Mercurial > repos > iuc > bcftools_concat

diff bcftools_concat.xml @ 24:c3c930926708 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 08:14:09 +0000
parents 03e0645395d2
children
line wrap: on
line diff
--- a/bcftools_concat.xml	Sun Aug 18 10:18:33 2024 +0000
+++ b/bcftools_concat.xml	Tue Dec 02 08:14:09 2025 +0000
@@ -1,15 +1,13 @@
-<?xml version='1.0' encoding='utf-8'?>
 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Concatenate or combine VCF/BCF files</description>
     <macros>
         <token name="@EXECUTABLE@">concat</token>
         <import>macros.xml</import>
     </macros>
-    <expand macro="bio_tools" />
-    <expand macro="requirements" />
-    <expand macro="version_command" />
+    <expand macro="bio_tools"/>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
     <command detect_errors="aggressive"><![CDATA[
-@PREPARE_ENV@
 @PREPARE_INPUT_FILES@
 #set $section = $sec_restrict
 @PREPARE_REGIONS_FILE@
@@ -53,9 +51,9 @@
 #end if
     ]]></command>
     <inputs>
-        <expand macro="macro_inputs" />
+        <expand macro="macro_inputs"/>
         <section name="sec_restrict" expanded="false" title="Restrict to">
-            <expand macro="macro_restrict" />
+            <expand macro="macro_region_restrict"/>
         </section>
         <section name="sec_default" expanded="true" title="Concat Options">
             <conditional name="mode">
@@ -91,28 +89,25 @@
                         </when>
                         <when value="no"/>
                     </conditional>
-                    <param name="ligate" type="boolean" truevalue="--ligate" falsevalue="" label="Ligate"
-                           help="Ligate phased VCFs by matching phase at overlapping haplotypes" />
+                    <param name="ligate" type="boolean" truevalue="--ligate" falsevalue="" label="Ligate" help="Ligate phased VCFs by matching phase at overlapping haplotypes"/>
                     <param name="ligate_mode" type="select" optional="true" label="Ligate mode" help="It allows finer control of --ligate behavior">
                         <option value="--ligate-warn">Ligate warn: Drop sites that are present in one chunk but absent in the other (--ligate-warn)</option>
                         <option value="--ligate-force">Ligate force: Kepp sites that are present only in one chunk (--ligate-force)</option>
                     </param>
                 </when>
             </conditional>
-            <param name="compact_PS" type="boolean" truevalue="--compact-PS" falsevalue="" label="Compact Ps"
-                   help="Do not output PS tag at each site, only at the start of a new phase set block." />
-            <param name="min_PQ" type="integer" label="Min Pq" value="30" optional="true"
-                   help="Break phase set if phasing quality is lower than &lt;int&gt;" />
+            <param name="compact_PS" type="boolean" truevalue="--compact-PS" falsevalue="" label="Compact Ps" help="Do not output PS tag at each site, only at the start of a new phase set block."/>
+            <param name="min_PQ" type="integer" label="Min Pq" value="30" optional="true" help="Break phase set if phasing quality is lower than &lt;int&gt;"/>
         </section>
-        <expand macro="macro_select_output_type" />
+        <expand macro="macro_select_output_type"/>
     </inputs>
     <outputs>
         <expand macro="macro_vcf_output"/>
     </outputs>
     <tests>
         <test>
-            <param name="input_files" ftype="vcf" value="concat.1.b.vcf,concat.1.a.vcf" />
-            <param name="output_type" value="v" />
+            <param name="input_files" ftype="vcf" value="concat.1.b.vcf,concat.1.a.vcf"/>
+            <param name="output_type" value="v"/>
             <output name="output_file">
                 <assert_contents>
                     <has_text_matching expression="1\t100"/>
@@ -121,9 +116,13 @@
             </output>
         </test>
         <test>
-            <param name="input_files" ftype="vcf" value="concat.1.b.vcf,concat.1.a.vcf" />
-            <param name="naive" value="no" />
-            <param name="output_type" value="v" />
+            <param name="input_files" ftype="vcf" value="concat.1.b.vcf,concat.1.a.vcf"/>
