Mercurial > repos > iuc > delly_filter

changeset 3:d2590fe6793f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d76130cdcb21f0390b4e68e733d38575fd5cc6c7"
author iuc
date Tue, 14 Dec 2021 19:06:53 +0000
parents 6184cfc70e28
children 74f9f312c713
files filter.xml macros.xml
diffstat 2 files changed, 10 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/filter.xml	Fri Jan 22 14:32:03 2021 +0000
+++ b/filter.xml	Tue Dec 14 19:06:53 2021 +0000
@@ -1,6 +1,7 @@
 <?xml version="1.0"?>
 <tool id="delly_filter" name="Delly filter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="18.01">
     <description>somatic or germline structural variants</description>
+    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -231,7 +232,7 @@
             </output>
             <output name="out_vcf">
                 <assert_contents>
-                    <has_n_lines n="142"/>
+                    <has_n_lines n="143"/>
                     <has_line line="##fileformat=VCFv4.2"/>
                     <has_line line="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO&#009;FORMAT&#009;NORMAL&#009;TUMOR"/>
                 </assert_contents>
--- a/macros.xml	Fri Jan 22 14:32:03 2021 +0000
+++ b/macros.xml	Tue Dec 14 19:06:53 2021 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">0.8.7</token>
+    <token name="@TOOL_VERSION@">0.9.1</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">delly</requirement>
-            <requirement type="package" version="1.10.2">bcftools</requirement>
+            <requirement type="package" version="1.12">bcftools</requirement>
         </requirements>
     </xml>
     <xml name="version_command">
@@ -16,7 +16,11 @@
             <citation type="doi">10.1093/bioinformatics/bts378</citation>
         </citations>
     </xml>
-	
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type="bio.tools">delly2</xref>
+        </xrefs>
+    </xml>
     <!-- command -->
 
     <token name="@BAM@"><![CDATA[
@@ -148,4 +152,4 @@
     <token name="@REFERENCES@"><![CDATA[
 More information are available on `GitHub <https://github.com/dellytools/delly>`_.
     ]]></token>
-</macros>
\ No newline at end of file
+</macros>