Mercurial > repos > earlhaminst > ete

annotate ete_homology_classifier.xml @ 12:dc32007a6b36 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit c568584f1eaa1366603b89db7e52994812f5d387
author earlhaminst
date Tue, 07 Jun 2022 08:58:05 +0000
parents 2db72467da51
children d40b9a7debe5
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
1 <tool id="ete_homology_classifier" name="Homology Classifier and Filter" version="@VERSION@">
8
16e925bf567e "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit ed32f2e6d8174873cefcbe141084f857f84b0586"
earlhaminst
parents: 5
diff changeset
2 <description>from a genetree using the ETE Toolkit</description>
5
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
3 <macros>
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
4 <import>ete_macros.xml</import>
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
5 <xml name="homologies_macro" token_label="" token_help="">
11
2db72467da51 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 67e136d433c0d925db362342919305b46fdffecd"
earlhaminst
parents: 8
diff changeset
6 <param name="homologies" type="select" multiple="true" optional="false" label="@LABEL@" help="@HELP@">
5
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
7 <option value="one-to-one" selected="true">one-to-one</option>
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
8 <option value="one-to-many" selected="true">one-to-many</option>
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
9 <option value="many-to-one" selected="true">many-to-one</option>
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
10 <option value="many-to-many" selected="true">many-to-many</option>
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
11 <option value="paralogs" selected="true">Paralogs</option>
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
12 </param>
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
13 </xml>
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
14 </macros>
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
15 <expand macro="requirements" />
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
16 <command detect_errors="exit_code">
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
17 <![CDATA[
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
18 python '$__tool_directory__/ete_homology_classifier.py'
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
19 --genetree '$genetreeFile'
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
20 --out_format '$format_type.out_format'
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
21 #if $format_type.homologies:
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
22 --filters $format_type.homologies
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
23 #end if
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
24 > $homology
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
25 ]]>
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
26 </command>
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
27 <inputs>
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
28 <param name="genetreeFile" type="data" format="nhx" label="GeneTree file" help="GeneTree in nhx format, where nodes are in form of geneid_species" />
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
29 <conditional name="format_type">
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
30 <param name="out_format" type="select" label="Output format">
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
31 <option value="tabular" selected="true">Tabular</option>
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
32 <option value="csv">One-line CSV</option>
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
33 </param>
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
34 <when value="tabular">
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
35 <expand macro="homologies_macro" label="Pair types to keep"/>
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
36 </when>
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
37 <when value="csv">
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
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" />
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
39 </when>
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
40 </conditional>
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
41 </inputs>
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
42 <outputs>
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
43 <data format="tabular" name="homology" label="${tool.name} on ${on_string}">
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
44 <change_format>
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
45 <when input="format_type.out_format" value="csv" format="csv" />
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
46 </change_format>
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
47 </data>
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
48 </outputs>
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
49 <tests>
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
50 <test>
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
51 <param name="genetreeFile" ftype="nhx" value="genetree.nhx" />
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
52 <param name="out_format" value="tabular"/>
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
53 <param name="homologies" value="one-to-one,one-to-many,many-to-one,many-to-many,paralogs" />
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
54 <output name="homology" file="11_homology.tabular" />
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
55 </test>
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
56 <test>
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
57 <param name="genetreeFile" ftype="nhx" value="11_genetree.nhx" />
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
58 <param name="out_format" value="csv"/>
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
59 <output name="homology" file="11_homology.csv" />
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
60 </test>
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
61 </tests>
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
62 <help>
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
63 <![CDATA[
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
64 Classify and filter Homology from single GeneTree by utilising the `ETE Toolkit`_.
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
65
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
66 .. _ETE Toolkit: http://etetoolkit.org/
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
67
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
68 **Output format:**
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
69
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
70 *tabular*:
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
71
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
72 ====================== ======================== ============
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
73 gene_1 gene_2 homology
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
74 ====================== ======================== ============
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
75 insr_rattusnorvegicus insr_musmusculus one-to-one
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
76 insr_rattusnorvegicus insr_homosapiens one-to-one
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
77 insr_rattusnorvegicus insr_pantroglodytes one-to-one
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
78 insr_rattusnorvegicus insr_susscrofa one-to-one
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
79 insr_musmusculus insr_homosapiens one-to-one
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
80 insr_musmusculus insr_pantroglodytes one-to-one
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
81 insr_musmusculus insr_susscrofa one-to-one
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
82 insr_homosapiens insr_pantroglodytes one-to-one
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
83 insr_homosapiens insr_susscrofa one-to-one
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
84 insr_pantroglodytes insr_susscrofa one-to-one
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
85 ====================== ======================== ============
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
86
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
87 \
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
88
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
89 *One-line CSV*::
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
90
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
91 insr_rattusnorvegicus,insr_musmusculus,insr_homosapiens,insr_pantroglodytes,insr_susscrofa
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
92 ]]>
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
93 </help>
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
94 <expand macro="citations" />
817031b8486d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit b97aee603b9acf29981719160e963a1efe2946d0
earlhaminst
parents:
diff changeset
95 </tool>