+            <section name="sec_default">
+                <conditional name="mode">
+                    <param name="naive" value="no"/>
+                </conditional>
+            </section>
+            <param name="output_type" value="v"/>
             <output name="output_file">
                 <assert_contents>
                     <has_text_matching expression="1\t100"/>
@@ -132,9 +131,16 @@
             </output>
         </test>
         <test>
-            <param name="input_files" ftype="vcf" value="concat.2.b.vcf,concat.2.a.vcf" />
-            <param name="allow_overlaps" value="yes" />
-            <param name="output_type" value="v" />
+            <param name="input_files" ftype="vcf" value="concat.2.b.vcf,concat.2.a.vcf"/>
+            <section name="sec_default">
+                <conditional name="mode">
+                    <param name="naive" value="no"/>
+                    <conditional name="overlaps">
+                        <param name="allow_overlaps" value="yes"/>
+                    </conditional>
+                </conditional>
+            </section>
+            <param name="output_type" value="v"/>
             <output name="output_file">
                 <assert_contents>
                     <has_text_matching expression="2\t140\t.\tA\tG"/>
@@ -143,10 +149,17 @@
             </output>
         </test>
         <test>
-            <param name="input_files" ftype="vcf" value="concat.2.b.vcf,concat.2.a.vcf" />
-            <param name="allow_overlaps" value="yes" />
-            <param name="rm_dups" value="none" />
-            <param name="output_type" value="v" />
+            <param name="input_files" ftype="vcf" value="concat.2.b.vcf,concat.2.a.vcf"/>
+            <section name="sec_default">
+                <conditional name="mode">
+                    <param name="naive" value="no"/>
+                    <conditional name="overlaps">
+                        <param name="allow_overlaps" value="yes"/>
+                        <param name="rm_dups" value="none"/>
+                    </conditional>
+                </conditional>
+            </section>
+            <param name="output_type" value="v"/>
             <output name="output_file">
                 <assert_contents>
                     <has_text_matching expression="2\t160\t.\tTAAAA"/>
@@ -155,10 +168,18 @@
         </test>
         <!-- Test region overlap-->
         <test>
-            <param name="input_files" ftype="vcf" value="concat.1.b.vcf,concat.1.a.vcf" />
-            <param name="output_type" value="v" />
+            <param name="input_files" ftype="vcf" value="concat.1.b.vcf,concat.1.a.vcf"/>
+            <param name="output_type" value="v"/>
             <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>
+                    <repeat name="region_specs">
+                        <param name="chrom" value="3" />
+                    </repeat>
+                </conditional>
             </section>
             <output name="output_file">
                 <assert_contents>
@@ -167,13 +188,13 @@
                 </assert_contents>
             </output>
             <assert_command>
-                <has_text text="--regions-overlap" />
+                <has_text text="--regions-overlap"/>
             </assert_command>
         </test>
         <!-- Test ligate options -->
         <test>
-            <param name="input_files" ftype="vcf" value="concat.1.b.vcf,concat.1.a.vcf" />
-            <param name="output_type" value="v" />
+            <param name="input_files" ftype="vcf" value="concat.1.b.vcf,concat.1.a.vcf"/>
+            <param name="output_type" value="v"/>
             <section name="sec_default">
                 <conditional name="mode">
                     <conditional name="overlaps">
@@ -190,7 +211,7 @@
                 </assert_contents>
             </output>
             <assert_command>
-                <has_text text="--ligate-warn" />
+                <has_text text="--ligate-warn"/>
             </assert_command>
         </test>
     </tests>
@@ -211,7 +232,7 @@
 
 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
 
-@BCFTOOLS_WIKI@
+@BCFTOOLS_HOWTOS@
     ]]></help>
-    <expand macro="citations" />
+    <expand macro="citations"/>
 </tool>