Mercurial > repos > iuc > bcftools_view

diff bcftools_view.xml @ 27:c6c23f9ef8d6 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 07:51:20 +0000
parents 9dac1d55dbfe
children
line wrap: on
line diff
--- a/bcftools_view.xml	Sun Aug 18 09:54:45 2024 +0000
+++ b/bcftools_view.xml	Tue Dec 02 07:51:20 2025 +0000
@@ -14,7 +14,6 @@
     <expand macro="requirements" />
     <expand macro="version_command" />
     <command detect_errors="aggressive"><![CDATA[
-@PREPARE_ENV@
 @PREPARE_INPUT_FILE@
 #set $section = $sec_restrict
 @PREPARE_TARGETS_FILE@
@@ -102,8 +101,8 @@
         <expand macro="macro_input" />
         <section name="sec_restrict" expanded="false" title="Restrict to">
             <expand macro="macro_apply_filters" />
-            <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>
@@ -201,8 +200,6 @@
             </param>
             <param name="compression_level" type="integer" min="0" max="9" label="Compression Level" optional="True"
                    help="Compression level: 0 uncompressed, 1 best speed, 9 best compression" />
-            <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets File"
-                   help="Inverts the query/filtering applied by Targets File" />
         </section>
         <expand macro="macro_select_output_type" />
     </inputs>
@@ -212,10 +209,14 @@
     <tests>
         <test>
             <param name="input_file" ftype="vcf" value="view.vcf" />
-            <param name="min_ac" value="1" />
-            <param name="max_ac" value="1" />
-            <param name="samples" value="NA00002" />
-            <param name="types" value="snps" />
+            <section name="sec_filter">
+                <param name="min_ac" value="1" />
+                <param name="max_ac" value="1" />
+                <param name="types" value="snps" />
+            </section>
+            <section name="sec_subset">
+                <param name="samples" value="NA00002" />
+            </section>
             <param name="output_type" value="v" />
             <output name="output_file">
                 <assert_contents>
@@ -226,10 +227,14 @@
         </test>
         <test>
             <param name="input_file" ftype="bcf" value="view.bcf" />
-            <param name="min_ac" value="1" />
-            <param name="max_ac" value="1" />
-            <param name="samples" value="NA00002" />
-            <param name="types" value="snps" />
+            <section name="sec_filter">
+                <param name="min_ac" value="1" />
+                <param name="max_ac" value="1" />
+                <param name="types" value="snps" />
+            </section>
+            <section name="sec_subset">
+                <param name="samples" value="NA00002" />
+            </section>
             <param name="output_type" value="v" />
             <output name="output_file">
                 <assert_contents>
@@ -240,13 +245,17 @@
         </test>
         <test>
             <param name="input_file" ftype="vcf" value="view.vcf" />
-            <param name="known_or_novel" value="--novel" />
-            <param name="private" value="--exclude-private" />
-            <param name="samples" value="NA00003" />
+            <section name="sec_filter">
+                <param name="known_or_novel" value="--novel" />
+                <param name="private" value="--exclude-private" />
+            </section>
+            <section name="sec_subset">
+                <param name="samples" value="NA00003" />
+            </section>
             <section name="sec_restrict">
                 <conditional name="regions">
                     <param name="regions_src" value="regions"/>
-                    <repeat name="regions">
+                    <repeat name="region_specs">
                         <param name="chrom" value="Y" />
                         <param name="start" value="20" />
                     </repeat>
@@ -265,14 +274,18 @@
         </test>
         <test>
             <param name="input_file" ftype="vcf" value="view.vcf" />
-            <param name="known_or_novel" value="--known" />
-            <param name="private" value="--exclude-private" />
-            <param name="apply_filters" value="PASS" />
-            <param name="samples" value="NA00003" />
+            <section name="sec_filter">
+                <param name="known_or_novel" value="--known" />
+                <param name="private" value="--exclude-private" />
+            </section>
+            <section name="sec_subset">
+                <param name="samples" value="NA00003" />
+            </section>
             <section name="sec_restrict">
+                <param name="apply_filters" value="PASS" />
                 <conditional name="regions">
                     <param name="regions_src" value="regions"/>
-                    <repeat name="regions">
+                    <repeat name="region_specs">
                         <param name="chrom" value="Y" />
                         <param name="start" value="20" />
                     </repeat>
@@ -288,8 +301,12 @@
         </test>
         <test>
             <param name="input_file" ftype="vcf" value="view.vcf" />
-            <param name="private" value="--private" />
-            <param name="samples" value="NA00003" />
+            <section name="sec_filter">
+                <param name="private" value="--private" />
+            </section>
+            <section name="sec_subset">
+                <param name="samples" value="NA00003" />
