Mercurial > repos > iuc > bcftools_reheader

diff bcftools_reheader.xml @ 25:da7365baa407 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
author iuc
date Tue, 02 Dec 2025 07:58:37 +0000
parents d0933084cba7
children
line wrap: on
line diff
--- a/bcftools_reheader.xml	Sun Aug 18 09:48:17 2024 +0000
+++ b/bcftools_reheader.xml	Tue Dec 02 07:58:37 2025 +0000
@@ -9,7 +9,6 @@
     <expand macro="requirements" />
     <expand macro="version_command" />
     <command detect_errors="aggressive"><![CDATA[
-@PREPARE_ENV@
 @PREPARE_INPUT_FILE@
 bcftools @EXECUTABLE@
 
@@ -74,7 +73,9 @@
     <tests>
         <test>
             <param name="input_file" ftype="vcf" value="reheader.vcf" />
-            <param name="header" ftype="vcf" value="reheader.hdr" />
+            <section name="sec_default">
+                <param name="header" ftype="vcf" value="reheader.hdr" />
+            </section>
             <param name="output_type" value="v" />
             <output name="output_file">
                 <assert_contents>
@@ -86,8 +87,12 @@
         </test>
         <test>
             <param name="input_file" ftype="vcf" value="reheader.vcf" />
-            <param name="samples_src" value="history" />
-            <param name="sample_file" ftype="tabular" value="reheader.samples" />
+            <section name="sec_default">
+                <conditional name="rename_samples">
+                    <param name="samples_src" value="history" />
+                    <param name="sample_file" ftype="tabular" value="reheader.samples" />
+                </conditional>
+            </section>
             <param name="output_type" value="v" />
             <output name="output_file">
                 <assert_contents>
@@ -98,8 +103,12 @@
         </test>
         <test>
             <param name="input_file" ftype="vcf" value="reheader.vcf" />
-            <param name="samples_src" value="history" />
-            <param name="sample_file" ftype="tabular" value="reheader.samples2" />
+            <section name="sec_default">
+                <conditional name="rename_samples">
+                    <param name="samples_src" value="history" />
+                    <param name="sample_file" ftype="tabular" value="reheader.samples2" />
+                </conditional>
+            </section>
             <param name="output_type" value="v" />
             <output name="output_file">
                 <assert_contents>
@@ -144,7 +153,7 @@
 
 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
 
-@BCFTOOLS_WIKI@
+@BCFTOOLS_HOWTOS@
 ]]>
     </help>
     <expand macro="citations" />