Mercurial > repos > iuc > bcftools_annotate

diff bcftools_annotate.xml @ 26:bba9853e1fdc 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 07:55:02 +0000
parents 65d418d476a5
children
line wrap: on
line diff
--- a/bcftools_annotate.xml	Sun Aug 18 09:38:22 2024 +0000
+++ b/bcftools_annotate.xml	Tue Dec 02 07:55:02 2025 +0000
@@ -9,7 +9,6 @@
     <expand macro="requirements" />
     <expand macro="version_command" />
     <command detect_errors="aggressive"><![CDATA[
-@PREPARE_ENV@
 @PREPARE_INPUT_FILE@
 #set $annotation_file = None
 #set $annotation_hdr = None
@@ -175,7 +174,7 @@
             <expand macro="macro_include" />
             <expand macro="macro_exclude" />
             <expand macro="macro_collapse" />
-            <expand macro="macro_restrict" />
+            <expand macro="macro_region_restrict" />
             <expand macro="macro_samples" />
         </section>
         <expand macro="macro_select_output_type" />
@@ -186,10 +185,14 @@
     <tests>
         <test>
             <param name="input_file" ftype="vcf" value="annotate.vcf" />
-            <param name="anno_fmt" value="tab" />
-            <param name="annotations" value="annotate.tab" />
-            <param name="header_file" value="annotate.hdr" />
-            <param name="columns" value="CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL" />
+            <section name="sec_annofile">
+                <conditional name="annofile">
+                    <param name="anno_fmt" value="tab" />
+                    <param name="annotations" value="annotate.tab" />
+                    <param name="header_file" value="annotate.hdr" />
+                </conditional>
+                <param name="columns" value="CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL" />
+            </section>
             <param name="output_type" value="v" />
             <output name="output_file">
                 <assert_contents>
@@ -218,9 +221,13 @@
         </test>
         <test>
             <param name="input_file" ftype="vcf" value="annotate.vcf" />
-            <param name="anno_fmt" value="vcf" />
-            <param name="annotations" value="annots.vcf" />
-            <param name="columns" value="STR,ID,QUAL,FILTER" />
+            <section name="sec_annofile">
+                <conditional name="annofile">
+                    <param name="anno_fmt" value="vcf" />
+                    <param name="annotations" value="annots.vcf" />
+                </conditional>
+                <param name="columns" value="STR,ID,QUAL,FILTER" />
+            </section>
             <param name="output_type" value="v" />
             <output name="output_file">
                 <assert_contents>
@@ -231,9 +238,13 @@
         </test>
         <test>
             <param name="input_file" ftype="vcf" value="annotate.vcf" />
-            <param name="anno_fmt" value="vcf" />
-            <param name="annotations" value="annots.bcf" />
-            <param name="columns" value="STR,ID,QUAL,FILTER" />
+            <section name="sec_annofile">
+                <conditional name="annofile">
+                    <param name="anno_fmt" value="vcf" />
+                    <param name="annotations" value="annots.bcf" />
+                </conditional>
+                <param name="columns" value="STR,ID,QUAL,FILTER" />
+            </section>
             <param name="output_type" value="v" />
             <output name="output_file">
                 <assert_contents>
@@ -244,9 +255,13 @@
         </test>
         <test>
             <param name="input_file" ftype="vcf" value="annotate2.vcf" />
-            <param name="anno_fmt" value="vcf" />
-            <param name="annotations" value="annots2.vcf" />
-            <param name="columns" value="ID,QUAL,FILTER,INFO,FMT" />
+            <section name="sec_annofile">
+                <conditional name="annofile">
+                    <param name="anno_fmt" value="vcf" />
+                    <param name="annotations" value="annots2.vcf" />
+                </conditional>
+                <param name="columns" value="ID,QUAL,FILTER,INFO,FMT" />
+            </section>
             <param name="output_type" value="v" />
             <output name="output_file">
                 <assert_contents>
@@ -257,10 +272,16 @@
         </test>
         <test>
             <param name="input_file" ftype="vcf" value="annotate2.vcf" />
-            <param name="anno_fmt" value="vcf" />
-            <param name="annotations" value="annots2.vcf" />
-            <param name="columns" value="ID,QUAL,FILTER,INFO,FMT" />
-            <param name="samples" value="A" />
+            <section name="sec_annofile">
+                <conditional name="annofile">
+                    <param name="anno_fmt" value="vcf" />
+                    <param name="annotations" value="annots2.vcf" />
+                </conditional>
+                <param name="columns" value="ID,QUAL,FILTER,INFO,FMT" />
+            </section>
+            <section name="sec_restrict">
+                <param name="samples" value="A" />
+            </section>
             <param name="output_type" value="v" />
             <output name="output_file">
                 <assert_contents>
@@ -271,8 +292,14 @@
         </test>
         <test>
             <param name="input_file" ftype="vcf" value="annotate3.vcf" />
-            <param name="anno_fmt" value="none" />
-            <param name="remove" value="ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL" />
+            <section name="sec_annofile">
+                <conditional name="annofile">
+                    <param name="anno_fmt" value="none" />
+                </conditional>
+            </section>
+            <section name="sec_annotate">
+                <param name="remove" value="ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL" />
+            </section>
             <param name="output_type" value="v" />
             <output name="output_file">
                 <assert_contents>
@@ -282,8 +309,14 @@
         </test>
         <test>
             <param name="input_file" ftype="vcf" value="annotate3.vcf" />
-            <param name="anno_fmt" value="none" />
-            <param name="remove" value="FORMAT" />
+            <section name="sec_annofile">
+                <conditional name="annofile">
+                    <param name="anno_fmt" value="none" />
+                </conditional>
+            </section>
+            <section name="sec_annotate">
+                <param name="remove" value="FORMAT" />
+            </section>
             <param name="output_type" value="v" />
             <output name="output_file">
                 <assert_contents>
@@ -294,11 +327,22 @@
         <!-- Test region overlap option -->
         <test>
             <param name="input_file" ftype="vcf" value="annotate3.vcf" />
-            <param name="anno_fmt" value="none" />
-            <param name="remove" value="FORMAT" />
+            <section name="sec_annofile">
+                <conditional name="annofile">
+                    <param name="anno_fmt" value="none" />
+                </conditional>
+            </section>
+            <section name="sec_annotate">
+                <param name="remove" value="FORMAT" />
+            </section>
             <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>
+                </conditional>
             </section>
             <output name="output_file">
                 <assert_contents>
@@ -312,12 +356,16 @@
         <!-- Test min overlap option -->
         <test>
             <param name="input_file" ftype="vcf" value="annotate3.vcf" />
-            <param name="anno_fmt" value="none" />
-            <param name="remove" value="FORMAT" />
-            <param name="output_type" value="v" />
             <section name="sec_annofile">
+                <conditional name="annofile">
+                    <param name="anno_fmt" value="none" />
+                </conditional>
                 <param name="min_overlap" value="0.5"/>
             </section>
+            <section name="sec_annotate">
+                <param name="remove" value="FORMAT" />
+            </section>
+            <param name="output_type" value="v" />
             <output name="output_file">
                 <assert_contents>
                     <not_has_text text="GT:X:PL:Y:AA" />
@@ -366,7 +414,7 @@
 
 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
 
-@BCFTOOLS_WIKI@
+@BCFTOOLS_HOWTOS@
 ]]>
     </help>
     <expand macro="citations" />