
         </section>
@@ -60,6 +59,7 @@
                 <option value=".">. missing (. or ./., keeps ploidy)</option>
                 <option value="0">0 reference allele (e.g. 0/0 or 0, keeps ploidy)</option>
                 <option value="c:GT">c:GT custom genotype (e.g. 0/0, 0, 0/1, m/M, overrides ploidy)</option>
+                <option value="c:./.">c:./. missing genotype with arbitrary ploidy</option>
                 <option value="M">M major allele</option>
                 <option value="m">m minor (the second most common) allele (e.g. 1/1 or 1, keeps ploidy)</option>
                 <option value="p">p phased genotype</option>
@@ -74,8 +74,10 @@
     <tests>
         <test>
             <param name="input_file" ftype="vcf" value="plugin1.vcf" />
-            <param name="target_gt" value="." />
-            <param name="new_gt" value="0" />
+            <section name="sec_plugin">
+                <param name="target_gt" value="." />
+                <param name="new_gt" value="0" />
+            </section>
             <param name="output_type" value="v" />
             <output name="output_file">
                 <assert_contents>
@@ -100,6 +102,20 @@
                 </assert_contents>
             </output>
         </test>
+        <test>
+            <param name="input_file" ftype="vcf" value="plugin1.vcf" />
+            <section name="sec_plugin">
+                <param name="target_gt" value="." />
+                <param name="new_gt" value="c:./." />
+            </section>
+            <param name="output_type" value="v" />
+            <output name="output_file">
+                <assert_contents>
+                    <has_text text="GT" />
+                    <has_text text="DP4=1,2,3,4;INDEL;STR=test" />
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help><![CDATA[
 =====================================