Mercurial > repos > iuc > intermine_galaxy_exchange
comparison intermine_galaxy_exchange.xml @ 0:3d09554c8a47 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange commit 562a034dbd23e37f1a994b1987a7cc0ec08be1a2
author | iuc |
---|---|
date | Mon, 09 Jul 2018 14:11:23 -0400 |
parents | |
children | 5673140f2d5a |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:3d09554c8a47 |
---|---|
1 <tool id="galaxy_intermine_exchange" name="Create InterMine Interchange" version="0.0.1"> | |
2 <description>Dataset</description> | |
3 <requirements> | |
4 <requirement type="package" version="8.25">coreutils</requirement> | |
5 </requirements> | |
6 <command detect_errors="exit_code"><![CDATA[ | |
7 awk -F \$'\t' ' { | |
8 #if str($feature_text): | |
9 f = "${feature_text}"; | |
10 #else: | |
11 f = \$${feature_column}; | |
12 #end if | |
13 | |
14 #if str($feature_id_text): | |
15 i = "${feature_id_text}"; | |
16 #else: | |
17 i = \$${feature_id_column}; | |
18 #end if | |
19 | |
20 #if str($organism_text): | |
21 o = "${organism_text}"; | |
22 #elif $organism_column: | |
23 o = \$${organism_column}; | |
24 #else: | |
25 o= ""; | |
26 #end if | |
27 | |
28 print f, i, o; } ' OFS=\$'\t' '${input_tabular}' > '${intermine_output}' | |
29 ]]> | |
30 </command> | |
31 <inputs> | |
32 <param name="input_tabular" type="data" format="txt" multiple="False" optional="False" label="Tabular file"/> | |
33 <param name="feature_column" type="data_column" data_ref="input_tabular" optional="False" label="Feature Type column" value="1"/> | |
34 <param name="feature_text" type="text" value="" optional="True" label="Feature Type" help="Optional, will override column selection with static text value"/> | |
35 <param name="feature_id_column" type="data_column" data_ref="input_tabular" optional="False" label="Feature column Identifier" value="2"/> | |
36 <param name="feature_id_text" type="text" value="" optional="True" label="Feature Type" help="Optional, will override column selection with static text value"/> | |
37 <param name="organism_column" type="data_column" data_ref="input_tabular" optional="True" label="Feature column Identifier" value="3"/> | |
38 <param name="organism_text" type="text" value="" optional="True" label="Feature Type" help="Optional, will override column selection with static text value"/> | |
39 </inputs> | |
40 <outputs> | |
41 <data format="intermine_tabular" name="intermine_output"/> | |
42 </outputs> | |
43 <tests> | |
44 <test> | |
45 <param name="input_tabular" value="intermine-format-example.tsv" ftype="tabular"/> | |
46 <param name="feature_column" value="1"/> | |
47 <param name="feature_id_text" value=""/> | |
48 <param name="feature_id_column" value="2"/> | |
49 <param name="feature_text" value=""/> | |
50 <param name="forganism_column" value="2"/> | |
51 <param name="organism_text" value=""/> | |
52 <output name="tabular_output" file="intermine-format-example.tsv" ftype="intermine_tabular"/> | |
53 </test> | |
54 </tests> | |
55 <help> | |
56 <![CDATA[ | |
57 InterMine-Galaxy exchange format | |
58 ================================ | |
59 This file format exists as an intermediate step to import from Galaxy to InterMines and is not in itself a data format intended to be used for data storage or any purpose apart from Galaxy->InterMine interoperability. | |
60 | |
61 This file has two mandatory columns and one optional column | |
62 | |
63 Column 1 (mandatory) | |
64 -------------------- | |
65 **Type of identifier**, e.g. `Gene` or `Protein`. Must be a class in the `InterMine data model`_. Gene or Protein is always a safe option. | |
66 | |
67 Column 2 (mandatory) | |
68 -------------------- | |
69 **Identifier** this could be, as an example, a gene symbol like `GATA1` or another other identifier, e.g. `FBGN0000099` or perhaps a protein accession, or some other identifier. | |
70 | |
71 Column 3 (optional) | |
72 ------------------- | |
73 **Organism name** - e.g. `H. sapiens` or `Drosophila melanogaster`. This is optional and does not have to be precise, but is good to provide if it is known. | |
74 | |
75 ---- | |
76 | |
77 For additional information, please see: | |
78 | |
79 - https://github.com/intermine/galaxy-integration/blob/master/intermine-file-format/intermine-format-definition.md | |
80 - https://raw.githubusercontent.com/intermine/galaxy-integration/master/intermine-file-format/intermine-format-example.tsv | |
81 | |
82 .. _InterMine data model: http://intermine.readthedocs.io/en/latest/data-model/model/#a-short-example | |
83 ]]> | |
84 </help> | |
85 <citations> | |
86 <citation type="doi">10.1093/nar/gku301</citation> | |
87 </citations> | |
88 </tool> |