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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 11:29:58 +0000
parents 1b52f0c8ad7f
children
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0:1b52f0c8ad7f 1:d6c074a93c51
1 <tool id='aegean_parseval' name='AEGeAn ParsEval' version='@TOOL_VERSION@' profile='20.01'> 1 <tool id="aegean_parseval" name="AEGeAn ParsEval" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
2 <description> compare two sets of gene annotations for the same sequence.</description> 2 <description> compare two sets of gene annotations for the same sequence.</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>parseval --version</version_command> 9 <version_command>parseval --version</version_command>
10 <command detect_errors='exit_code'> 10 <command detect_errors="exit_code">
11 <![CDATA[ 11 <![CDATA[
12 #if $output_type == 'html' 12 #if $output_type == "html"
13 mkdir -p '${output_html.extra_files_path}' && 13 mkdir -p "${output_html.extra_files_path}" &&
14 #end if 14 #end if
15 parseval '$referencegff3' '$predictiongff3' 15 parseval "$referencegff3" "$predictiongff3"
16 --delta $delta 16 --delta $delta
17 --maxtrans $maxtrans 17 --maxtrans $maxtrans
18 -w 18 -w
19 #if $refrlabel 19 #if $refrlabel
20 --refrlabel '$refrlabel' 20 --refrlabel "$refrlabel"
21 #end if 21 #end if
22 #if $predlabel 22 #if $predlabel
23 --predlabel '$predlabel' 23 --predlabel "$predlabel"
24 #end if 24 #end if
25 #if $output_type =='text' 25 #if $output_type =="text"
26 -f 'text' 26 -f "text"
27 -o '$output_txt' 27 -o "$output_txt"
28 #else if $output_type == 'html' 28 #else if $output_type == "html"
29 -f 'html' 29 -f "html"
30 -o '${output_html.files_path}' && 30 -o "${output_html.files_path}" &&
31 echo "</div> </body> </html>" >> '${output_html.files_path}'/index.html && 31 echo "</div> </body> </html>" >> "${output_html.files_path}"/index.html &&
32 cp '${output_html.files_path}'/index.html '$output_html' 32 cp "${output_html.files_path}"/index.html "$output_html"
33 #end if 33 #end if
34 ]]> 34 ]]>
35 </command> 35 </command>
36 <inputs> 36 <inputs>
37 <param name='referencegff3' type='data' format='gff3' label="Reference GFF3 file"/> 37 <param name="referencegff3" type="data" format="gff3" label="Reference GFF3 file"/>
38 <param name='predictiongff3' type='data' format='gff3' label="Prediction GFF3 file"/> 38 <param name="predictiongff3" type="data" format="gff3" label="Prediction GFF3 file"/>
39 <param argument='--delta' type='integer' 39 <param argument="--delta" type="integer"
40 min='0' max='20' value='0' 40 min="0" max="20" value="0"
41 label='Number of nucleotides to extend gene loci'/> 41 label="Number of nucleotides to extend gene loci"/>
42 <param argument='--maxtrans' type='integer' 42 <param argument="--maxtrans" type="integer"
43 min='1' max='50' value='32' 43 min="1" max="50" value="32"
44 label='Maximum transcript allowed per locus' /> 44 label="Maximum transcript allowed per locus" />
45 <param name='output_type' type='select' 45 <param name="output_type" type="select"
46 label='Select the output type'> 46 label="Select the output type">
47 <option value='text'>Text</option> 47 <option value="text">Text</option>
48 <option value='html'>HTML</option> 48 <option value="html">HTML</option>
49 </param> 49 </param>
50 <param argument='--refrlabel' type='text' 50 <param argument="--refrlabel" type="text"
51 value='' optional='true' 51 value="" optional="true"
52 label='Reference annotations' 52 label="Reference annotations"
53 help='Optional label for reference annotations'/> 53 help="Optional label for reference annotations"/>
54 <param argument='--predlabel' type='text' 54 <param argument="--predlabel" type="text"
55 value='' optional='true' 55 value="" optional="true"
56 label='Prediction annotations' 56 label="Prediction annotations"
57 help='Optional label for prediction annotations'/> 57 help="Optional label for prediction annotations"/>
58 </inputs> 58 </inputs>
59 <outputs> 59 <outputs>
60 <data name='output_txt' format='txt'> 60 <data name="output_txt" format="txt" label="${tool.name} on ${on_string}: text">
61 <filter>output_type == 'text'</filter> 61 <filter>output_type == "text"</filter>
62 </data> 62 </data>
63 <data name='output_html' format='html' from_work_dir="output.html"> 63 <data name="output_html" format="html" from_work_dir="output.html" label="${tool.name} on ${on_string}: HTML">
64 <filter>output_type == 'html'</filter> 64 <filter>output_type == "html"</filter>
65 </data> 65 </data>
66 </outputs> 66 </outputs>
