Mercurial > repos > iuc > aegean_parseval

annotate parseval.xml @ 0:1b52f0c8ad7f draft

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/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
author iuc
date Sun, 03 Jan 2021 14:58:02 +0000
parents
children d6c074a93c51
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
1 <tool id='aegean_parseval' name='AEGeAn ParsEval' version='@TOOL_VERSION@' profile='20.01'>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
2 <description> compare two sets of gene annotations for the same sequence.</description>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
3 <macros>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
4 <import>macros.xml</import>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
5 </macros>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
6 <expand macro='xrefs'/>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
7 <expand macro='edam_ontology'/>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
8 <expand macro='requirements'/>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
9 <version_command>parseval --version</version_command>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
10 <command detect_errors='exit_code'>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
11 <![CDATA[
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
12 #if $output_type == 'html'
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
13 mkdir -p '${output_html.extra_files_path}' &&
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
14 #end if
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
15 parseval '$referencegff3' '$predictiongff3'
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
16 --delta $delta
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
17 --maxtrans $maxtrans
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
18 -w
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
19 #if $refrlabel
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
20 --refrlabel '$refrlabel'
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
21 #end if
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
22 #if $predlabel
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
23 --predlabel '$predlabel'
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
24 #end if
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
25 #if $output_type =='text'
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
26 -f 'text'
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
27 -o '$output_txt'
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
28 #else if $output_type == 'html'
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
29 -f 'html'
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
30 -o '${output_html.files_path}' &&
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
31 echo "</div> </body> </html>" >> '${output_html.files_path}'/index.html &&
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
32 cp '${output_html.files_path}'/index.html '$output_html'
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
33 #end if
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
34 ]]>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
35 </command>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
36 <inputs>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
37 <param name='referencegff3' type='data' format='gff3' label="Reference GFF3 file"/>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
38 <param name='predictiongff3' type='data' format='gff3' label="Prediction GFF3 file"/>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
39 <param argument='--delta' type='integer'
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
40 min='0' max='20' value='0'
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
41 label='Number of nucleotides to extend gene loci'/>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
42 <param argument='--maxtrans' type='integer'
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
43 min='1' max='50' value='32'
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
44 label='Maximum transcript allowed per locus' />
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
45 <param name='output_type' type='select'
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
46 label='Select the output type'>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
47 <option value='text'>Text</option>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
48 <option value='html'>HTML</option>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
49 </param>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
50 <param argument='--refrlabel' type='text'
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
51 value='' optional='true'
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
52 label='Reference annotations'
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
53 help='Optional label for reference annotations'/>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
54 <param argument='--predlabel' type='text'
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
55 value='' optional='true'
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
56 label='Prediction annotations'
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
57 help='Optional label for prediction annotations'/>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
58 </inputs>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
59 <outputs>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
60 <data name='output_txt' format='txt'>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
61 <filter>output_type == 'text'</filter>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
62 </data>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
63 <data name='output_html' format='html' from_work_dir="output.html">
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
64 <filter>output_type == 'html'</filter>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
65 </data>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
66 </outputs>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
67 <tests>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
68 <test expect_num_outputs="1">
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
69 <param name='referencegff3' value='TAIR9_GFF3_genes.gff'/>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
70 <param name='predictiongff3' value='TAIR10_GFF3_genes.gff'/>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
71 <param name='delta' value='5'/>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
72 <param name='maxtrans' value='20'/>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
73 <output name='output_txt' file='parseval_output_test1.txt' lines_diff='8'/>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
74 </test>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
75 <test expect_num_outputs="1">
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
76 <param name='referencegff3' value='TAIR9_GFF3_genes.gff'/>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
77 <param name='predictiongff3' value='TAIR10_GFF3_genes.gff'/>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
78 <output name='output_txt' file='parseval_output_test2.txt' lines_diff='8'/>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
79 </test>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
80 <test expect_num_outputs="1">
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
81 <param name='referencegff3' value='TAIR9_GFF3_genes.gff'/>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
82 <param name='predictiongff3' value='TAIR10_GFF3_genes.gff'/>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
83 <param name='delta' value='10'/>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
