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comparison phylogeny_load_tree.xml @ 0:b44be6289549 draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
author gga
date Thu, 21 Jun 2018 08:42:08 -0400
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-1:000000000000 0:b44be6289549
1 <?xml version="1.0"?>
2 <tool id="phylogeny_load_tree" name="Chado load trees" version="@WRAPPER_VERSION@.0">
3 <description>for phylogeny module</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <code file="chado.py"/>
9 <command detect_errors="aggressive"><![CDATA[
10 @AUTH@
11
12 chakin phylogeny load_tree
13 '$newick'
14 '$analysis_id'
15
16 #if $name:
17 --name '$name'
18 #end if
19 #if $xref_db:
20 --xref_db '$xref_db'
21 #end if
22 #if $xref_accession:
23 --xref_accession '$xref_accession'
24 #end if
25 #if $match_on_name:
26 $match_on_name
27 #end if
28 #if $prefix:
29 --prefix '$prefix'
30 #end if
31
32 | jq -S . > $results
33 ]]></command>
34 <inputs>
35 <!-- arguments -->
36 <param name="newick" label="Newick" argument="newick" type="data" format="txt" help="Newick file to load (or directory containing multiple newick files to load)" />
37 <param argument="--analysis_id"
38 type="select"
39 dynamic_options="list_analyses()"
40 label="Analysis" />
41
42 <!-- options -->
43 <param name="name" label="Name" argument="name" type="text" help="The name given to the phylotree entry in the database" />
44 <param name="xref_db" label="Xref db" argument="xref_db" value="null" type="text" help="The name of the db to link dbxrefs for the trees" />
45 <param name="xref_accession" label="Xref Accession" argument="xref_accession" type="text" help="The accession to use for dbxrefs for the trees (assumed same as name unless otherwise specified)" />
46 <param name="match_on_name" label="Match On Name" argument="match_on_name" type="boolean" truevalue="--match_on_name" falsevalue="" help="Match polypeptide features using their name instead of their uniquename" />
47 <param name="prefix" label="Prefix" argument="prefix" type="text" help="Comma-separated list of prefix to be removed from identifiers (e.g species prefixes when loading OrthoFinder output)" />
48 <expand macro="wait_for"/>
49
50 </inputs>
51 <outputs>
52 <data format="json" name="results"/>
53 </outputs>
54 <help>
55 Load a phylogenetic tree (Newick format) into Chado db
56
57 @HELP@
58 </help>
59 </tool>