Repository 'biom_normalize_table'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/biom_normalize_table

Changeset 0:a03e97724306 (2019-09-11)
Next changeset 1:be44ed503d2b (2020-01-24)
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
added:
biom_normalize_table.xml
macros.xml
test-data/biom_from_uc.biom
test-data/input_abundance_1.biom1
test-data/input_abundance_1.tabular
test-data/input_abundance_taxonomy_1.tabular
test-data/input_taxonomy_1.tabular
test-data/normalized_presence_absence_observations.biom
test-data/normalized_relative_abund_samples.biom
test-data/observation_subsetting
test-data/output_1.biom1.re
test-data/output_taxonomy_1.biom1.re
test-data/sample_subsetting
test-data/subset_observations.biom
test-data/subset_samples.biom
test-data/summarize
test-data/summarize_qualitative_observations
test-data/uc_table.uc
b
diff -r 000000000000 -r a03e97724306 biom_normalize_table.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/biom_normalize_table.xml Wed Sep 11 12:41:04 2019 -0400
[
@@ -0,0 +1,50 @@
+<tool id="biom_normalize_table" name="Normalize" version="@VERSION@.1">
+    <description>a BIOM table</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <command detect_errors="exit_code">
+        <![CDATA[
+            biom normalize-table
+              --input-fp '$input_fp'
+              --output-fp '$output_fp'
+              $relative_abund
+              $presence_absence
+              --axis '$axis'
+        ]]>
+    </command>
+    <inputs>
+        <param name="input_fp" argument="--input-fp" type="data" format="biom1" label="BIOM table to normalize" />
+        <param name="relative_abund" argument="--relative-abund" type="boolean" checked="True" truevalue="--relative-abund" falsevalue="" label="Convert table to relative abundance" />
+        <param name="presence_absence" argument="--presence-absence" type="boolean" checked="True" truevalue="--presence-absence" falsevalue="" label="Convert table to presence/absence" />
+        <param argument="--axis" type="select" label="The axis to normalize over">
+            <option value="sample" selected="True">Sample</option>
+            <option value="observation">Observation</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data format="biom1" name="output_fp"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_fp" value="input_abundance_1.biom1" />
+            <param name="relative_abund" value="--relative-abund" />
+            <param name="presence_absence" value="" />
+            <param name="axis" value="sample" />
+            <output name="output_fp" value="normalized_relative_abund_samples.biom" ftype="biom1" compare="sim_size"/>
+        </test>
+        <test>
+            <param name="input_fp" value="input_abundance_1.biom1" />
+            <param name="relative_abund" value="" />
+            <param name="presence_absence" value="--presence-absence" />
+            <param name="axis" value="observation" />
+            <output name="output_fp" value="normalized_presence_absence_observations.biom" ftype="biom1" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+Normalize the values of a BIOM table through various methods. Relative abundance will take the relative abundance of each observation in terms of samples or observations.  Presence absensece will convert observations to 1's and 0's based on presence of the observation.
