# HG changeset patch
# User iuc
# Date 1635024327 0
# Node ID ff46c0cea2f7d0137b15fdeb607403cf620d6c99
# Parent  51e935a2032b00081668aaf67cae4d991a76c940
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 4ca0a67fd4126f8b2a135b6cb7894042e980b39a"

diff -r 51e935a2032b -r ff46c0cea2f7 biom_add_metadata.xml
--- a/biom_add_metadata.xml	Fri Jan 24 21:39:11 2020 +0000
+++ b/biom_add_metadata.xml	Sat Oct 23 21:25:27 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="biom_add_metadata" name="Add metadata" version="@VERSION@.1">
+<tool id="biom_add_metadata" name="Add metadata" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>to a BIOM table</description>
     <macros>
         <import>macros.xml</import>
diff -r 51e935a2032b -r ff46c0cea2f7 macros.xml
--- a/macros.xml	Fri Jan 24 21:39:11 2020 +0000
+++ b/macros.xml	Sat Oct 23 21:25:27 2021 +0000
@@ -1,11 +1,13 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="2.1.5">biom-format</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">biom-format</requirement>
             <yield/>
         </requirements>
     </xml>
-    <token name="@VERSION@">2.1.5</token>
+    <token name="@TOOL_VERSION@">2.1.10</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">20.05</token>
     <xml name="version_command">
         <version_command>biom --version</version_command>
     </xml>
diff -r 51e935a2032b -r ff46c0cea2f7 test-data/output_1.biom1.re
--- a/test-data/output_1.biom1.re	Fri Jan 24 21:39:11 2020 +0000
+++ b/test-data/output_1.biom1.re	Sat Oct 23 21:25:27 2021 +0000
@@ -1,1 +1,1 @@
-\{\"id\"\:\ \"None\"\,\"format\"\:\ \"Biological\ Observation\ Matrix\ 1\.0\.0\"\,\"format\_url\"\:\ \"http\:\/\/biom\-format\.org\"\,\"matrix\_type\"\:\ \"sparse\"\,\"generated\_by\"\:\ \"BIOM\-Format\ 2\.1\.5\"\,\"date\"\:\ \".*\"\,\"type\"\:\ \"OTU\ table\"\,\"matrix\_element\_type\"\:\ \"float\"\,\"shape\"\:\ \[19\,\ 2\]\,\"data\"\:\ \[\[1\,0\,160\.0\]\,\[1\,1\,242\.0\]\,\[6\,0\,1\.0\]\,\[6\,1\,1\.0\]\,\[7\,0\,3\.0\]\,\[7\,1\,4\.0\]\,\[12\,0\,13\.0\]\,\[12\,1\,36\.0\]\,\[14\,0\,1\.0\]\,\[14\,1\,5\.0\]\,\[15\,0\,1\.0\]\,\[16\,0\,1\.0\]\,\[16\,1\,3\.0\]\]\,\"rows\"\:\ \[\{\"id\"\:\ \"2\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"3\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"4\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"5\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"8\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"9\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"10\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"11\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"12\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"14\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"15\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"16\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"17\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"18\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"22\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"23\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"25\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"28\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"29\"\,\ \"metadata\"\:\ null\}\]\,\"columns\"\:\ \[\{\"id\"\:\ \"SAMPLE\_1\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"SAMPLE\_2\"\,\ \"metadata\"\:\ null\}\]\}
+\{\"id\"\:\ \"None\"\,\"format\"\:\ \"Biological\ Observation\ Matrix\ 1\.0\.0\"\,\"format\_url\"\:\ \"http\:\/\/biom\-format\.org\"\,\"matrix\_type\"\:\ \"sparse\"\,\"generated\_by\"\:\ \"BIOM\-Format\ \d+\.\d+\.\d+\"\,\"date\"\:\ \".*\"\,\"type\"\:\ \"OTU\ table\"\,\"matrix\_element\_type\"\:\ \"float\"\,\"shape\"\:\ \[19\,\ 2\]\,\"data\"\:\ \[\[1\,0\,160\.0\]\,\[1\,1\,242\.0\]\,\[6\,0\,1\.0\]\,\[6\,1\,1\.0\]\,\[7\,0\,3\.0\]\,\[7\,1\,4\.0\]\,\[12\,0\,13\.0\]\,\[12\,1\,36\.0\]\,\[14\,0\,1\.0\]\,\[14\,1\,5\.0\]\,\[15\,0\,1\.0\]\,\[16\,0\,1\.0\]\,\[16\,1\,3\.0\]\]\,\"rows\"\:\ \[\{\"id\"\:\ \"2\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"3\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"4\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"5\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"8\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"9\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"10\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"11\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"12\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"14\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"15\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"16\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"17\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"18\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"22\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"23\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"25\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"28\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"29\"\,\ \"metadata\"\:\ null\}\]\,\"columns\"\:\ \[\{\"id\"\:\ \"SAMPLE\_1\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"SAMPLE\_2\"\,\ \"metadata\"\:\ null\}\]\}
