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comparison tbl2gff3.xml @ 0:965674d88d34 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
author iuc
date Tue, 07 Jul 2020 04:20:40 -0400
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children 4a7f4b0cc0a3
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-1:000000000000 0:965674d88d34
1 <tool id="tbl2gff3" name="Table to GFF3" version="1.1">
2 <description></description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <command detect_errors="exit_code">
8 <![CDATA[
9 python '$__tool_directory__/tbl2gff3.py'
10 '$table'
11 '$rid'
12 '$begin'
13 '$end'
14
15 #if $type:
16 --type '$type'
17 #end if
18
19 #if $score:
20 --score '$score'
21 #end if
22
23 #if $source:
24 --source '$source'
25 #end if
26
27 #if str($strand.strand_select) != "none":
28 --strand_${strand.strand_select} '${strand.strand}'
29 #end if
30
31 #for $a in $attributes
32 -a '${a.key}:${a.val}'
33 #end for
34
35 > '$output'
36 ]]></command>
37 <inputs>
38 <param label="Table" name="table" type="data" format="tabular"/>
39
40 <param name="rid" type="text" value="1" label="Record ID column or value" optional="false" help="@HELP@"/>
41 <param name="begin" type="text" value="" optional="false" label="Feature start column or value" help="@HELP@"/>
42 <param name="end" type="text" value="" optional="false" label="Feature end column or value" help="@HELP@"/>
43 <param name="type" type="text" value="sequence_feature" label="Feature type column or value" help="@HELP@"/>
44 <param name="score" type="text" value="" label="Feature score column or value" help="@HELP@"/>
45 <param name="source" type="text" value="tbl2gff3" label="Feature source column or value" help="@HELP@"/>
46
47
48 <conditional name="strand">
49 <param name="strand_select" type="select" label="Strand">
50 <option value="none">Not specified</option>
51 <option value="column">From Column</option>
52 <option value="value">Specify Value</option>
53 </param>
54 <when value="none" />
55 <when value="column" >
56 <param name="strand" type="text" value="" label="Strand column" />
57 </when>
58 <when value="value">
59 <param name="strand" type="integer" value="1" min="-1" max="1" label="Strand value" />
60 </when>
61 </conditional>
62
63 <repeat name="attributes" title="Qualifiers" help="Other columns can be turned into qualifiers with arbitrary keys and values">
64 <param name="key" type="text" value="key" label="Name of the qualifier"/>
65 <param name="val" type="text" value="" label="Qualifier value column or raw text" help="@HELP@"/>
66 </repeat>
67
68 </inputs>
69 <outputs>
70 <data format="gff3" name="output"/>
71 </outputs>
72 <tests>
73 <test>
74 <param name="table" ftype="tabular" value="input.tab" />
75 <param name="rid" value="1" />
76 <param name="begin" value="5" />
77 <param name="end" value="6" />
78 <param name="score" value="14" />
79 <conditional name="strand">
80 <param name="strand_select" value="value"/>
81 <param name="strand" value="1"/>
82 </conditional>
83 <repeat name="attributes">
84 <param name="key" value="e-value" />
85 <param name="val" value="7" />
86 </repeat>
87 <repeat name="attributes">
88 <param name="key" value="hit" />
89 <param name="val" value="9" />
90 </repeat>
91 <repeat name="attributes">
92 <param name="key" value="GI" />
93 <param name="val" value="11" />
94 </repeat>
95 <repeat name="attributes">
96 <param name="key" value="test" />
97 <param name="val" value="one" />
98 </repeat>
99 <repeat name="attributes">
100 <param name="key" value="test" />
101 <param name="val" value="two" />
102 </repeat>
103
104 <output name="output" file="blast.gff3" />
105
106 </test>
107 </tests>
108 <help><![CDATA[
109 **What it does**
110
111 Convert a table into GFF3. This is not a very complex or advanced tool, it won't produce GFF with hierarchy, just flat gff3 which may be sufficient for visualisation purposes.
112
113 ]]></help>
114 <citations>
115 </citations>
116 </tool>
117