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comparison ete_species_tree_generator.xml @ 3:077021c45b96 draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
author earlhaminst
date Mon, 12 Mar 2018 12:51:48 -0400
parents 03c10736e497
children f1eca1158f21
comparison
equal deleted inserted replaced
2:03c10736e497 3:077021c45b96
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <stdio> 7 <stdio>
8 <!-- Anything other than zero is an error --> 8 <!-- Anything other than zero is an error -->
9 <exit_code range="1:" /> 9 <exit_code range="1:" />
10 </stdio> 10 </stdio>
11 <command> 11 <command><![CDATA[
12 <![CDATA[
13 python '$__tool_directory__/ete_species_tree_generator.py' 12 python '$__tool_directory__/ete_species_tree_generator.py'
14 -s '$speciesFile' 13 -s '$speciesFile'
15 -d $database 14 -d $database
16 -o '$outputFile' 15 -o '$outputFile'
17 #if $output_format.treebest == 'yes' 16 #if $output_format.treebest == 'yes'
18 -f 8 17 -f 8
19 #else 18 #else
20 -f ${output_format.format_selector} 19 -f ${output_format.format_selector}
21 #end if 20 #end if
22 -t $output_format.treebest 21 -t $output_format.treebest
23 ]]> 22 ]]></command>
24 </command>
25 <inputs> 23 <inputs>
26 <param name="speciesFile" type="data" format="txt" label="Species file" help="List with one species per line" /> 24 <param name="speciesFile" type="data" format="txt" label="Species file" help="List with one species per line" />
27 <param name="database" type="data" format="sqlite" label="(ETE3) Taxonomy Database" help="The sqlite formatted Taxonomy used by ETE3 (which is derived from NCBI taxonomy)" /> 25 <param name="database" type="data" format="sqlite" label="(ETE3) Taxonomy Database" help="The sqlite formatted Taxonomy used by ETE3 (which is derived from NCBI taxonomy)" />
28 <conditional name="output_format"> 26 <conditional name="output_format">
29 <param name="treebest" type="select" label="Use in TreeBest" help="Select yes if specie tree to be used in TreeBest"> 27 <param name="treebest" type="select" label="Use in TreeBest" help="Select yes if specie tree to be used in TreeBest">
62 <has_text text=")root;" /> 60 <has_text text=")root;" />
63 </assert_contents> 61 </assert_contents>
64 </output> 62 </output>
65 </test> 63 </test>
66 </tests> 64 </tests>
67 <help> 65 <help><![CDATA[
68 <![CDATA[
69 Generate a species tree from a list of species using the `ETE Toolkit`_. 66 Generate a species tree from a list of species using the `ETE Toolkit`_.
70 67
71 .. _ETE Toolkit: http://etetoolkit.org/ 68 .. _ETE Toolkit: http://etetoolkit.org/
72 69
73 **Output format:** 70 **Output format:**
85 7 leaf branches + all names ((D:0.723274,F:0.567784)E,(B:0.279326,H:0.756049)B); 82 7 leaf branches + all names ((D:0.723274,F:0.567784)E,(B:0.279326,H:0.756049)B);
86 8 all names ((D,F)E,(B,H)B); 83 8 all names ((D,F)E,(B,H)B);
87 9 leaf names ((D,F),(B,H)); 84 9 leaf names ((D,F),(B,H));
88 100 topology only ((,),(,)); 85 100 topology only ((,),(,));
89 ======= ============================================= ======================================================================================== 86 ======= ============================================= ========================================================================================
90 ]]> 87 ]]></help>
91 </help>
92 <expand macro="citations" /> 88 <expand macro="citations" />
93 </tool> 89 </tool>