Add biotols for mothur (#5576)

galaxyproject · Dec 3, 2023 · f3a3113 · f3a3113
1 parent b6e175a
commit f3a3113
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diff --git a/tools/mothur/align.check.xml b/tools/mothur/align.check.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>

diff --git a/tools/mothur/align.seqs.xml b/tools/mothur/align.seqs.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>

diff --git a/tools/mothur/amova.xml b/tools/mothur/amova.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>

diff --git a/tools/mothur/anosim.xml b/tools/mothur/anosim.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>

diff --git a/tools/mothur/bin.seqs.xml b/tools/mothur/bin.seqs.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>

diff --git a/tools/mothur/biom.info.xml b/tools/mothur/biom.info.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>

diff --git a/tools/mothur/chimera.bellerophon.xml b/tools/mothur/chimera.bellerophon.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>

diff --git a/tools/mothur/chimera.ccode.xml b/tools/mothur/chimera.ccode.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>

diff --git a/tools/mothur/chimera.check.xml b/tools/mothur/chimera.check.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>

diff --git a/tools/mothur/chimera.perseus.xml b/tools/mothur/chimera.perseus.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>

diff --git a/tools/mothur/chimera.pintail.xml b/tools/mothur/chimera.pintail.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>

diff --git a/tools/mothur/chimera.slayer.xml b/tools/mothur/chimera.slayer.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>

diff --git a/tools/mothur/chimera.uchime.xml b/tools/mothur/chimera.uchime.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>

diff --git a/tools/mothur/chimera.vsearch.xml b/tools/mothur/chimera.vsearch.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements">
         <requirement type="package" version="2.6.0">vsearch</requirement>
     </expand>

diff --git a/tools/mothur/chop.seqs.xml b/tools/mothur/chop.seqs.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>

diff --git a/tools/mothur/classify.otu.xml b/tools/mothur/classify.otu.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>

diff --git a/tools/mothur/classify.seqs.xml b/tools/mothur/classify.seqs.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>

diff --git a/tools/mothur/classify.tree.xml b/tools/mothur/classify.tree.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>

diff --git a/tools/mothur/clearcut.xml b/tools/mothur/clearcut.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>

diff --git a/tools/mothur/cluster.classic.xml b/tools/mothur/cluster.classic.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>

diff --git a/tools/mothur/cluster.fragments.xml b/tools/mothur/cluster.fragments.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>

diff --git a/tools/mothur/cluster.split.xml b/tools/mothur/cluster.split.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements">
         <requirement type="package" version="2.6.0">vsearch</requirement>
     </expand>

diff --git a/tools/mothur/cluster.xml b/tools/mothur/cluster.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements">
         <requirement type="package" version="2.6.0">vsearch</requirement>
     </expand>

diff --git a/tools/mothur/collect.shared.xml b/tools/mothur/collect.shared.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>

diff --git a/tools/mothur/collect.single.xml b/tools/mothur/collect.single.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>

diff --git a/tools/mothur/consensus.seqs.xml b/tools/mothur/consensus.seqs.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>

diff --git a/tools/mothur/cooccurrence.xml b/tools/mothur/cooccurrence.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>

diff --git a/tools/mothur/corr.axes.xml b/tools/mothur/corr.axes.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>

diff --git a/tools/mothur/count.groups.xml b/tools/mothur/count.groups.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>

diff --git a/tools/mothur/count.seqs.xml b/tools/mothur/count.seqs.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>

diff --git a/tools/mothur/create.database.xml b/tools/mothur/create.database.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>

diff --git a/tools/mothur/degap.seqs.xml b/tools/mothur/degap.seqs.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>

diff --git a/tools/mothur/deunique.seqs.xml b/tools/mothur/deunique.seqs.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>

diff --git a/tools/mothur/deunique.tree.xml b/tools/mothur/deunique.tree.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>

diff --git a/tools/mothur/dist.seqs.xml b/tools/mothur/dist.seqs.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>

diff --git a/tools/mothur/dist.shared.xml b/tools/mothur/dist.shared.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>

diff --git a/tools/mothur/fastq.info.xml b/tools/mothur/fastq.info.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>

diff --git a/tools/mothur/filter.seqs.xml b/tools/mothur/filter.seqs.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>

diff --git a/tools/mothur/filter.shared.xml b/tools/mothur/filter.shared.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>

diff --git a/tools/mothur/get.communitytype.xml b/tools/mothur/get.communitytype.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>

diff --git a/tools/mothur/get.coremicrobiome.xml b/tools/mothur/get.coremicrobiome.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>

diff --git a/tools/mothur/get.dists.xml b/tools/mothur/get.dists.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>

diff --git a/tools/mothur/get.group.xml b/tools/mothur/get.group.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>

diff --git a/tools/mothur/get.groups.xml b/tools/mothur/get.groups.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>

diff --git a/tools/mothur/get.label.xml b/tools/mothur/get.label.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>

diff --git a/tools/mothur/get.lineage.xml b/tools/mothur/get.lineage.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>

diff --git a/tools/mothur/get.mimarkspackage.xml b/tools/mothur/get.mimarkspackage.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>

diff --git a/tools/mothur/get.otulabels.xml b/tools/mothur/get.otulabels.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>

diff --git a/tools/mothur/get.otulist.xml b/tools/mothur/get.otulist.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>

diff --git a/tools/mothur/get.oturep.xml b/tools/mothur/get.oturep.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>