+    ]]></help>
+    <expand macro="citations" />
+</tool>
b
diff -r 000000000000 -r a03e97724306 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Wed Sep 11 12:41:04 2019 -0400
b
@@ -0,0 +1,18 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="2.1.5">biom-format</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <token name="@VERSION@">2.1.5</token>
+    <xml name="version_command">
+        <version_command>biom --version</version_command>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1186/2047-217X-1-7</citation>
+            <yield/>
+        </citations>
+    </xml>
+</macros>
b
diff -r 000000000000 -r a03e97724306 test-data/biom_from_uc.biom
b
Binary file test-data/biom_from_uc.biom has changed
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diff -r 000000000000 -r a03e97724306 test-data/input_abundance_1.biom1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_abundance_1.biom1 Wed Sep 11 12:41:04 2019 -0400
[
@@ -0,0 +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": "2016-05-26T17:20:40.263567","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}]}
\ No newline at end of file
b
diff -r 000000000000 -r a03e97724306 test-data/input_abundance_1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_abundance_1.tabular Wed Sep 11 12:41:04 2019 -0400
b
@@ -0,0 +1,20 @@
+ID SAMPLE_1 SAMPLE_2
+2 0 0
+3 160 242
+4 0 0
+5 0 0
+8 0 0
+9 0 0
+10 1 1
+11 3 4
+12 0 0
+14 0 0
+15 0 0
+16 0 0
+17 13 36
+18 0 0
+22 1 5
+23 1 0
+25 1 3
+28 0 0
+29 0 0
b
diff -r 000000000000 -r a03e97724306 test-data/input_abundance_taxonomy_1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_abundance_taxonomy_1.tabular Wed Sep 11 12:41:04 2019 -0400
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@@ -0,0 +1,20 @@
+#ID SAMPLE_1 SAMPLE_2 taxonomy
+2 0 0 d__Archaea
+3 160 242 d__Bacteria
+4 0 0 d__Archaea;p__Crenarchaeota
+5 0 0 d__Archaea;p__Euryarchaeota
+8 0 0 d__Bacteria;p__AC1
+9 0 0 d__Bacteria;p__AD3
+10 1 1 d__Bacteria;p__Acidobacteria
+11 3 4 d__Bacteria;p__Actinobacteria
+12 0 0 d__Bacteria;p__AncK6
+14 0 0 d__Bacteria;p__Armatimonadetes
+15 0 0 d__Bacteria;p__BHI80-139
+16 0 0 d__Bacteria;p__BRC1
+17 13 36 d__Bacteria;p__Bacteroidetes
+18 0 0 d__Bacteria;p__CD12
+22 1 5 d__Bacteria;p__Chlorobi
+23 1 0 d__Bacteria;p__Chloroflexi
+25 1 3 d__Bacteria;p__Cyanobacteria
+28 0 0 d__Bacteria;p__EM19
+29 0 0 d__Bacteria;p__EM3
b
diff -r 000000000000 -r a03e97724306 test-data/input_taxonomy_1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_taxonomy_1.tabular Wed Sep 11 12:41:04 2019 -0400
b
@@ -0,0 +1,20 @@
+#ID taxonomy
+2 d__Archaea
+3 d__Bacteria
+4 d__Archaea;p__Crenarchaeota
+5 d__Archaea;p__Euryarchaeota
+8 d__Bacteria;p__AC1
+9 d__Bacteria;p__AD3
+10 d__Bacteria;p__Acidobacteria
+11 d__Bacteria;p__Actinobacteria
+12 d__Bacteria;p__AncK6
+14 d__Bacteria;p__Armatimonadetes
+15 d__Bacteria;p__BHI80-139
+16 d__Bacteria;p__BRC1
+17 d__Bacteria;p__Bacteroidetes
+18 d__Bacteria;p__CD12
+22 d__Bacteria;p__Chlorobi
+23 d__Bacteria;p__Chloroflexi
+25 d__Bacteria;p__Cyanobacteria
+28 d__Bacteria;p__EM19
+29 d__Bacteria;p__EM3
b
diff -r 000000000000 -r a03e97724306 test-data/normalized_presence_absence_observations.biom
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Binary file test-data/normalized_presence_absence_observations.biom has changed
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diff -r 000000000000 -r a03e97724306 test-data/normalized_relative_abund_samples.biom
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Binary file test-data/normalized_relative_abund_samples.biom has changed
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diff -r 000000000000 -r a03e97724306 test-data/observation_subsetting
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/observation_subsetting Wed Sep 11 12:41:04 2019 -0400
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@@ -0,0 +1,2 @@
+11
+23
\ No newline at end of file
