Mercurial > repos > iuc > bcftools_plugin_frameshifts

diff bcftools_plugin_frameshifts.xml @ 25:7c7cf05cdb1e draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
author iuc
date Tue, 02 Dec 2025 07:47:59 +0000
parents 5bd73b287e3b
children
line wrap: on
line diff
--- a/bcftools_plugin_frameshifts.xml	Sun Aug 18 09:50:12 2024 +0000
+++ b/bcftools_plugin_frameshifts.xml	Tue Dec 02 07:47:59 2025 +0000
@@ -9,7 +9,6 @@
     <expand macro="requirements" />
     <expand macro="version_command" />
     <command detect_errors="aggressive"><![CDATA[
-@PREPARE_ENV@
 @PREPARE_INPUT_FILE@
 #set $section = $sec_restrict
 @PREPARE_TARGETS_FILE@
@@ -41,8 +40,8 @@
         <param name="exons" type="data" format="bed"
         label="Exons File" help="BED file describing exons" />
         <section name="sec_restrict" expanded="false" title="Restrict to">
-            <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>
@@ -59,8 +58,7 @@
             <output name="output_file" ftype="vcf">
                 <assert_contents>
                     <has_line_matching expression="##INFO=&lt;ID=OOF,.+" />
-                    <has_line_matching expression="1&#09;3106154&#09;.&#09;CAAA&#09;C&#09;.+&#09;.+&#09;OOF=0.+" />
-                    <has_line_matching expression="1&#09;3106154&#09;.&#09;C&#09;CT&#09;.+&#09;.+&#09;OOF=1.+" />
+                    <has_line_matching expression="1\t3106154\t.\tCAAA\tC\t342\tPASS\tOOF=-1.+"/>
                 </assert_contents>
             </output>
         </test>