Mercurial > repos > iuc > aegean_parseval

annotate parseval.xml @ 1:d6c074a93c51 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 11:29:58 +0000
parents 1b52f0c8ad7f
children
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d6c074a93c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit 669dd4d406e86aee7d83e7420dced981c180d805
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1 <tool id="aegean_parseval" name="AEGeAn ParsEval" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
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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"
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3 <macros>
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4 <import>macros.xml</import>
1b52f0c8ad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
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5 </macros>
1
d6c074a93c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit 669dd4d406e86aee7d83e7420dced981c180d805
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6 <expand macro="edam_ontology"/>
d6c074a93c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit 669dd4d406e86aee7d83e7420dced981c180d805
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7 <expand macro="xrefs"/>
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8 <expand macro="requirements"/>
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9 <version_command>parseval --version</version_command>
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10 <command detect_errors="exit_code">
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11 <![CDATA[
1
d6c074a93c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit 669dd4d406e86aee7d83e7420dced981c180d805
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12 #if $output_type == "html"
d6c074a93c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit 669dd4d406e86aee7d83e7420dced981c180d805
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13 mkdir -p "${output_html.extra_files_path}" &&
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14 #end if
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15 parseval "$referencegff3" "$predictiongff3"
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16 --delta $delta
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17 --maxtrans $maxtrans
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18 -w
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19 #if $refrlabel
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20 --refrlabel "$refrlabel"
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21 #end if
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22 #if $predlabel
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23 --predlabel "$predlabel"
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24 #end if
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25 #if $output_type =="text"
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26 -f "text"
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27 -o "$output_txt"
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28 #else if $output_type == "html"
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29 -f "html"
d6c074a93c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit 669dd4d406e86aee7d83e7420dced981c180d805
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30 -o "${output_html.files_path}" &&
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31 echo "</div> </body> </html>" >> "${output_html.files_path}"/index.html &&
d6c074a93c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit 669dd4d406e86aee7d83e7420dced981c180d805
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32 cp "${output_html.files_path}"/index.html "$output_html"
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33 #end if
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34 ]]>
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35 </command>
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36 <inputs>
1
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37 <param name="referencegff3" type="data" format="gff3" label="Reference GFF3 file"/>
d6c074a93c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit 669dd4d406e86aee7d83e7420dced981c180d805
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38 <param name="predictiongff3" type="data" format="gff3" label="Prediction GFF3 file"/>
d6c074a93c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit 669dd4d406e86aee7d83e7420dced981c180d805
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39 <param argument="--delta" type="integer"
d6c074a93c51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit 669dd4d406e86aee7d83e7420dced981c180d805
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40 min="0" max="20" value="0"
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41 label="Number of nucleotides to extend gene loci"/>
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42 <param argument="--maxtrans" type="integer"
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43 min="1" max="50" value="32"
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44 label="Maximum transcript allowed per locus" />
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45 <param name="output_type" type="select"
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46 label="Select the output type">
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47 <option value="text">Text</option>
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48 <option value="html">HTML</option>
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49 </param>
1
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50 <param argument="--refrlabel" type="text"
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51 value="" optional="true"
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52 label="Reference annotations"
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53 help="Optional label for reference annotations"/>
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54 <param argument="--predlabel" type="text"
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55 value="" optional="true"
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56 label="Prediction annotations"
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57 help="Optional label for prediction annotations"/>
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58 </inputs>
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59 <outputs>
1
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60 <data name="output_txt" format="txt" label="${tool.name} on ${on_string}: text">
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61 <filter>output_type == "text"</filter>
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62 </data>
1
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63 <data name="output_html" format="html" from_work_dir="output.html" label="${tool.name} on ${on_string}: HTML">
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64 <filter>output_type == "html"</filter>
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65 </data>
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66 </outputs>
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67 <tests>
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68 <test expect_num_outputs="1">
1
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69 <param name="referencegff3" value="TAIR9_GFF3_genes.gff" ftype="gff3"/>
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70 <param name="predictiongff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>
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71 <param name="delta" value="5"/>
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72 <param name="maxtrans" value="20"/>
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73 <output name="output_txt" file="parseval_output_test1.txt" lines_diff="8"/>
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74 </test>
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75 <test expect_num_outputs="1">
1
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76 <param name="referencegff3" value="TAIR9_GFF3_genes.gff" ftype="gff3"/>
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77 <param name="predictiongff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>
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78 <output name="output_txt" file="parseval_output_test2.txt" lines_diff="8"/>
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79 </test>
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80 <test expect_num_outputs="1">
1
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81 <param name="referencegff3" value="TAIR9_GFF3_genes.gff" ftype="gff3"/>
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82 <param name="predictiongff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>
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83 <param name="delta" value="10"/>
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84 <param name="maxtrans" value="10"/>
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85 <output name="output_txt" file="parseval_output_test3.txt" lines_diff="8"/>
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86 </test>
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87 <test expect_num_outputs="1">
1
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88 <param name="referencegff3" value="TAIR9_GFF3_genes.gff" ftype="gff3"/>
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89 <param name="predictiongff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>
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90 <param name="output_type" value="html"/>
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91 <output name="output_html" file="parseval_output_test4.html" lines_diff="8"/>
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92 </test>
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93 <test expect_num_outputs="1">
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94 <param name="referencegff3" value="TAIR9_GFF3_genes.gff" ftype="gff3"/>
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95 <param name="predictiongff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>
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96 <param name="output_type" value="html"/>
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97 <param name="delta" value="10"/>
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98 <param name="maxtrans" value="10"/>
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99 <output name="output_html" file="parseval_output_test5.html" lines_diff="8"/>
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100 </test>
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101 <test expect_num_outputs="1">
1
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102 <param name="referencegff3" value="TAIR9_GFF3_genes.gff" ftype="gff3"/>
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103 <param name="predictiongff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>
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104 <param name="output_type" value="text"/>
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105 <param name="refrlabel" value="example_ref_label"/>
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106 <param name="predlabel" value="example_pred_label"/>
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107 <output name="output_txt" file="parseval_output_test6.txt" lines_diff="8"/>
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108 </test>
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109 </tests>
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110 <help>
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111 <![CDATA[
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112 .. class:: infomark
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113
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114 **Purpose**
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115
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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.
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117
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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.
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119
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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.
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121
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122 -----
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123
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124 .. class:: infomark
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125
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126 **Input**
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127
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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.
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129
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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.
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131
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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.
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133
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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.
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135
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136 -----
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137
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138 .. class:: infomark
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139
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140 **Output**
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141
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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.
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143
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144
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145 ]]>
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146 </help>
1
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147 <expand macro="citations"/>
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148 </tool>