Mercurial > repos > greg > plant_tribes_gene_family_scaffold_updater
comparison gene_family_scaffold_updater.xml @ 0:2b0906489073 draft default tip
Uploaded
author | greg |
---|---|
date | Tue, 21 Aug 2018 13:00:21 -0400 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:2b0906489073 |
---|---|
1 <tool id="plant_tribes_gene_family_scaffold_updater" name="Update PlantTribes scaffold" version="@WRAPPER_VERSION@.0.0"> | |
2 <description>with a new genome</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <requirements> | |
7 <requirement type="package" version="2.7.1">blast</requirement> | |
8 <requirement type="package" version="3.1b2">hmmer</requirement> | |
9 <requirement type="package" version="7.313">mafft</requirement> | |
10 <requirement type="package" version="5.22.0">perl</requirement> | |
11 <requirement type="package" version="1.641">perl-dbi</requirement> | |
12 <requirement type="package" version="3.5.3">perl-dbd-pg</requirement> | |
13 </requirements> | |
14 <command detect_errors="exit_code"><![CDATA[ | |
15 perl '$__tool_directory__/gene_family_scaffold_updater.pl' | |
16 --database_connection_string '$__app__.config.plant_tribes_database_connection' | |
17 --proteins '$input_proteins' | |
18 --coding_sequences '$input_coding_sequences' | |
19 --scaffold '$GALAXY_DATA_INDEX_DIR/plant_tribes/scaffolds/$scaffold' | |
20 --species_name '$species_name' | |
21 --species_code '$species_code' | |
22 --species_family '$species_family' | |
23 --species_order '$species_order' | |
24 --species_group '$species_group' | |
25 --species_clade '$species_clade' | |
26 --rooting_order_species_code '$rooting_order_species_code' | |
27 --num_threads \${GALAXY_SLOTS:-4} | |
28 &>'$output']]></command> | |
29 <inputs> | |
30 <expand macro="param_scaffold"/> | |
31 <param name="input_proteins" format="fasta" type="data" label="Proteins fasta file"> | |
32 <validator type="empty_field"/> | |
33 </param> | |
34 <param name="input_coding_sequences" format="fasta" type="data" label="Coding sequences fasta file"> | |
35 <validator type="empty_field"/> | |
36 </param> | |
37 <param name="species_name" type="text" value="" label="Species name"> | |
38 <validator type="empty_field"/> | |
39 </param> | |
40 <param name="species_code" type="text" value="" label="Species code"> | |
41 <validator type="empty_field"/> | |
42 </param> | |
43 <param name="species_family" type="text" value="" label="Species family"> | |
44 <validator type="empty_field"/> | |
45 </param> | |
46 <param name="species_order" type="text" value="" label="Species order"> | |
47 <validator type="empty_field"/> | |
48 </param> | |
49 <param name="species_group" type="text" value="" label="Species group"> | |
50 <validator type="empty_field"/> | |
51 </param> | |
52 <param name="species_clade" type="text" value="" label="Species clade"> | |
53 <validator type="empty_field"/> | |
54 </param> | |
55 <param name="rooting_order_species_code" type="text" label="Species code for rooting order" help="The new species above will be placed immediately after this species code in the rooting order configuration file"> | |
56 <validator type="empty_field"/> | |
57 </param> | |
58 </inputs> | |
59 <outputs> | |
60 <data name="output" format="txt"/> | |
61 </outputs> | |
62 <tests> | |
63 <test> | |
64 <!--Testing this tool is a bit difficult at the current time.--> | |
65 </test> | |
66 </tests> | |
67 <help> | |
68 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary | |
69 analyses of genome-scale gene families and transcriptomes. This tool adds a new genome to a scaffold installed into Galaxy | |
70 by the PlantTribes Scaffolds Downloader data manager tool. | |
71 | |
72 ----- | |
73 | |
74 **Required options** | |
75 | |
76 * **Proteins fasta file** - amino acids (proteins) sequences fasta file for new genome. | |
77 * **Coding sequences fasta file** - corresponding coding sequences (CDS) fasta file for new genome. | |
78 * **Gene family scaffold** - one of the PlantTribes gene family scaffolds, installed into Galaxy by the PlantTribes Scaffold Data Manager tool. | |
79 </help> | |
80 <citations> | |
81 <citation type="bibtex"> | |
82 @unpublished{None, | |
83 author = {Eric Wafula}, | |
84 title = {None}, | |
85 year = {None}, | |
86 eprint = {None}, | |
87 url = {https://github.com/dePamphilis/PlantTribes}} | |
88 </citation> | |
89 </citations> | |
90 </tool> | |
91 |