Mercurial > repos > gga > chado_phylogeny_load_tree

annotate phylogeny_load_tree.xml @ 14:2df919635d8a 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 bc69ce09372c8c2701b726c326e671af279adb4d
author gga
date Thu, 11 Jul 2019 08:34:19 -0400
parents 8d44d72730ed
children 16753eb6b170
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
b44be6289549 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
1 <?xml version="1.0"?>
14
2df919635d8a planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit bc69ce09372c8c2701b726c326e671af279adb4d
gga
parents: 13
diff changeset
2 <tool id="phylogeny_load_tree" name="Chado load trees" version="@WRAPPER_VERSION@.2">
0
b44be6289549 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
3 <description>for phylogeny module</description>
b44be6289549 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
4 <macros>
b44be6289549 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
5 <import>macros.xml</import>
b44be6289549 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
6 </macros>
b44be6289549 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
7 <expand macro="requirements"/>
b44be6289549 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
8 <code file="chado.py"/>
b44be6289549 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
9 <command detect_errors="aggressive"><![CDATA[
10
2e38005d5205 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents: 8
diff changeset
10 #if $input.input_type == "archive":
2e38005d5205 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents: 8
diff changeset
11 mkdir 'newick_arch/' &&
2e38005d5205 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents: 8
diff changeset
12 tar -C 'newick_arch/' -xzvf '${input.newick_arch}' > /dev/null &&
0
b44be6289549 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
13 #end if
10
2e38005d5205 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents: 8
diff changeset
14
13
8d44d72730ed planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 12
diff changeset
15 @START_PSQL@ &&
12
4812a8770a8c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 703eb9ed2bdf6380db14c0af6a7cb1a85fab6d3f
gga
parents: 11
diff changeset
16
10
2e38005d5205 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents: 8
diff changeset
17 chakin phylogeny load_tree
5
31f6e0f70e41 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit a1460ea4dbbd5c6ff6576b2d6db8aaa04b0061a7
gga
parents: 0
diff changeset
18
31f6e0f70e41 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit a1460ea4dbbd5c6ff6576b2d6db8aaa04b0061a7
gga
parents: 0
diff changeset
19 $match_on_name
31f6e0f70e41 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit a1460ea4dbbd5c6ff6576b2d6db8aaa04b0061a7
gga
parents: 0
diff changeset
20
0
b44be6289549 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
21 #if $prefix:
b44be6289549 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
22 --prefix '$prefix'
b44be6289549 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
23 #end if
b44be6289549 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
24
10
2e38005d5205 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents: 8
diff changeset
25 #if $xref_db:
2e38005d5205 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents: 8
diff changeset
26 --xref_db '$xref_db'
2e38005d5205 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents: 8
diff changeset
27 #end if
2e38005d5205 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents: 8
diff changeset
28
12
4812a8770a8c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 703eb9ed2bdf6380db14c0af6a7cb1a85fab6d3f
gga
parents: 11
diff changeset
29 #if $input.input_type == "file":
10
2e38005d5205 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents: 8
diff changeset
30 #if $name:
2e38005d5205 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents: 8
diff changeset
31 --name '$name'
2e38005d5205 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents: 8
diff changeset
32 #end if
2e38005d5205 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents: 8
diff changeset
33
2e38005d5205 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents: 8
diff changeset
34 #if $xref_accession:
2e38005d5205 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents: 8
diff changeset
35 --xref_accession '$xref_accession'
2e38005d5205 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents: 8
diff changeset
36 #end if
2e38005d5205 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents: 8
diff changeset
37
2e38005d5205 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents: 8
diff changeset
38 '$newick'
2e38005d5205 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents: 8
diff changeset
39 #else
2e38005d5205 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents: 8
diff changeset
40 'newick_arch/'
2e38005d5205 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents: 8
diff changeset
41 #end if
2e38005d5205 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents: 8
diff changeset
42
12
4812a8770a8c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 703eb9ed2bdf6380db14c0af6a7cb1a85fab6d3f
gga
parents: 11
diff changeset
43 '$analysis_id' > '$results'
13
8d44d72730ed planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 12
diff changeset
