# HG changeset patch
# User iuc
# Date 1518778663 18000
# Node ID 83dc1b4ee3234aa5cce6f7669168cae39828e875
# Parent  4d1fb16ff86ab8eb74d938018b6e0e3b6d51e2c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit commit 8564cf195c7700975710c13f900a787e2801bb9d

diff -r 4d1fb16ff86a -r 83dc1b4ee323 get_term_id_vs_term_def.xml
--- a/get_term_id_vs_term_def.xml	Fri Nov 10 11:31:44 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,49 +0,0 @@
-<tool id="onto_tk_term_id_vs_term_def" name="Get all the term IDs and term definitions" version="@VERSION@.0">
-    <description>of a given OBO ontology</description>
-    <macros>
-        <import>onto_macros.xml</import>
-    </macros>
-    <expand macro="requirements" />
-    <command detect_errors="aggressive">
-        get_term_id_vs_term_def.pl
-        -f '$input' > '$output'
-    </command>
-    <inputs>
-        <expand macro="input_ontology" />
-    </inputs>
-    <outputs>
-        <data format="tabular" name="output">
-            <actions>
-                <action name="column_names" type="metadata" default="term ID,term definition" />
-            </actions>
-        </data>
-    </outputs>
-    <tests>
-        <test>
-            <param name="input" value="pre_cco_core.obo"/>
-            <output name="output" file="term_id_vs_term_def.tab"/>
-        </test>
-    </tests>
-    <help>
-
-.. class:: infomark
-
-Generates a flat file with two columns (TAB separated) with the term_id and term_definition from the elements of the given OBO ontology.
-
-
-**Example**
-
-If you ask for the term IDs and terms definitions of the Gene Ontology, you will get::
-
-  GO:0006285	The formation of an AP site, a deoxyribose sugar with a missing base, by DNA glycosylase which recognizes an altered base in DNA and catalyzes its hydrolytic removal. This sugar phosphate is the substrate recognized by the AP endonuclease, which cuts the DNA phosphodiester backbone at the 5' side of the altered site to leave a gap which is subsequently repaired.
-  GO:0043527	A multimeric protein complex involved in the methylation of specific nucleotides in tRNA.
-  GO:0005593	Any collagen polymer associated with collagen fibrils and in which the collagen monomers contain two or more relatively short triple-helical domains connected by non-triple-helical sequences; the acronym FACIT stands for fibril-associated collagen with interrupted triple helix.
-  GO:0015777	The directed movement of teichoic acid into, out of, within or between cells by means of some external agent such as a transporter or pore. Teichoic acid is any polymer occurring in the cell wall, membrane or capsule of Gram-positive bacteria and containing chains of glycerol phosphate or ribitol phosphate residues.
-  GO:0047104	Catalysis of the reaction: NAD+ + CoA + palmitaldehyde = NADH + palmityl-CoA.
-  GO:0018302	The incorporation of iron into a 4Fe-4S iron-sulfur cluster via tris-L-cysteinyl-L-N1'-histidino tetrairon tetrasulfide.
-  ...
-  ...
-
-    </help>
-    <expand macro="citations" />
-</tool>
diff -r 4d1fb16ff86a -r 83dc1b4ee323 term_id_vs_term_def.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/term_id_vs_term_def.xml	Fri Feb 16 05:57:43 2018 -0500
@@ -0,0 +1,49 @@
+<tool id="onto_tk_term_id_vs_term_def" name="Get all the term IDs and term definitions" version="@VERSION@.0">
+    <description>of a given OBO ontology</description>
+    <macros>
+        <import>onto_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="aggressive">
+        get_term_id_vs_term_def.pl
+        -f '$input' | sort > '$output'
+    </command>
+    <inputs>
+        <expand macro="input_ontology" />
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="pre_cco_core.obo"/>
+            <output name="output">
+                <assert_contents>
+                    <has_text text="Any process that modulates the frequency, rate or extent of the cell cycle process" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+
+.. class:: infomark
+
+Generates a flat file with two columns (TAB separated) with the term_id and term_definition from the elements of the given OBO ontology.
+
+
+**Example**
+
+If you ask for the term IDs and terms definitions of the Gene Ontology, you will get::
+
+  GO:0006285	The formation of an AP site, a deoxyribose sugar with a missing base, by DNA glycosylase which recognizes an altered base in DNA and catalyzes its hydrolytic removal. This sugar phosphate is the substrate recognized by the AP endonuclease, which cuts the DNA phosphodiester backbone at the 5' side of the altered site to leave a gap which is subsequently repaired.
+  GO:0043527	A multimeric protein complex involved in the methylation of specific nucleotides in tRNA.
+  GO:0005593	Any collagen polymer associated with collagen fibrils and in which the collagen monomers contain two or more relatively short triple-helical domains connected by non-triple-helical sequences; the acronym FACIT stands for fibril-associated collagen with interrupted triple helix.
+  GO:0015777	The directed movement of teichoic acid into, out of, within or between cells by means of some external agent such as a transporter or pore. Teichoic acid is any polymer occurring in the cell wall, membrane or capsule of Gram-positive bacteria and containing chains of glycerol phosphate or ribitol phosphate residues.
+  GO:0047104	Catalysis of the reaction: NAD+ + CoA + palmitaldehyde = NADH + palmityl-CoA.
+  GO:0018302	The incorporation of iron into a 4Fe-4S iron-sulfur cluster via tris-L-cysteinyl-L-N1'-histidino tetrairon tetrasulfide.
+  ...
+  ...
+
+    </help>
+    <expand macro="citations" />
+</tool>