+            </section>
             <param name="output_type" value="v" />
             <output name="output_file">
                 <assert_contents>
@@ -300,7 +317,9 @@
         </test>
         <test>
             <param name="input_file" ftype="vcf" value="view.vcf" />
-            <param name="include" value="QUAL==999 &amp;&amp; (FS&lt;20 || FS&gt;=41.02) &amp;&amp; ICF&gt;-0.1 &amp;&amp; HWE*2&gt;1.2" />
+            <section name="sec_restrict">
+                <param name="include" value="QUAL==999 &amp;&amp; (FS&lt;20 || FS&gt;=41.02) &amp;&amp; ICF&gt;-0.1 &amp;&amp; HWE*2&gt;1.2" />
+            </section>
             <param name="output_type" value="v" />
             <output name="output_file">
                 <assert_contents>
@@ -311,7 +330,9 @@
         </test>
         <test>
             <param name="input_file" ftype="vcf" value="view.vcf" />
-            <param name="phased" value="--phased" />
+            <section name="sec_filter">
+                <param name="phased" value="--phased" />
+            </section>
             <param name="output_type" value="v" />
             <output name="output_file">
                 <assert_contents>
@@ -322,7 +343,9 @@
         </test>
         <test>
             <param name="input_file" ftype="vcf" value="view.vcf" />
-            <param name="phased" value="--exclude-phased" />
+            <section name="sec_filter">
+                <param name="phased" value="--exclude-phased" />
+            </section>
             <param name="output_type" value="v" />
             <output name="output_file">
                 <assert_contents>
@@ -333,11 +356,15 @@
         </test>
         <test>
             <param name="input_file" ftype="vcf" value="view.vcf" />
-            <param name="min_alleles" value="2" />
-            <param name="max_alleles" value="2" />
-            <param name="min_af" value="0.3" />
-            <param name="max_af" value="0.7" />
-            <param name="header" value="--header-only" />
+            <section name="sec_filter">
+                <param name="min_alleles" value="2" />
+                <param name="max_alleles" value="2" />
+                <param name="min_af" value="0.3" />
+                <param name="max_af" value="0.7" />
+            </section>
+            <section name="sec_output">
+                <param name="header" value="--header-only" />
+            </section>
             <param name="output_type" value="v" />
             <output name="output_file">
                 <assert_contents>
@@ -348,8 +375,12 @@
         </test>
         <test>
             <param name="input_file" ftype="vcf" value="view.vcf" />
-            <param name="uncalled" value="--uncalled" />
-            <param name="header" value="--no-header" />
+            <section name="sec_filter">
+                <param name="uncalled" value="--uncalled" />
+            </section>
+            <section name="sec_output">
+                <param name="header" value="--no-header" />
+            </section>
             <param name="output_type" value="v" />
             <output name="output_file">
                 <assert_contents>
@@ -360,8 +391,12 @@
         </test>
         <test>
             <param name="input_file" ftype="vcf" value="view.vcf" />
-            <param name="exclude_types" value="snps" />
-            <param name="drop_genotypes" value="true" />
+            <section name="sec_filter">
+                <param name="exclude_types" value="snps" />
+            </section>
+            <section name="sec_output">
+                <param name="drop_genotypes" value="true" />
+            </section>
             <param name="output_type" value="v" />
             <output name="output_file">
                 <assert_contents>
@@ -373,9 +408,11 @@
         </test>
         <test>
             <param name="input_file" ftype="vcf" value="view.vcf" />
-            <param name="phased" value="--phased" />
+            <section name="sec_filter">
+                <param name="phased" value="--phased" />
+                <param name="select_genotype" value="^het" />
+            </section>
             <param name="output_type" value="v" />
-            <param name="select_genotype" value="^het" />
             <output name="output_file">
                 <assert_contents>
                     <has_text text="--genotype ^het" />
@@ -387,13 +424,22 @@
         <!-- Test region overlap option -->
         <test>
             <param name="input_file" ftype="vcf" value="view.vcf" />
-            <param name="min_ac" value="1" />
-            <param name="max_ac" value="1" />
-            <param name="samples" value="NA00002" />
-            <param name="types" value="snps" />
+            <section name="sec_filter">
+                <param name="min_ac" value="1" />
+                <param name="max_ac" value="1" />
+                <param name="types" value="snps" />
+            </section>
+            <section name="sec_subset">
+                <param name="samples" value="NA00002" />
+            </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="20" />
+                    </repeat>
+                </conditional>
             </section>
             <output name="output_file">
                 <assert_contents>
@@ -419,7 +465,7 @@
 
 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
 
-@BCFTOOLS_WIKI@
+@BCFTOOLS_HOWTOS@
 ]]>
     </help>
     <expand macro="citations" />