67 <tests> 67 <tests>
68 <test expect_num_outputs="1"> 68 <test expect_num_outputs="1">
69 <param name='referencegff3' value='TAIR9_GFF3_genes.gff'/> 69 <param name="referencegff3" value="TAIR9_GFF3_genes.gff" ftype="gff3"/>
70 <param name='predictiongff3' value='TAIR10_GFF3_genes.gff'/> 70 <param name="predictiongff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>
71 <param name='delta' value='5'/> 71 <param name="delta" value="5"/>
72 <param name='maxtrans' value='20'/> 72 <param name="maxtrans" value="20"/>
73 <output name='output_txt' file='parseval_output_test1.txt' lines_diff='8'/> 73 <output name="output_txt" file="parseval_output_test1.txt" lines_diff="8"/>
74 </test> 74 </test>
75 <test expect_num_outputs="1"> 75 <test expect_num_outputs="1">
76 <param name='referencegff3' value='TAIR9_GFF3_genes.gff'/> 76 <param name="referencegff3" value="TAIR9_GFF3_genes.gff" ftype="gff3"/>
77 <param name='predictiongff3' value='TAIR10_GFF3_genes.gff'/> 77 <param name="predictiongff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>
78 <output name='output_txt' file='parseval_output_test2.txt' lines_diff='8'/> 78 <output name="output_txt" file="parseval_output_test2.txt" lines_diff="8"/>
79 </test> 79 </test>
80 <test expect_num_outputs="1"> 80 <test expect_num_outputs="1">
81 <param name='referencegff3' value='TAIR9_GFF3_genes.gff'/> 81 <param name="referencegff3" value="TAIR9_GFF3_genes.gff" ftype="gff3"/>
82 <param name='predictiongff3' value='TAIR10_GFF3_genes.gff'/> 82 <param name="predictiongff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>
83 <param name='delta' value='10'/> 83 <param name="delta" value="10"/>
84 <param name='maxtrans' value='10'/> 84 <param name="maxtrans" value="10"/>
85 <output name='output_txt' file='parseval_output_test3.txt' lines_diff='8'/> 85 <output name="output_txt" file="parseval_output_test3.txt" lines_diff="8"/>
86 </test> 86 </test>
87 <test expect_num_outputs="1"> 87 <test expect_num_outputs="1">
88 <param name='referencegff3' value='TAIR9_GFF3_genes.gff'/> 88 <param name="referencegff3" value="TAIR9_GFF3_genes.gff" ftype="gff3"/>
89 <param name='predictiongff3' value='TAIR10_GFF3_genes.gff'/> 89 <param name="predictiongff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>
90 <param name='output_type' value='html'/> 90 <param name="output_type" value="html"/>
91 <output name='output_html' file='parseval_output_test4.html' lines_diff='8'/> 91 <output name="output_html" file="parseval_output_test4.html" lines_diff="8"/>
92 </test> 92 </test>
93 <test expect_num_outputs="1"> 93 <test expect_num_outputs="1">
94 <param name='referencegff3' value='TAIR9_GFF3_genes.gff'/> 94 <param name="referencegff3" value="TAIR9_GFF3_genes.gff" ftype="gff3"/>
95 <param name='predictiongff3' value='TAIR10_GFF3_genes.gff'/> 95 <param name="predictiongff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>
96 <param name='output_type' value='html'/> 96 <param name="output_type" value="html"/>
97 <param name='delta' value='10'/> 97 <param name="delta" value="10"/>
98 <param name='maxtrans' value='10'/> 98 <param name="maxtrans" value="10"/>
99 <output name='output_html' file='parseval_output_test5.html' lines_diff='8'/> 99 <output name="output_html" file="parseval_output_test5.html" lines_diff="8"/>
100 </test> 100 </test>
101 <test expect_num_outputs="1"> 101 <test expect_num_outputs="1">
102 <param name='referencegff3' value='TAIR9_GFF3_genes.gff'/> 102 <param name="referencegff3" value="TAIR9_GFF3_genes.gff" ftype="gff3"/>
103 <param name='predictiongff3' value='TAIR10_GFF3_genes.gff'/> 103 <param name="predictiongff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>
104 <param name='output_type' value='text'/> 104 <param name="output_type" value="text"/>
105 <param name='refrlabel' value='example_ref_label'/> 105 <param name="refrlabel" value="example_ref_label"/>
106 <param name='predlabel' value='example_pred_label'/> 106 <param name="predlabel" value="example_pred_label"/>
107 <output name='output_txt' file='parseval_output_test6.txt' lines_diff='8'/> 107 <output name="output_txt" file="parseval_output_test6.txt" lines_diff="8"/>
108 </test> 108 </test>
109 </tests> 109 </tests>
110 <help> 110 <help>
111 <![CDATA[ 111 <![CDATA[
112 .. class:: infomark 112 .. class:: infomark
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. 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.
143 143
144 144
145 ]]> 145 ]]>
146 </help> 146 </help>
147 <expand macro='citations'/> 147 <expand macro="citations"/>
148 </tool> 148 </tool>