| Previous changeset 3:bd46669113b9 (2021-06-26) Next changeset 5:33c99804a32f (2022-04-18) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 4ca0a67fd4126f8b2a135b6cb7894042e980b39a" |
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modified:
biom_convert.xml macros.xml test-data/output_1.biom1.re test-data/output_taxonomy_1.biom1.re |
| b |
| diff -r bd46669113b9 -r 54ccb7e1f49a biom_convert.xml --- a/biom_convert.xml Sat Jun 26 19:09:19 2021 +0000 +++ b/biom_convert.xml Sat Oct 23 21:30:47 2021 +0000 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="biom_convert" name="Convert" version="@VERSION@.4"> +<tool id="biom_convert" name="Convert" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>between BIOM table formats</description> <macros> <import>macros.xml</import> |
| b |
| diff -r bd46669113b9 -r 54ccb7e1f49a macros.xml --- a/macros.xml Sat Jun 26 19:09:19 2021 +0000 +++ b/macros.xml Sat Oct 23 21:30:47 2021 +0000 |
| b |
| @@ -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> |
| b |
| diff -r bd46669113b9 -r 54ccb7e1f49a test-data/output_1.biom1.re --- a/test-data/output_1.biom1.re Sat Jun 26 19:09:19 2021 +0000 +++ b/test-data/output_1.biom1.re Sat Oct 23 21:30:47 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\"\:\ \[\{\"id\"\:\ \"SAMPLE\_1\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"SAMPLE\_2\"\,\ \"metadata\"\:\ null\}\]\} |
| b |
| diff -r bd46669113b9 -r 54ccb7e1f49a test-data/output_taxonomy_1.biom1.re --- a/test-data/output_taxonomy_1.biom1.re Sat Jun 26 19:09:19 2021 +0000 +++ b/test-data/output_taxonomy_1.biom1.re Sat Oct 23 21:30:47 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\"\:\ \[\{\"id\"\:\ \"SAMPLE\_1\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"SAMPLE\_2\"\,\ \"metadata\"\:\ null\}\]\} |