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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 11:30:13 +0000
parents 1dd7adc21b6d
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0:1dd7adc21b6d 1:8dc7512c9dc9
1 <tool id="aegean_gaeval" name="AEGeAn GAEVAL" version="@TOOL_VERSION@" profile="20.01"> 1 <tool id="aegean_gaeval" name="AEGeAn GAEVAL" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
2 <description> compute coverage and integrity scores for gene models using transcript alignments.</description> 2 <description> compute coverage and integrity scores for gene models using transcript alignments.</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>gaeval --version</version_command> 9 <version_command>gaeval --version</version_command>
10 <command detect_errors='exit_code'> 10 <command detect_errors="exit_code">
11 <![CDATA[ 11 <![CDATA[
12 gaeval '$alignmentgff3' '$genesgff3' 12 gaeval "$alignmentgff3" "$genesgff3"
13 -a $weights.alpha 13 -a $weights.alpha
14 -b $weights.beta 14 -b $weights.beta
15 -g $weights.gamma 15 -g $weights.gamma
16 -e $weights.epsilon 16 -e $weights.epsilon
17 -c $expected.expcds 17 -c $expected.expcds
18 -5 $expected.exp5putr 18 -5 $expected.exp5putr
19 -3 $expected.exp3putr > '$output' 19 -3 $expected.exp3putr > "$output"
20 ]]> 20 ]]>
21 </command> 21 </command>
22 <inputs> 22 <inputs>
23 <param name='alignmentgff3' type='data' format='gff3' label='Alignment GFF3 file' /> 23 <param name="alignmentgff3" type="data" format="gff3" label="Alignment GFF3 file" />
24 <param name='genesgff3' type='data' format='gff3' label='Genes GFF3 file'/> 24 <param name="genesgff3" type="data" format="gff3" label="Genes GFF3 file"/>
25 <!-- Weight options --> 25 <!-- Weight options -->
26 <section name='weights' 26 <section name="weights"
27 title='Weights for calculating integrity score' 27 title="Weights for calculating integrity score"
28 expanded='False'> 28 expanded="False">
29 <param argument='--alpha' type='float' 29 <param argument="--alpha" type="float"
30 min='0' max='1' value='0.6' 30 min="0" max="1" value="0.6"
31 label='Introns confirmed, or % expected CDS lenght for single-exon genes' 31 label="Introns confirmed, or % expected CDS lenght for single-exon genes"
32 help='The percentage of introns confirmed by an alignment gap; for single-exon gene predictions lacking introns, it represents the ratio of the observed CDS length to the expected CDS length. '/> 32 help="The percentage of introns confirmed by an alignment gap; for single-exon gene predictions lacking introns, it represents the ratio of the observed CDS length to the expected CDS length. "/>
33 <param argument='--beta' type='float' 33 <param argument="--beta" type="float"
34 min='0' max='1' value='0.3' 34 min="0" max="1" value="0.3"
35 label='Exon coverage' 35 label="Exon coverage"
36 help='Overall percentage of individual exons spanned by at least one sequencing read.'/> 36 help="Overall percentage of individual exons spanned by at least one sequencing read."/>
37 <param argument='--gamma' type='float' 37 <param argument="--gamma" type="float"
38 min='0' max='1' value='0.05' 38 min="0" max="1" value="0.05"
39 label='% expected 5’ UTR length' 39 label="% expected 5’ UTR length"
40 help='The ratio of the observed 5’ UTR length to the expected 5’ UTR length.'/> 40 help="The ratio of the observed 5’ UTR length to the expected 5’ UTR length."/>
41 <param argument='--epsilon' type='float' 41 <param argument="--epsilon" type="float"
42 min='0' max='1' value='0.05' 42 min="0" max="1" value="0.05"
43 label='% expected 3’ UTR lenght' 43 label="% expected 3’ UTR lenght"
44 help='The ratio of the observed 3’ UTR length to the expected 3’ UTR length.'/> 44 help="The ratio of the observed 3’ UTR length to the expected 3’ UTR length."/>
45 </section> 45 </section>
46 <!-- Expected feature lenght options --> 46 <!-- Expected feature lenght options -->
47 <section name='expected' 47 <section name="expected"