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diff -r 000000000000 -r a03e97724306 test-data/output_1.biom1.re
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_1.biom1.re Wed Sep 11 12:41:04 2019 -0400
[
@@ -0,0 +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\"\:\ \[\{\"id\"\:\ \"SAMPLE\_1\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"SAMPLE\_2\"\,\ \"metadata\"\:\ null\}\]\}
b
diff -r 000000000000 -r a03e97724306 test-data/output_taxonomy_1.biom1.re
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_taxonomy_1.biom1.re Wed Sep 11 12:41:04 2019 -0400
[
@@ -0,0 +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\"\:\ \[\{\"id\"\:\ \"SAMPLE\_1\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"SAMPLE\_2\"\,\ \"metadata\"\:\ null\}\]\}
b
diff -r 000000000000 -r a03e97724306 test-data/sample_subsetting
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample_subsetting Wed Sep 11 12:41:04 2019 -0400
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@@ -0,0 +1,1 @@
+SAMPLE_1
\ No newline at end of file
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diff -r 000000000000 -r a03e97724306 test-data/subset_observations.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/subset_observations.biom Wed Sep 11 12:41:04 2019 -0400
[
@@ -0,0 +1,23 @@
+{
+"id": "None"
+,
+"format": "Biological Observation Matrix 1.0.0"
+,
+"format_url": "http://biom-format.org"
+,
+"type": "OTU table"
+,
+"generated_by": "BIOM-Format 2.1.5"
+,
+"date": "2016-05-26T17:20:40.263567"
+,
+"matrix_type": "sparse"
+,
+"matrix_element_type": "float"
+,
+"data": [[0,0,3.0],[0,1,4.0],[1,0,1.0]], "shape": [2, 2]
+,
+"rows": [{"id": "11", "metadata": null}, {"id": "23", "metadata": null}]
+,
+"columns": [{"id": "SAMPLE_1", "metadata": null},{"id": "SAMPLE_2", "metadata": null}]
+}
b
diff -r 000000000000 -r a03e97724306 test-data/subset_samples.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/subset_samples.biom Wed Sep 11 12:41:04 2019 -0400
[
@@ -0,0 +1,23 @@
+{
+"id": "None"
+,
+"format": "Biological Observation Matrix 1.0.0"
+,
+"format_url": "http://biom-format.org"
+,
+"type": "OTU table"
+,
+"generated_by": "BIOM-Format 2.1.5"
+,
+"date": "2016-05-26T17:20:40.263567"
+,
+"matrix_type": "sparse"
+,
+"matrix_element_type": "float"
+,
+"data": [[1,0,160.0],[6,0,1.0],[7,0,3.0],[12,0,13.0],[14,0,1.0],[15,0,1.0],[16,0,1.0]], "shape": [19, 1]
+,
+"columns": [{"id": "SAMPLE_1", "metadata": null}]
+,
+"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}]
+}
b
diff -r 000000000000 -r a03e97724306 test-data/summarize
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize Wed Sep 11 12:41:04 2019 -0400
b
@@ -0,0 +1,17 @@
+Num samples: 2
+Num observations: 19
+Total count: 471
+Table density (fraction of non-zero values): 0.342
+
+Counts/sample summary:
+ Min: 180.0
+ Max: 291.0
+ Median: 235.500
+ Mean: 235.500
+ Std. dev.: 55.500
+ Sample Metadata Categories: None provided
+ Observation Metadata Categories: None provided
+
+Counts/sample detail:
+SAMPLE_1: 180.0
+SAMPLE_2: 291.0
\ No newline at end of file
b
diff -r 000000000000 -r a03e97724306 test-data/summarize_qualitative_observations
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize_qualitative_observations Wed Sep 11 12:41:04 2019 -0400
b
@@ -0,0 +1,32 @@
+Num samples: 2
+Num observations: 19
+
+Sample/observations summary:
+ Min: 0
+ Max: 2
+ Median: 0.000
+ Mean: 0.684
+ Std. dev.: 0.921
+ Sample Metadata Categories: None provided
+ Observation Metadata Categories: None provided
+
+Observations/sample detail:
+2: 0
+16: 0
+12: 0
+8: 0
+4: 0
+18: 0
+9: 0
+29: 0
+5: 0
+28: 0
+14: 0
+15: 0
+23: 1
+10: 2
+17: 2
+25: 2
+22: 2
+11: 2
+3: 2
\ No newline at end of file
b
diff -r 000000000000 -r a03e97724306 test-data/uc_table.uc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/uc_table.uc Wed Sep 11 12:41:04 2019 -0400
b
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