Mercurial > repos > gga > askomics_integrate

comparison askomics.xml @ 0:d2aeb7a02bb2 draft default tip

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics commit f745b23c84a615bf434d717c8c0e553a012f0268
author gga
date Mon, 11 Sep 2017 05:48:41 -0400
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-1:000000000000 0:d2aeb7a02bb2
1 <?xml version="1.0"?>
2 <tool id="askomics_integrate" name="AskOmics" version="@WRAPPER_VERSION@">
3 <description>Data integration</description>
4
5 <macros>
6 <import>macros.xml</import>
7 </macros>
8
9 <expand macro='requirements' />
10
11 <stdio>
12 <exit_code range="1:" />
13 </stdio>
14
15 <command><![CDATA[
16 askocli integrate
17
18 #if @URL@
19 -a @URL@
20 #else
21 -a @ENV_URL@
22 #end if
23
24 --file-type '$input_format.format'
25
26 #if $input_format.format == "csv"
27
28 #if $input_format.opt.headers
29 --headers $input_format.opt.headers
30 #end if
31
32 #if $input_format.opt.col_type
33 -c $input_format.opt.col_type
34 #end if
35
36 #if $input_format.opt.key_col
37 --key-columns $input_format.opt.key_col
38 #end if
39
40 #if $input_format.opt.dis_col
41 --disabled-columns $input_format.opt.dis_col
42 #end if
43
44 #end if
45
46 #if $input_format.format == "gff"
47 -e $input_format.ent
48 -t '$input_format.tax'
49 #end if
50
51 #if $input_format.format == "bed"
52 --entity-name $input_format.ent_name
53 -t '$input_format.tax'
54 #end if
55
56 #if $advanced.uri
57 --uri $advanced.uri
58 #end if
59
60 $advanced.public
61
62 -k @APIKEY@
63
64 '$input'
65 > '$output'
66 ]]></command>
67
68 <inputs>
69 <expand macro='askomics_loc' />
70 <expand macro='askomics_auth' />
71
72 <conditional name="input_format">
73 <param type="select" name="format" label="Input format">
74 <option value="csv">CSV/TSV</option>
75 <option value="gff">GFF</option>
76 <option value="ttl">Turtle</option>
77 <option value="bed">BED</option>
78 </param>
79 <when value="csv">
80 <param format="tabular" name="input" type="data" label="Dataset to integrate" />
81 <section name='opt' title='Optional fields' expanded='false'>
82 <param name="headers" type="text" value="" optional="true" label="Headers (separated with spaces)" argument="--headers" />
83 <param name="col_type" type="text" value="" optional="true" label="Columns types (separated with spaces)" argument="-c" />
84 <param name="key_col" type="text" value="" optional="true" label="Key columns (separated with spaces)" argument="--key-columns" />
85 <param name="dis_col" type="text" value="" optional="true" label="Disabled columns (separated with spaces)" argument="--disabled-columns" />
86 </section>
87 </when>
88 <when value="gff">
89 <param format="gff3" name="input" type="data" label="Dataset to integrate" />
90 <param name="ent" type="text" value="transcript gene" label="Entities (separated with space)" argument="-e" />
91 <param name="tax" type="text" value="" label="Taxon" argument="-t" />
92 </when>
93 <when value="bed">
94 <param format="bed" name="input" type="data" label="Dataset to integrate" />
95 <param name="ent_name" type="text" value="" label="Entity name" argument="--entity-name" />
96 <param name="tax" type="text" value="" label="Taxon" argument="-t" />
97 </when>
98 <when value="ttl">
99 <param format="ttl" name="input" type="data" label="Dataset to integrate" />
100 </when>
101 </conditional>
102
103 <!-- Advanced fonctionalities -->
104 <section name="advanced" title="Advanced features" expanded="false">
105 <param name="uri" type="text" value="" label="Custom URI" argument="--uri" />
106 <param name="public" type="boolean" checked="false" truevalue="--public" falsevalue="" label="Integrate as a public dataset" argument="--public" />
107 </section>
108
109 </inputs>
110
111 <outputs>
112 <data format="txt" name="output" label="Integration of ${input_format.input.name}" />
113 </outputs>
114
115 <tests>
116 <test expect_failure='true' expect_exit_code='1'>
117 <expand macro='test_asko_loc' />
118 <expand macro='test_asko_auth' />
119 <conditional name='input_format'>
120 <param name='format' value='csv' />
121 <param name='input' value='people.tsv' />
122 </conditional>
123 </test>
124 </tests>
125
126 <help><![CDATA[
127 @HELP@
128 ]]></help>
129
130 <expand macro='citation' />
131 </tool>