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comparison canongff3.xml @ 1:c45c9dd066e2 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit 669dd4d406e86aee7d83e7420dced981c180d805
author iuc
date Sun, 11 Feb 2024 11:29:29 +0000
parents 3f438bf5475d
children
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0:3f438bf5475d 1:c45c9dd066e2
1 <tool id='aegean_canongff3' name=' AEGeAn CanonGFF3' version='@TOOL_VERSION@' profile='20.01'> 1 <tool id="aegean_canongff3" name="AEGeAn CanonGFF3" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
2 <description> pre-process GFF3 files, removing all features not directly related to protein-coding genes</description> 2 <description> pre-process GFF3 files, removing all features not directly related to protein-coding genes</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro='xrefs'/> 6 <expand macro="edam_ontology"/>
7 <expand macro='edam_ontology'/> 7 <expand macro="xrefs"/>
8 <expand macro='requirements'/> 8 <expand macro="requirements"/>
9 <version_command>canon-gff3 --version</version_command> 9 <version_command>canon-gff3 --version</version_command>
10 <command detect_errors='exit_code'> 10 <command detect_errors="exit_code">
11 <![CDATA[ 11 <![CDATA[
12 canon-gff3 '$gff3file' 12 canon-gff3 "$gff3file"
13 $infer 13 $infer
14 #if $source 14 #if $source
15 -s '$source' 15 -s "$source"
16 #end if 16 #end if
17 -o '$output' 17 -o "$output"
18 ]]> 18 ]]>
19 </command> 19 </command>
20 <inputs> 20 <inputs>
21 <param name='gff3file' type='data' format='gff3' label='GFF3 File' 21 <param name="gff3file" type="data" format="gff3" label="GFF3 File"
22 help="GFF3 annotation file" multiple='true' /> 22 help="GFF3 annotation file" multiple="true" />
23 <param argument='--infer' type='boolean' 23 <param argument="--infer" type="boolean"
24 truevalue='--infer' falsevalue='' 24 truevalue="--infer" falsevalue=""
25 label='Infer gene feature for transcripts lacking it' 25 label="Infer gene feature for transcripts lacking it"
26 help='For transcript features lacking an explicitly declared gene feature as a parent, create this feature on-they-fly'/> 26 help="For transcript features lacking an explicitly declared gene feature as a parent, create this feature on-they-fly"/>
27 <param argument='--source' type='text' 27 <param argument="--source" type="text"
28 value='' optional='true' 28 value="" optional="true"
29 label='Reset the source of each feature' 29 label="Reset the source of each feature"
30 help='Reset the source of each feature to the given value. Source keywords can be a program (e.g. RepeatMasker) or an organization (like TAIR)'> 30 help="Reset the source of each feature to the given value. Source keywords can be a program (e.g. RepeatMasker) or an organization (like TAIR)">
31 <validator type="regex" message="Please only use letters, numbers or underscores in sample label">^[\w]+$</validator> 31 <validator type="regex" message="Please only use letters, numbers or underscores in sample label">^[\w]+$</validator>
32 </param> 32 </param>
33 </inputs> 33 </inputs>
34 <outputs> 34 <outputs>
35 <data name='output' format='gff3' /> 35 <data name="output" format="gff3" />
36 </outputs> 36 </outputs>
37 <tests> 37 <tests>
38 <test> 38 <test>
39 <param name='gff3file' value='TAIR10_GFF3_genes.gff'/> 39 <param name="gff3file" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>
40 <output name='output' file='canon-output_test1.gff3'/> 40 <output name="output" file="canon-output_test1.gff3"/>
41 </test> 41 </test>
42 <test> 42 <test>
43 <param name='gff3file' value='TAIR10_GFF3_genes.gff'/> 43 <param name="gff3file" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>
44 <param name='source' value='test_source'/> 44 <param name="source" value="test_source"/>
45 <output name='output' file='canon-output_test2.gff3'/> 45 <output name="output" file="canon-output_test2.gff3"/>
46 </test> 46 </test>
47 <test> 47 <test>
48 <param name='gff3file' value='TAIR10_GFF3_genes.gff'/> 48 <param name="gff3file" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>
49 <param name='infer' value='true'/> 49 <param name="infer" value="true"/>
50 <output name='output' file='canon-output_test3.gff3'/> 50 <output name="output" file="canon-output_test3.gff3"/>
51 </test> 51 </test>
52 </tests> 52 </tests>
53 <help> 53 <help>
54 <![CDATA[ 54 <![CDATA[
55 .. class:: infomark 55 .. class:: infomark
76 76
77 CanonGFF3 output is a GFF3 file containing protein-coding genes from the provided input file(s). 77 CanonGFF3 output is a GFF3 file containing protein-coding genes from the provided input file(s).
78 78
79 ]]> 79 ]]>
80 </help> 80 </help>
81 <expand macro='citations'/> 81 <expand macro="citations"/>
82 </tool> 82 </tool>