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comparison ete_homology_classifier.xml @ 5:817031b8486d draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
author earlhaminst
date Thu, 10 May 2018 06:15:17 -0400
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children 16e925bf567e
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4:87b6de3ef63e 5:817031b8486d
1 <tool id="ete_homology_classifier" name="Homology Classifier and Filter" version="@VERSION@">
2 <description>from a genetree utilising the ETE Toolkit</description>
3 <macros>
4 <import>ete_macros.xml</import>
5 <xml name="homologies_macro" token_label="" token_help="">
6 <param name="homologies" type="select" multiple="true" optional="false" display="checkboxes" label="@LABEL@" help="@HELP@">
7 <option value="one-to-one" selected="true">one-to-one</option>
8 <option value="one-to-many" selected="true">one-to-many</option>
9 <option value="many-to-one" selected="true">many-to-one</option>
10 <option value="many-to-many" selected="true">many-to-many</option>
11 <option value="paralogs" selected="true">Paralogs</option>
12 </param>
13 </xml>
14 </macros>
15 <expand macro="requirements" />
16 <command detect_errors="exit_code">
17 <![CDATA[
18 python '$__tool_directory__/ete_homology_classifier.py'
19 --genetree '$genetreeFile'
20 --out_format '$format_type.out_format'
21 #if $format_type.homologies:
22 --filters $format_type.homologies
23 #end if
24 > $homology
25 ]]>
26 </command>
27 <inputs>
28 <param name="genetreeFile" type="data" format="nhx" label="GeneTree file" help="GeneTree in nhx format, where nodes are in form of geneid_species" />
29 <conditional name="format_type">
30 <param name="out_format" type="select" label="Output format">
31 <option value="tabular" selected="true">Tabular</option>
32 <option value="csv">One-line CSV</option>
33 </param>
34 <when value="tabular">
35 <expand macro="homologies_macro" label="Pair types to keep"/>
36 </when>
37 <when value="csv">
38 <expand macro="homologies_macro" label="Allowed homology types for the GeneTree" help="If the GeneTree contains any other homology type, then the output will be empty" />
39 </when>
40 </conditional>
41 </inputs>
42 <outputs>
43 <data format="tabular" name="homology" label="${tool.name} on ${on_string}">
44 <change_format>
45 <when input="format_type.out_format" value="csv" format="csv" />
46 </change_format>
47 </data>
48 </outputs>
49 <tests>
50 <test>
51 <param name="genetreeFile" ftype="nhx" value="genetree.nhx" />
52 <param name="out_format" value="tabular"/>
53 <param name="homologies" value="one-to-one,one-to-many,many-to-one,many-to-many,paralogs" />
54 <output name="homology" file="11_homology.tabular" />
55 </test>
56 <test>
57 <param name="genetreeFile" ftype="nhx" value="11_genetree.nhx" />
58 <param name="out_format" value="csv"/>
59 <output name="homology" file="11_homology.csv" />
60 </test>
61 </tests>
62 <help>
63 <![CDATA[
64 Classify and filter Homology from single GeneTree by utilising the `ETE Toolkit`_.
65
66 .. _ETE Toolkit: http://etetoolkit.org/
67
68 **Output format:**
69
70 *tabular*:
71
72 ====================== ======================== ============
73 gene_1 gene_2 homology
74 ====================== ======================== ============
75 insr_rattusnorvegicus insr_musmusculus one-to-one
76 insr_rattusnorvegicus insr_homosapiens one-to-one
77 insr_rattusnorvegicus insr_pantroglodytes one-to-one
78 insr_rattusnorvegicus insr_susscrofa one-to-one
79 insr_musmusculus insr_homosapiens one-to-one
80 insr_musmusculus insr_pantroglodytes one-to-one
81 insr_musmusculus insr_susscrofa one-to-one
82 insr_homosapiens insr_pantroglodytes one-to-one
83 insr_homosapiens insr_susscrofa one-to-one
84 insr_pantroglodytes insr_susscrofa one-to-one
85 ====================== ======================== ============
86
87 \
88
89 *One-line CSV*::
90
91 insr_rattusnorvegicus,insr_musmusculus,insr_homosapiens,insr_pantroglodytes,insr_susscrofa
92 ]]>
93 </help>
94 <expand macro="citations" />
95 </tool>