Mercurial > repos > iuc > bcftools_stats

diff bcftools_stats.xml @ 25:24e9954fec54 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 08:03:22 +0000
parents 913c052dfc71
children
line wrap: on
line diff
--- a/bcftools_stats.xml	Sun Aug 18 09:50:58 2024 +0000
+++ b/bcftools_stats.xml	Tue Dec 02 08:03:22 2025 +0000
@@ -8,11 +8,10 @@
     <expand macro="requirements">
         <expand macro="samtools_requirement"/>
         <expand macro="matplotlib_requirement" />
-        <requirement type="package" version="0.12.0">tectonic</requirement>
+        <requirement type="package" version="0.15.0">tectonic</requirement>
     </expand>
     <expand macro="version_command" />
     <command detect_errors="aggressive"><![CDATA[
-@PREPARE_ENV@
 #set $input_files = [$input_file]
 #if $inputB_file:
     #silent $input_files.append($inputB_file)
@@ -83,8 +82,8 @@
             <expand macro="macro_samples" />
             <expand macro="macro_apply_filters" />
             <expand macro="macro_collapse" />
-            <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>
@@ -202,7 +201,12 @@
             <param name="input_file" ftype="vcf" value="stats.b.vcf" />
             <param name="inputB_file" ftype="vcf" value="stats.a.vcf" />
             <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>
@@ -235,7 +239,7 @@
             <output name="output_file">
                 <assert_contents>
                     <has_text_matching expression="bcftools stats  --samples - "/>
-                    <has_text_matching expression="PSC\t0\tHG00101\t0\t0\t0\t0\t0\t0\t4.8"/>
+                    <has_text_matching expression="PSC\t0\tHG00101\t0\t0\t0\t0\t0\t0\t4.9"/>
                     <has_text_matching expression="PSI\t0\tHG00102\t0"/>
                 </assert_contents>
             </output>
@@ -260,7 +264,7 @@
 
 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
 
-@BCFTOOLS_WIKI@
+@BCFTOOLS_HOWTOS@
 ]]>
 </help>
     <expand macro="citations" />