changeset 0:e9f04f5172e4 draft

"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/extract_tree_order.xml	Fri Jan 24 17:35:19 2020 -0500
@@ -0,0 +1,54 @@
+<tool id="extract-tree-order" name="BioPython Phylo Parse Newick Leaf Order" version="1.0" profile="16.04">
+    <description>Convert a newick tree to an ordered list of its leaves</description>
+    <edam_topics>
+        <edam_topic>topic_0084</edam_topic>
+        <edam_topic>topic_0091</edam_topic>
+    </edam_topics>
+    <edam_operations>
+        <edam_operation>operation_0326</edam_operation>
+        <edam_operation>operation_3434</edam_operation>
+    </edam_operations>
+    <requirements>
+        <requirement type="package" version="3.7">python</requirement>
+        <requirement type="package" version="1.73">biopython</requirement>
+    </requirements>
+    <command detect_errors="aggressive"><![CDATA[
+        python -c \$'from Bio import Phylo\nfor clade in Phylo.read("$input", "newick").get_terminals(order="preorder"): print(clade.name)' > '$output'
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="newick" label="Input" />
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input" value="test-data/test.newick" ftype="newick" />
+            <output name="output" file="test-data/output.txt" ftype="txt" />
+        </test>
+    </tests>
+    <help><![CDATA[
+        Convert a newick tree to an ordered list of its leaves as determined by BioPython.Phylo 'preorder'.
+        
+        This is useful when tree order affects order of processing of the related data.
+        
+        For example, you may want to do pairwise alignment of the sequences for adjacent leaves.
+        
+        `('NC_008463':1.25269,('NC_002516':0.21042,'NC_018080':0.20913)0.940:0.00444,('NZ_CH482384':0.24749,('NC_011770':0.00035,('NZ_CP006982':0.00036,'NC_023066':0.00018)0.940:0.00019)1.000:0.18245)0.990:0.01335);`
+        
+        returns
+        
+        ```
+        NC_008463
+        NC_002516
+        NC_018080
+        NZ_CH482384
+        NC_011770
+        NZ_CP006982
+        NC_023066
+        ```
+    ]]></help>
+    <citations>
+        <citation type="doi">10.5281/zenodo.3364789</citation>
+    </citations>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.txt	Fri Jan 24 17:35:19 2020 -0500
@@ -0,0 +1,7 @@
+NC_008463
+NC_002516
+NC_018080
+NZ_CH482384
+NC_011770
+NZ_CP006982.ref
+NC_023066

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test.newick	Fri Jan 24 17:35:19 2020 -0500
@@ -0,0 +1,1 @@
+('NC_008463':1.25269,('NC_002516':0.21042,'NC_018080':0.20913)0.940:0.00444,('NZ_CH482384':0.24749,('NC_011770':0.00035,('NZ_CP006982.ref':0.00036,'NC_023066':0.00018)0.940:0.00019)1.000:0.18245)0.990:0.01335);