Mercurial > repos > gga > chado_phylogeny_load_tree

comparison phylogeny_load_tree.xml @ 10:2e38005d5205 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
author gga
date Mon, 25 Feb 2019 06:04:40 -0500
parents 2b4c9d801a1e
children 8f3b6bb4c05c
comparison
equal deleted inserted replaced
9:d344316d56b5 10:2e38005d5205
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="phylogeny_load_tree" name="Chado load trees" version="@WRAPPER_VERSION@.0"> 2 <tool id="phylogeny_load_tree" name="Chado load trees" version="@WRAPPER_VERSION@.1">
3 <description>for phylogeny module</description> 3 <description>for phylogeny module</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <code file="chado.py"/> 8 <code file="chado.py"/>
9 <command detect_errors="aggressive"><![CDATA[ 9 <command detect_errors="aggressive"><![CDATA[
10 @AUTH@ 10 @AUTH@
11 11
12 #if $input.input_type == "archive":
13 mkdir 'newick_arch/' &&
14 tar -C 'newick_arch/' -xzvf '${input.newick_arch}' > /dev/null &&
15 #end if
16
12 chakin phylogeny load_tree 17 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 18
26 $match_on_name 19 $match_on_name
27 20
28 #if $prefix: 21 #if $prefix:
29 --prefix '$prefix' 22 --prefix '$prefix'
30 #end if 23 #end if
31 24
25 #if $xref_db:
26 --xref_db '$xref_db'
27 #end if
28
29 #if $input.input_type == "archive":
30 #if $name:
31 --name '$name'
32 #end if
33
34 #if $xref_accession:
35 --xref_accession '$xref_accession'
36 #end if
37
38 '$newick'
39 #else
40 'newick_arch/'
41 #end if
42
43 '$analysis_id'
44
32 | jq -S . > $results 45 | jq -S . > $results
33 ]]></command> 46 ]]></command>
34 <inputs> 47 <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" 48 <param argument="analysis_id"
38 type="select" 49 type="select"
39 dynamic_options="list_analyses()" 50 dynamic_options="list_analyses()"
40 label="Analysis" /> 51 label="Analysis" />
41 52
53 <conditional name="input">
54 <param name="input_type" type="select" label="Input type">
55 <option value="file" selected="true">Newick file</option>
56 <option value="archive">Tar.gz archive of Newick files</option>
57 </param>
58 <when value="file">
59 <param name="newick" label="Newick" argument="newick" type="data" format="newick" help="Newick file to load" />
60 <param name="name" label="Name" argument="--name" type="text" help="The name given to the phylotree entry in the database" />
61 <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)" />
62 </when>
63 <when value="archive">
64 <param name="newick_arch" label="Newicks archive" type="data" format="tar" help="Archive of Newick files to load (must be at the root of the archive)" />
65 </when>
66 </conditional>
67
42 <!-- options --> 68 <!-- 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" /> 69 <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" /> 70 <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)" /> 71 <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"/> 72 <expand macro="wait_for"/>
49 73
50 </inputs> 74 </inputs>