48 title='Expected feature lenghts for calculating integrity score' 48 title="Expected feature lenghts for calculating integrity score"
49 expanded='False'> 49 expanded="False">
50 <param name='expcds' type='integer' 50 <param name="expcds" type="integer"
51 min='0' max='1000' value='400' 51 min="0" max="1000" value="400"
52 label='Expected CDs length (in bp) (-c)' /> 52 label="Expected CDs length (in bp) (-c)" />
53 <param name='exp5putr' type='integer' 53 <param name="exp5putr" type="integer"
54 min='0' max='1000' value='200' 54 min="0" max="1000" value="200"
55 label='Expected 5’ UTR length (-5)' /> 55 label="Expected 5’ UTR length (-5)" />
56 <param name='exp3putr' type='integer' 56 <param name="exp3putr" type="integer"
57 min='0' max='1000' value='100' 57 min="0" max="1000" value="100"
58 label='Expected 3’ UTR length (-3)' /> 58 label="Expected 3’ UTR length (-3)" />
59 </section> 59 </section>
60 </inputs> 60 </inputs>
61 <outputs> 61 <outputs>
62 <data name='output' format='tabular' /> 62 <data name="output" format="tabular" />
63 </outputs> 63 </outputs>
64 <tests> 64 <tests>
65 <test expect_num_outputs="1"> 65 <test expect_num_outputs="1">
66 <param name='alignmentgff3' value='TAIR10_GFF3_alignment.gff'/> 66 <param name="alignmentgff3" value="TAIR10_GFF3_alignment.gff" ftype="gff3"/>
67 <param name='genesgff3' value='TAIR10_GFF3_genes.gff'/> 67 <param name="genesgff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>
68 <output name='output' file='gaeval_output_test1.txt'/> 68 <output name="output" file="gaeval_output_test1.txt"/>
69 </test> 69 </test>
70 <test expect_num_outputs="1"> 70 <test expect_num_outputs="1">
71 <param name='alignmentgff3' value='TAIR10_GFF3_alignment.gff'/> 71 <param name="alignmentgff3" value="TAIR10_GFF3_alignment.gff" ftype="gff3"/>
72 <param name='genesgff3' value='TAIR10_GFF3_genes.gff'/> 72 <param name="genesgff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>
73 <section name='weights'> 73 <section name="weights">
74 <param name='alpha' value='0.5'/> 74 <param name="alpha" value="0.5"/>
75 <param name='beta' value='0.4'/> 75 <param name="beta" value="0.4"/>
76 <param name='gamma' value='0.05'/> 76 <param name="gamma" value="0.05"/>
77 <param name='epsion' value='0.05'/> 77 <param name="epsion" value="0.05"/>
78 </section> 78 </section>
79 <output name='output' file='gaeval_output_test2.txt'/> 79 <output name="output" file="gaeval_output_test2.txt"/>
80 </test> 80 </test>
81 <test expect_num_outputs="1"> 81 <test expect_num_outputs="1">
82 <param name='alignmentgff3' value='TAIR10_GFF3_alignment.gff'/> 82 <param name="alignmentgff3" value="TAIR10_GFF3_alignment.gff" ftype="gff3"/>
83 <param name='genesgff3' value='TAIR10_GFF3_genes.gff'/> 83 <param name="genesgff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>
84 <section name='expected'> 84 <section name="expected">
85 <param name='expcds' value='20'/> 85 <param name="expcds" value="20"/>
86 <param name='exp5putr' value='150'/> 86 <param name="exp5putr" value="150"/>
87 <param name='exp3putr' value='120'/> 87 <param name="exp3putr" value="120"/>
88 </section> 88 </section>
89 <output name='output' file='gaeval_output_test3.txt' lines_diff='2'/> 89 <output name="output" file="gaeval_output_test3.txt" lines_diff="2"/>
90 </test> 90 </test>
91 91
92 </tests> 92 </tests>
93 <help> 93 <help>
94 <![CDATA[ 94 <![CDATA[
124 124
125 GAEVAL computes coverage and integrity scores for each mRNA feature in the gene prediction input. The output will be identical to the input, except that each mRNA feature will have two new attribtues: gaeval_coverage and gaeval_integrity. 125 GAEVAL computes coverage and integrity scores for each mRNA feature in the gene prediction input. The output will be identical to the input, except that each mRNA feature will have two new attribtues: gaeval_coverage and gaeval_integrity.
126 126
127 ]]> 127 ]]>
128 </help> 128 </help>
129 <expand macro='citations'/> 129 <expand macro="citations"/>
130 </tool> 130 </tool>