update bamtools biotools

galaxyproject · Oct 31, 2023 · e0a888a · e0a888a
1 parent 244c02b
commit e0a888a
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Showing 7 changed files with 12 additions and 1 deletion.
diff --git a/tool_collections/bamtools/bamtools/bamtools.xml b/tool_collections/bamtools/bamtools/bamtools.xml
@@ -5,6 +5,7 @@
           <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
+    <expand macro="biotools"/>
     <command detect_errors="exit_code">
         <![CDATA[
             ##set up input files

diff --git a/tool_collections/bamtools/bamtools_filter/bamtools-filter.xml b/tool_collections/bamtools/bamtools_filter/bamtools-filter.xml
@@ -4,6 +4,7 @@
           <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
+    <expand macro="biotools"/>
     <command detect_errors="exit_code">
         <![CDATA[
             cp '$script_file' '$out_file2' &&

diff --git a/tool_collections/bamtools/bamtools_split/bamtools_split_mapped.xml b/tool_collections/bamtools/bamtools_split/bamtools_split_mapped.xml
@@ -4,6 +4,7 @@
           <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
+    <expand macro="biotools"/>
     <command>
         <![CDATA[
             ln -s '${input_bam}' 'localbam.bam' &&

diff --git a/tool_collections/bamtools/bamtools_split/bamtools_split_paired.xml b/tool_collections/bamtools/bamtools_split/bamtools_split_paired.xml
@@ -4,6 +4,7 @@
           <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
+    <expand macro="biotools"/>
     <command>
         <![CDATA[
             ln -s '${input_bam}' 'localbam.bam' &&

diff --git a/tool_collections/bamtools/bamtools_split/bamtools_split_ref.xml b/tool_collections/bamtools/bamtools_split/bamtools_split_ref.xml
@@ -4,6 +4,7 @@
           <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
+    <expand macro="biotools"/>
     <command>
         <![CDATA[
             ln -s '${input_bam}' 'localbam.bam' &&

diff --git a/tool_collections/bamtools/bamtools_split/bamtools_split_tag.xml b/tool_collections/bamtools/bamtools_split/bamtools_split_tag.xml
@@ -4,6 +4,7 @@
           <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
+    <expand macro="biotools"/>
     <command>
         <![CDATA[
             #import re

diff --git a/tool_collections/bamtools/macros.xml b/tool_collections/bamtools/macros.xml
@@ -7,9 +7,14 @@
             <requirement type="package" version="1.4.1">samtools</requirement>
         </requirements>
     </xml>
+    <xml name="biotools">
+        <xrefs>
+            <xref type="bio.tools">bamtools</xref>
+        </xrefs>
+    </xml>
     <xml name="citations">
         <citations>
             <citation type="doi">10.1093/bioinformatics/btr174</citation>
         </citations>
     </xml>
-</macros>
+</macros>