diff -r 51e935a2032b -r ff46c0cea2f7 test-data/output_taxonomy_1.biom1.re
--- a/test-data/output_taxonomy_1.biom1.re	Fri Jan 24 21:39:11 2020 +0000
+++ b/test-data/output_taxonomy_1.biom1.re	Sat Oct 23 21:25:27 2021 +0000
@@ -1,1 +1,1 @@
-\{\"id\"\:\ \"None\"\,\"format\"\:\ \"Biological\ Observation\ Matrix\ 1\.0\.0\"\,\"format\_url\"\:\ \"http\:\/\/biom\-format\.org\"\,\"matrix\_type\"\:\ \"sparse\"\,\"generated\_by\"\:\ \"BIOM\-Format\ 2\.1\.5\"\,\"date\"\:\ \".*\"\,\"type\"\:\ \"OTU\ table\"\,\"matrix\_element\_type\"\:\ \"float\"\,\"shape\"\:\ \[19\,\ 2\]\,\"data\"\:\ \[\[1\,0\,160\.0\]\,\[1\,1\,242\.0\]\,\[6\,0\,1\.0\]\,\[6\,1\,1\.0\]\,\[7\,0\,3\.0\]\,\[7\,1\,4\.0\]\,\[12\,0\,13\.0\]\,\[12\,1\,36\.0\]\,\[14\,0\,1\.0\]\,\[14\,1\,5\.0\]\,\[15\,0\,1\.0\]\,\[16\,0\,1\.0\]\,\[16\,1\,3\.0\]\]\,\"rows\"\:\ \[\{\"id\"\:\ \"2\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Archaea\"\]\}\}\,\{\"id\"\:\ \"3\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\]\}\}\,\{\"id\"\:\ \"4\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Archaea\"\,\ \"p\_\_Crenarchaeota\"\]\}\}\,\{\"id\"\:\ \"5\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Archaea\"\,\ \"p\_\_Euryarchaeota\"\]\}\}\,\{\"id\"\:\ \"8\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_AC1\"\]\}\}\,\{\"id\"\:\ \"9\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_AD3\"\]\}\}\,\{\"id\"\:\ \"10\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_Acidobacteria\"\]\}\}\,\{\"id\"\:\ \"11\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_Actinobacteria\"\]\}\}\,\{\"id\"\:\ \"12\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_AncK6\"\]\}\}\,\{\"id\"\:\ \"14\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_Armatimonadetes\"\]\}\}\,\{\"id\"\:\ \"15\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_BHI80\-139\"\]\}\}\,\{\"id\"\:\ \"16\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_BRC1\"\]\}\}\,\{\"id\"\:\ \"17\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_Bacteroidetes\"\]\}\}\,\{\"id\"\:\ \"18\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_CD12\"\]\}\}\,\{\"id\"\:\ \"22\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_Chlorobi\"\]\}\}\,\{\"id\"\:\ \"23\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_Chloroflexi\"\]\}\}\,\{\"id\"\:\ \"25\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_Cyanobacteria\"\]\}\}\,\{\"id\"\:\ \"28\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_EM19\"\]\}\}\,\{\"id\"\:\ \"29\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_EM3\"\]\}\}\]\,\"columns\"\:\ \[\{\"id\"\:\ \"SAMPLE\_1\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"SAMPLE\_2\"\,\ \"metadata\"\:\ null\}\]\}
+\{\"id\"\:\ \"None\"\,\"format\"\:\ \"Biological\ Observation\ Matrix\ 1\.0\.0\"\,\"format\_url\"\:\ \"http\:\/\/biom\-format\.org\"\,\"matrix\_type\"\:\ \"sparse\"\,\"generated\_by\"\:\ \"BIOM\-Format\ \d+\.\d+\.\d+\"\,\"date\"\:\ \".*\"\,\"type\"\:\ \"OTU\ table\"\,\"matrix\_element\_type\"\:\ \"float\"\,\"shape\"\:\ \[19\,\ 2\]\,\"data\"\:\ \[\[1\,0\,160\.0\]\,\[1\,1\,242\.0\]\,\[6\,0\,1\.0\]\,\[6\,1\,1\.0\]\,\[7\,0\,3\.0\]\,\[7\,1\,4\.0\]\,\[12\,0\,13\.0\]\,\[12\,1\,36\.0\]\,\[14\,0\,1\.0\]\,\[14\,1\,5\.0\]\,\[15\,0\,1\.0\]\,\[16\,0\,1\.0\]\,\[16\,1\,3\.0\]\]\,\"rows\"\:\ \[\{\"id\"\:\ \"2\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Archaea\"\]\}\}\,\{\"id\"\:\ \"3\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\]\}\}\,\{\"id\"\:\ \"4\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Archaea\"\,\ \"p\_\_Crenarchaeota\"\]\}\}\,\{\"id\"\:\ \"5\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Archaea\"\,\ \"p\_\_Euryarchaeota\"\]\}\}\,\{\"id\"\:\ \"8\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_AC1\"\]\}\}\,\{\"id\"\:\ \"9\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_AD3\"\]\}\}\,\{\"id\"\:\ \"10\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_Acidobacteria\"\]\}\}\,\{\"id\"\:\ \"11\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_Actinobacteria\"\]\}\}\,\{\"id\"\:\ \"12\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_AncK6\"\]\}\}\,\{\"id\"\:\ \"14\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_Armatimonadetes\"\]\}\}\,\{\"id\"\:\ \"15\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_BHI80\-139\"\]\}\}\,\{\"id\"\:\ \"16\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_BRC1\"\]\}\}\,\{\"id\"\:\ \"17\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_Bacteroidetes\"\]\}\}\,\{\"id\"\:\ \"18\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_CD12\"\]\}\}\,\{\"id\"\:\ \"22\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_Chlorobi\"\]\}\}\,\{\"id\"\:\ \"23\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_Chloroflexi\"\]\}\}\,\{\"id\"\:\ \"25\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_Cyanobacteria\"\]\}\}\,\{\"id\"\:\ \"28\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_EM19\"\]\}\}\,\{\"id\"\:\ \"29\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_EM3\"\]\}\}\]\,\"columns\"\:\ \[\{\"id\"\:\ \"SAMPLE\_1\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"SAMPLE\_2\"\,\ \"metadata\"\:\ null\}\]\}