Mercurial > repos > iuc > bcftools_roh

diff bcftools_roh.xml @ 25:a85677f5a2ab draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
author iuc
date Tue, 02 Dec 2025 07:53:42 +0000
parents 39cac1b56d93
children
line wrap: on
line diff
--- a/bcftools_roh.xml	Sun Aug 18 09:57:18 2024 +0000
+++ b/bcftools_roh.xml	Tue Dec 02 07:53:42 2025 +0000
@@ -8,7 +8,6 @@
     <expand macro="requirements" />
     <expand macro="version_command" />
     <command detect_errors="aggressive"><![CDATA[
-@PREPARE_ENV@
 @PREPARE_INPUT_FILE@
 #set $section = $sec_restrict
 @PREPARE_TARGETS_FILE@
@@ -78,8 +77,8 @@
     <inputs>
         <expand macro="macro_input" />
         <section name="sec_restrict" expanded="false" 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_samples" />
         </section>
         <section name="sec_general" expanded="true" title="Roh General Options">
@@ -124,8 +123,10 @@
     <tests>
         <test>
             <param name="input_file" ftype="vcf" value="roh.vcf" />
-            <param name="AF_dflt" value="0.4" />
-            <param name="GTs_only" value="30" />
+            <section name="sec_general">
+                <param name="AF_dflt" value="0.4" />
+                <param name="GTs_only" value="30" />
+            </section>
             <output name="output_file">
                 <assert_contents>
                     <has_text_matching expression="ST\tsample\t1"/>
@@ -135,8 +136,10 @@
         </test>
         <test>
             <param name="input_file" ftype="vcf" value="roh.vcf" />
-            <param name="AF_dflt" value="0.4" />
-            <param name="GTs_only" value="30" />
+            <section name="sec_general">
+                <param name="AF_dflt" value="0.4" />
+                <param name="GTs_only" value="30" />
+            </section>
             <param name="output_type" value="r" />
             <output name="output_file">
                 <assert_contents>
@@ -148,11 +151,13 @@
         <!-- Test ignore homref and include noalt-->
         <test>
             <param name="input_file" ftype="vcf" value="roh.vcf" />
-            <param name="AF_dflt" value="0.4" />
-            <param name="GTs_only" value="30" />
+            <section name="sec_general">
+                <param name="AF_dflt" value="0.4" />
+                <param name="GTs_only" value="30" />
+                <param name="ignore_homref" value="true"/>
+                <param name="include_noalt" value="true"/>
+            </section>
             <param name="output_type" value="r" />
-            <param name="ignore_homref" value="true"/>
-            <param name="include_noalt" value="true"/>
             <output name="output_file">
                 <assert_contents>
                     <not_has_text text="ST"/>
@@ -172,7 +177,12 @@
                 <param name="GTs_only" value="30" />
             </section>
             <section name="sec_restrict">
-                <param name="regions_overlap" value="1"/>
+                <conditional name="regions">
+                    <param name="regions_src" value="regions" />
+                    <repeat name="region_specs">
+                        <param name="chrom" value="1" />
+                    </repeat>
+                </conditional>
             </section>
             <output name="output_file">
                 <assert_contents>
@@ -197,7 +207,7 @@
 
 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
 
-@BCFTOOLS_WIKI@
+@BCFTOOLS_HOWTOS@
 ]]>
    </help>
     <expand macro="citations" />