Mercurial > repos > iuc > tbl2gff3

annotate tbl2gff3.xml @ 1:d9eb9f753fa6 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit db75a8489a1f61ea30abe9b91f6febac8b34204f"
author iuc
date Thu, 03 Dec 2020 16:59:00 +0000
parents 63f6b6ca0e97
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
d9eb9f753fa6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit db75a8489a1f61ea30abe9b91f6febac8b34204f"
iuc
parents: 0
diff changeset
1 <tool id="tbl2gff3" name="Table to GFF3" version="1.2">
0
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
2 <description></description>
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
3 <macros>
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
4 <import>macros.xml</import>
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
5 </macros>
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
6 <expand macro="requirements"/>
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
7 <command detect_errors="exit_code">
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
8 <![CDATA[
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
9 python '$__tool_directory__/tbl2gff3.py'
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
10 '$table'
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
11 '$rid'
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
12 '$begin'
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
13 '$end'
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
14
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
15 #if $type:
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
16 --type '$type'
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
17 #end if
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
18
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
19 #if $score:
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
20 --score '$score'
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
21 #end if
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
22
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
23 #if $source:
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
24 --source '$source'
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
25 #end if
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
26
1
d9eb9f753fa6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit db75a8489a1f61ea30abe9b91f6febac8b34204f"
iuc
parents: 0
diff changeset
27 #if str($strand.strand_select) == 'infer':
d9eb9f753fa6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit db75a8489a1f61ea30abe9b91f6febac8b34204f"
iuc
parents: 0
diff changeset
28 --strand_infer
d9eb9f753fa6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit db75a8489a1f61ea30abe9b91f6febac8b34204f"
iuc
parents: 0
diff changeset
29 #else if str($strand.strand_select) != "none":
0
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
30 --strand_${strand.strand_select} '${strand.strand}'
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
31 #end if
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
32
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
33 #for $a in $attributes
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
34 -a '${a.key}:${a.val}'
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
35 #end for
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
36
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
37 > '$output'
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
38 ]]></command>
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
39 <inputs>
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
40 <param label="Table" name="table" type="data" format="tabular"/>
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
41
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
42 <param name="rid" type="text" value="1" label="Record ID column or value" optional="false" help="@HELP@"/>
1
d9eb9f753fa6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit db75a8489a1f61ea30abe9b91f6febac8b34204f"
iuc
parents: 0
diff changeset
43 <param name="begin" type="text" value="" optional="false" label="Start column or value" help="@HELP@"/>
d9eb9f753fa6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit db75a8489a1f61ea30abe9b91f6febac8b34204f"
iuc
parents: 0
diff changeset
44 <param name="end" type="text" value="" optional="false" label="End column or value" help="@HELP@"/>
d9eb9f753fa6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit db75a8489a1f61ea30abe9b91f6febac8b34204f"
iuc
parents: 0
diff changeset
45 <param name="type" type="text" value="sequence_feature" label="Type column or value" help="@HELP@"/>
d9eb9f753fa6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit db75a8489a1f61ea30abe9b91f6febac8b34204f"
iuc
parents: 0
diff changeset
46 <param name="score" type="text" value="" label="Score column or value" help="@HELP@"/>
d9eb9f753fa6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit db75a8489a1f61ea30abe9b91f6febac8b34204f"
iuc
parents: 0
diff changeset
47 <param name="source" type="text" value="tbl2gff3" label="Source column or value" help="@HELP@"/>
0
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
48
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
49
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
50 <conditional name="strand">
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
51 <param name="strand_select" type="select" label="Strand">
1
d9eb9f753fa6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit db75a8489a1f61ea30abe9b91f6febac8b34204f"
iuc
parents: 0
diff changeset
52 <option value="infer">Infer</option>
0
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
53 <option value="none">Not specified</option>
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
54 <option value="column">From Column</option>
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
55 <option value="value">Specify Value</option>
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
56 </param>
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
57 <when value="none" />
1
d9eb9f753fa6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit db75a8489a1f61ea30abe9b91f6febac8b34204f"
iuc
parents: 0
diff changeset
58 <when value="infer" />
0
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
59 <when value="column" >
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
60 <param name="strand" type="text" value="" label="Strand column" />
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
61 </when>
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
62 <when value="value">
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
63 <param name="strand" type="integer" value="1" min="-1" max="1" label="Strand value" />
