Mercurial > repos > gga > chado_phylogeny_load_tree

comparison phylogeny_load_tree.xml @ 12:4812a8770a8c draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 703eb9ed2bdf6380db14c0af6a7cb1a85fab6d3f
author gga
date Wed, 27 Mar 2019 17:32:01 -0400
parents 8f3b6bb4c05c
children 8d44d72730ed
comparison
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11:8f3b6bb4c05c 12:4812a8770a8c
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@
11
12 #if $input.input_type == "archive": 10 #if $input.input_type == "archive":
13 mkdir 'newick_arch/' && 11 mkdir 'newick_arch/' &&
14 tar -C 'newick_arch/' -xzvf '${input.newick_arch}' > /dev/null && 12 tar -C 'newick_arch/' -xzvf '${input.newick_arch}' > /dev/null &&
15 #end if 13 #end if
14
15 @AUTH@
16 16
17 chakin phylogeny load_tree 17 chakin phylogeny load_tree
18 18
19 $match_on_name 19 $match_on_name
20 20
24 24
25 #if $xref_db: 25 #if $xref_db:
26 --xref_db '$xref_db' 26 --xref_db '$xref_db'
27 #end if 27 #end if
28 28
29 #if $input.input_type == "archive": 29 #if $input.input_type == "file":
30 #if $name: 30 #if $name:
31 --name '$name' 31 --name '$name'
32 #end if 32 #end if
33 33
34 #if $xref_accession: 34 #if $xref_accession:
38 '$newick' 38 '$newick'
39 #else 39 #else
40 'newick_arch/' 40 'newick_arch/'
41 #end if 41 #end if
42 42
43 '$analysis_id' 43 '$analysis_id' > '$results'
44
45 | jq -S . > '$results'
46 ]]></command> 44 ]]></command>
47 <inputs> 45 <inputs>
48 <param argument="analysis_id" 46 <param argument="analysis_id"
49 type="select" 47 type="select"
50 dynamic_options="list_analyses()" 48 dynamic_options="list_analyses()"
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)" /> 69 <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)" />
72 <expand macro="wait_for"/> 70 <expand macro="wait_for"/>
73 71
74 </inputs> 72 </inputs>
75 <outputs> 73 <outputs>
76 <data format="json" name="results"/> 74 <data format="txt" name="results"/>
77 </outputs> 75 </outputs>
78 <help> 76 <help>
79 Load a phylogenetic tree (Newick format) into Chado db 77 Load a phylogenetic tree (Newick format) into Chado db
80 78
81 @HELP@ 79 @HELP@