84 <param name='maxtrans' value='10'/>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
85 <output name='output_txt' file='parseval_output_test3.txt' lines_diff='8'/>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
86 </test>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
87 <test expect_num_outputs="1">
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
88 <param name='referencegff3' value='TAIR9_GFF3_genes.gff'/>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
89 <param name='predictiongff3' value='TAIR10_GFF3_genes.gff'/>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
90 <param name='output_type' value='html'/>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
91 <output name='output_html' file='parseval_output_test4.html' lines_diff='8'/>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
92 </test>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
93 <test expect_num_outputs="1">
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
94 <param name='referencegff3' value='TAIR9_GFF3_genes.gff'/>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
95 <param name='predictiongff3' value='TAIR10_GFF3_genes.gff'/>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
96 <param name='output_type' value='html'/>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
97 <param name='delta' value='10'/>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
98 <param name='maxtrans' value='10'/>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
99 <output name='output_html' file='parseval_output_test5.html' lines_diff='8'/>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
100 </test>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
101 <test expect_num_outputs="1">
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
102 <param name='referencegff3' value='TAIR9_GFF3_genes.gff'/>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
103 <param name='predictiongff3' value='TAIR10_GFF3_genes.gff'/>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
104 <param name='output_type' value='text'/>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
105 <param name='refrlabel' value='example_ref_label'/>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
106 <param name='predlabel' value='example_pred_label'/>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
107 <output name='output_txt' file='parseval_output_test6.txt' lines_diff='8'/>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
108 </test>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
109 </tests>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
110 <help>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
111 <![CDATA[
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
112 .. class:: infomark
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
113
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
114 **Purpose**
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
115
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
116 ParsEval is a program for comparing two sets of gene annotations for the same sequence. The most common use cases for ParsEval are as follows.
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
117
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
118 - You are annotating a newly assembled genome. The optimal parameter settings for annotation are not clear initially, so you do some exploratory data analysis and try several different parameter settings. You can use ParsEval to identify the similarities and differences between the different annotations you have produced.
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
119
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
120 - You are doing a genome-wide analysis of genes in your favorite organism. There is a gene annotation available from the consortium that sequenced and assembled the genome, but there is a different annotation available at NCBI. Again, ParsEval is the best way to compare these two annotations to quickly identify their similarities and differences.
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
121
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
122 -----
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
123
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
124 .. class:: infomark
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
125
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
126 **Input**
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
127
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
128 Input for ParsEval is two sets of annotations in GFF3 format. ParsEval uses the GenomeTools GFF3 parser, which strictly enforces syntax rules laid out in the GFF3 specification. ParsEval itself does some additional checks on the data to make sure valid comparisons are possible. Any features not directly related to protein-coding genes are ignored.
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
129
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
130 ParsEval will infer features implicitly encoded in the data. For example, if a gene annotation declares 6 exon features but no intron features, ParsEval will infer the 5 corresponding intron features from the exon boundaries. However, if ParsEval sees any intron features in a gene model it will assume all introns are declared explicitly. Violations of that assumption will likely elicit a program error.
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
131
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
132 ParsEval is pretty flexible in handling various common conventions for encoding gene structure: exons + start/stop codons, exons + CDS, CDS + UTRs, etc. Any subset of features that completely captures the gene’s exon/intron structure, CDS(s), and UTRs should be handled correctly.
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
133
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
134 ParsEval requires that gene isoforms be encoded using the feature type mRNA (as opposed to transcript, primary_transcript, or other valid SO terms). For mRNA features lacking an explicitly declared gene parent, ParsEval will create one. Note, however, that ParsEval will treat all such transcripts as belonging to separate distinct genes, which will erroneously inflate summary statistics reported by ParsEval.
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
135
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
136 -----
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
137
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
138 .. class:: infomark
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
139
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
140 **Output**
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
141
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
142 ParsEval output includes a variety of similarity statistics that measure the agreement between the two annotations. Our use of agreement here instead of accuracy is intentional: except in a very few rare cases, you will not be comparing a prediction to a true high-quality “gold standard.” It is much more common to compare two annotation sets whose relative quality is unknown. ParsEval uses the terms reference and prediction only to distinguish the two sets: it makes no assumptions as to their relative quality.
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
143
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
144
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
145 ]]>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
146 </help>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
147 <expand macro='citations'/>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
iuc
parents:
diff changeset
148 </tool>