44
14
2df919635d8a planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit bc69ce09372c8c2701b726c326e671af279adb4d
gga
parents: 13
diff changeset
45 @ZIP_PSQL@
0
b44be6289549 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
46 ]]></command>
b44be6289549 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
47 <inputs>
13
8d44d72730ed planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 12
diff changeset
48 <expand macro="psql_target"/>
8
2b4c9d801a1e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit f5c5d81fc9781371e12b91c0d609b9201587cda5
gga
parents: 5
diff changeset
49 <param argument="analysis_id"
0
b44be6289549 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
50 type="select"
b44be6289549 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
51 dynamic_options="list_analyses()"
b44be6289549 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
52 label="Analysis" />
b44be6289549 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
53
10
2e38005d5205 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents: 8
diff changeset
54 <conditional name="input">
2e38005d5205 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents: 8
diff changeset
55 <param name="input_type" type="select" label="Input type">
2e38005d5205 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents: 8
diff changeset
56 <option value="file" selected="true">Newick file</option>
2e38005d5205 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents: 8
diff changeset
57 <option value="archive">Tar.gz archive of Newick files</option>
2e38005d5205 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents: 8
diff changeset
58 </param>
2e38005d5205 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents: 8
diff changeset
59 <when value="file">
2e38005d5205 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents: 8
diff changeset
60 <param name="newick" label="Newick" argument="newick" type="data" format="newick" help="Newick file to load" />
2e38005d5205 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents: 8
diff changeset
61 <param name="name" label="Name" argument="--name" type="text" help="The name given to the phylotree entry in the database" />
2e38005d5205 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents: 8
diff changeset
62 <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)" />
2e38005d5205 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents: 8
diff changeset
63 </when>
2e38005d5205 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents: 8
diff changeset
64 <when value="archive">
2e38005d5205 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents: 8
diff changeset
65 <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)" />
2e38005d5205 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents: 8
diff changeset
66 </when>
2e38005d5205 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents: 8
diff changeset
67 </conditional>
2e38005d5205 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents: 8
diff changeset
68
0
b44be6289549 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
69 <!-- options -->
8
2b4c9d801a1e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit f5c5d81fc9781371e12b91c0d609b9201587cda5
gga
parents: 5
diff changeset
70 <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" />
2b4c9d801a1e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit f5c5d81fc9781371e12b91c0d609b9201587cda5
gga
parents: 5
diff changeset
71 <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" />
2b4c9d801a1e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit f5c5d81fc9781371e12b91c0d609b9201587cda5
gga
parents: 5
diff changeset
72 <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)" />
0
b44be6289549 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
73 <expand macro="wait_for"/>
b44be6289549 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
74
b44be6289549 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
75 </inputs>
b44be6289549 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
76 <outputs>
12
4812a8770a8c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 703eb9ed2bdf6380db14c0af6a7cb1a85fab6d3f
gga
parents: 11
diff changeset
77 <data format="txt" name="results"/>
13
8d44d72730ed planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 12
diff changeset
78 <data format="postgresql" name="outfile" from_work_dir="postgresql_out.tar.bz2" label="${tool.name} on ${on_string}">
8d44d72730ed planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 12
diff changeset
79 <filter>psql_target['method'] == "pgtools"</filter>
8d44d72730ed planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 12
diff changeset
80 </data>
0
b44be6289549 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
81 </outputs>
b44be6289549 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
82 <help>
b44be6289549 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
83 Load a phylogenetic tree (Newick format) into Chado db
b44be6289549 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
84
b44be6289549 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
85 @HELP@
b44be6289549 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
86 </help>
b44be6289549 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
87 </tool>