Mercurial > repos > brinkmanlab > extract_tree_order

annotate extract_tree_order.xml @ 1:ddf5427278ee draft

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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit a7380cf90205de589a64fe0105ea957402d62300"
author brinkmanlab
date Tue, 16 Jun 2020 12:50:07 -0400
parents e9f04f5172e4
children eb980e8bb133
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e9f04f5172e4 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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1 <tool id="extract-tree-order" name="BioPython Phylo Parse Newick Leaf Order" version="1.0" profile="16.04">
e9f04f5172e4 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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2 <description>Convert a newick tree to an ordered list of its leaves</description>
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3 <edam_topics>
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4 <edam_topic>topic_0084</edam_topic>
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5 <edam_topic>topic_0091</edam_topic>
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6 </edam_topics>
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7 <edam_operations>
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8 <edam_operation>operation_0326</edam_operation>
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9 <edam_operation>operation_3434</edam_operation>
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10 </edam_operations>
e9f04f5172e4 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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11 <requirements>
e9f04f5172e4 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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12 <requirement type="package" version="3.7">python</requirement>
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ddf5427278ee "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit a7380cf90205de589a64fe0105ea957402d62300"
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13 <requirement type="package" version="1.76">biopython</requirement>
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14 </requirements>
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15 <command detect_errors="aggressive"><![CDATA[
e9f04f5172e4 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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16 python -c \$'from Bio import Phylo\nfor clade in Phylo.read("$input", "newick").get_terminals(order="preorder"): print(clade.name)' > '$output'
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17 ]]></command>
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18 <inputs>
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19 <param name="input" type="data" format="newick" label="Input" />
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20 </inputs>
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21 <outputs>
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22 <data name="output" format="txt" />
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23 </outputs>
e9f04f5172e4 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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24 <tests>
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25 <test expect_num_outputs="1">
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26 <param name="input" value="test-data/test.newick" ftype="newick" />
e9f04f5172e4 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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27 <output name="output" file="test-data/output.txt" ftype="txt" />
e9f04f5172e4 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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28 </test>
e9f04f5172e4 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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29 </tests>
e9f04f5172e4 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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30 <help><![CDATA[
e9f04f5172e4 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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31 Convert a newick tree to an ordered list of its leaves as determined by BioPython.Phylo 'preorder'.
e9f04f5172e4 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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32
e9f04f5172e4 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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33 This is useful when tree order affects order of processing of the related data.
e9f04f5172e4 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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34
e9f04f5172e4 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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35 For example, you may want to do pairwise alignment of the sequences for adjacent leaves.
e9f04f5172e4 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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e9f04f5172e4 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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37 `('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);`
e9f04f5172e4 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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38
e9f04f5172e4 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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39 returns
e9f04f5172e4 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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40
e9f04f5172e4 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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41 ```
e9f04f5172e4 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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42 NC_008463
e9f04f5172e4 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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43 NC_002516
e9f04f5172e4 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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44 NC_018080
e9f04f5172e4 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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45 NZ_CH482384
e9f04f5172e4 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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46 NC_011770
e9f04f5172e4 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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47 NZ_CP006982
e9f04f5172e4 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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48 NC_023066
e9f04f5172e4 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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49 ```
e9f04f5172e4 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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50 ]]></help>
e9f04f5172e4 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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51 <citations>
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52 <citation type="doi">10.5281/zenodo.3364789</citation>
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53 </citations>
e9f04f5172e4 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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54 </tool>