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
64 </when>
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
65 </conditional>
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
66
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
67 <repeat name="attributes" title="Qualifiers" help="Other columns can be turned into qualifiers with arbitrary keys and values">
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
68 <param name="key" type="text" value="key" label="Name of the qualifier"/>
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
69 <param name="val" type="text" value="" label="Qualifier value column or raw text" help="@HELP@"/>
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
70 </repeat>
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
71
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
72 </inputs>
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
73 <outputs>
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
74 <data format="gff3" name="output"/>
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
75 </outputs>
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
76 <tests>
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
77 <test>
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
78 <param name="table" ftype="tabular" value="input.tab" />
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
79 <param name="rid" value="1" />
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
80 <param name="begin" value="5" />
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
81 <param name="end" value="6" />
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
82 <param name="score" value="14" />
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
83 <conditional name="strand">
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
84 <param name="strand_select" value="value"/>
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
85 <param name="strand" value="1"/>
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
86 </conditional>
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
87 <repeat name="attributes">
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
88 <param name="key" value="e-value" />
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
89 <param name="val" value="7" />
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
90 </repeat>
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
91 <repeat name="attributes">
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
92 <param name="key" value="hit" />
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
93 <param name="val" value="9" />
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
94 </repeat>
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
95 <repeat name="attributes">
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
96 <param name="key" value="GI" />
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
97 <param name="val" value="11" />
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
98 </repeat>
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
99 <repeat name="attributes">
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
100 <param name="key" value="test" />
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
101 <param name="val" value="one" />
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
102 </repeat>
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
103 <repeat name="attributes">
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
104 <param name="key" value="test" />
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
105 <param name="val" value="two" />
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
106 </repeat>
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
107
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
108 <output name="output" file="blast.gff3" />
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
109
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
110 </test>
1
d9eb9f753fa6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit db75a8489a1f61ea30abe9b91f6febac8b34204f"
iuc
parents: 0
diff changeset
111 <test>
d9eb9f753fa6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit db75a8489a1f61ea30abe9b91f6febac8b34204f"
iuc
parents: 0
diff changeset
112 <param name="table" ftype="tabular" value="infer.tab" />
d9eb9f753fa6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit db75a8489a1f61ea30abe9b91f6febac8b34204f"
iuc
parents: 0
diff changeset
113 <param name="rid" value="1" />
d9eb9f753fa6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit db75a8489a1f61ea30abe9b91f6febac8b34204f"
iuc
parents: 0
diff changeset
114 <param name="begin" value="2" />
d9eb9f753fa6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit db75a8489a1f61ea30abe9b91f6febac8b34204f"
iuc
parents: 0
diff changeset
115 <param name="end" value="3" />
d9eb9f753fa6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit db75a8489a1f61ea30abe9b91f6febac8b34204f"
iuc
parents: 0
diff changeset
116 <conditional name="strand">
d9eb9f753fa6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit db75a8489a1f61ea30abe9b91f6febac8b34204f"
iuc
parents: 0
diff changeset
117 <param name="strand_select" value="infer"/>
d9eb9f753fa6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit db75a8489a1f61ea30abe9b91f6febac8b34204f"
iuc
parents: 0
diff changeset
118 </conditional>
d9eb9f753fa6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit db75a8489a1f61ea30abe9b91f6febac8b34204f"
iuc
parents: 0
diff changeset
119 <output name="output" file="infer.gff3" />
d9eb9f753fa6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit db75a8489a1f61ea30abe9b91f6febac8b34204f"
iuc
parents: 0
diff changeset
120
d9eb9f753fa6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit db75a8489a1f61ea30abe9b91f6febac8b34204f"
iuc
parents: 0
diff changeset
121 </test>
0
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
122 </tests>
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
123 <help><![CDATA[
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
124 **What it does**
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
125
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
126 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.
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
127
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
128 ]]></help>
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
129 <citations>
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
130 </citations>
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
131 </tool>
63f6b6ca0e97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
iuc
parents:
diff changeset
132