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comparison tbl2gff3.xml @ 1:4a7f4b0cc0a3 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit db75a8489a1f61ea30abe9b91f6febac8b34204f"
author iuc
date Thu, 03 Dec 2020 16:59:23 +0000
parents 965674d88d34
children
comparison
equal deleted inserted replaced
0:965674d88d34 1:4a7f4b0cc0a3
1 <tool id="tbl2gff3" name="Table to GFF3" version="1.1"> 1 <tool id="tbl2gff3" name="Table to GFF3" version="1.2">
2 <description></description> 2 <description></description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
22 22
23 #if $source: 23 #if $source:
24 --source '$source' 24 --source '$source'
25 #end if 25 #end if
26 26
27 #if str($strand.strand_select) != "none": 27 #if str($strand.strand_select) == 'infer':
28 --strand_infer
29 #else if str($strand.strand_select) != "none":
28 --strand_${strand.strand_select} '${strand.strand}' 30 --strand_${strand.strand_select} '${strand.strand}'
29 #end if 31 #end if
30 32
31 #for $a in $attributes 33 #for $a in $attributes
32 -a '${a.key}:${a.val}' 34 -a '${a.key}:${a.val}'
36 ]]></command> 38 ]]></command>
37 <inputs> 39 <inputs>
38 <param label="Table" name="table" type="data" format="tabular"/> 40 <param label="Table" name="table" type="data" format="tabular"/>
39 41
40 <param name="rid" type="text" value="1" label="Record ID column or value" optional="false" help="@HELP@"/> 42 <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@"/> 43 <param name="begin" type="text" value="" optional="false" label="Start column or value" help="@HELP@"/>
42 <param name="end" type="text" value="" optional="false" label="Feature end column or value" help="@HELP@"/> 44 <param name="end" type="text" value="" optional="false" label="End column or value" help="@HELP@"/>
43 <param name="type" type="text" value="sequence_feature" label="Feature type column or value" help="@HELP@"/> 45 <param name="type" type="text" value="sequence_feature" label="Type column or value" help="@HELP@"/>
44 <param name="score" type="text" value="" label="Feature score column or value" help="@HELP@"/> 46 <param name="score" type="text" value="" label="Score column or value" help="@HELP@"/>
45 <param name="source" type="text" value="tbl2gff3" label="Feature source column or value" help="@HELP@"/> 47 <param name="source" type="text" value="tbl2gff3" label="Source column or value" help="@HELP@"/>
46 48
47 49
48 <conditional name="strand"> 50 <conditional name="strand">
49 <param name="strand_select" type="select" label="Strand"> 51 <param name="strand_select" type="select" label="Strand">
52 <option value="infer">Infer</option>
50 <option value="none">Not specified</option> 53 <option value="none">Not specified</option>
51 <option value="column">From Column</option> 54 <option value="column">From Column</option>
52 <option value="value">Specify Value</option> 55 <option value="value">Specify Value</option>
53 </param> 56 </param>
54 <when value="none" /> 57 <when value="none" />
58 <when value="infer" />
55 <when value="column" > 59 <when value="column" >
56 <param name="strand" type="text" value="" label="Strand column" /> 60 <param name="strand" type="text" value="" label="Strand column" />
57 </when> 61 </when>
58 <when value="value"> 62 <when value="value">
59 <param name="strand" type="integer" value="1" min="-1" max="1" label="Strand value" /> 63 <param name="strand" type="integer" value="1" min="-1" max="1" label="Strand value" />
102 </repeat> 106 </repeat>
103 107
104 <output name="output" file="blast.gff3" /> 108 <output name="output" file="blast.gff3" />
105 109
106 </test> 110 </test>
111 <test>
112 <param name="table" ftype="tabular" value="infer.tab" />
113 <param name="rid" value="1" />
114 <param name="begin" value="2" />
115 <param name="end" value="3" />
116 <conditional name="strand">
117 <param name="strand_select" value="infer"/>
118 </conditional>
119 <output name="output" file="infer.gff3" />
120
121 </test>
107 </tests> 122 </tests>
108 <help><![CDATA[ 123 <help><![CDATA[
109 **What it does** 124 **What it does**
110 125
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. 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.