Mercurial > repos > iuc > homer_gtf_to_annotations

comparison homer_gtf_to_annotation.xml @ 0:8ebb6520eef4 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/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
author iuc
date Sun, 08 Aug 2021 11:04:17 +0000
parents
children 7c5da353e460
comparison
equal deleted inserted replaced
-1:000000000000 0:8ebb6520eef4
1 <tool id="homer_gtf_to_annotations" name="Converts GTF to Annotations file for Homer" version="@TOOL_VERSION@+galaxy0" profile="20.05">
2 <macros>
3 <import>macros.xml</import>
4 </macros>
5 <expand macro="requirements"/>
6 <command detect_errors="exit_code"><![CDATA[
7 ## Run parseGTF.pl
8 parseGTF.pl $gtf_file ann
9 ## Different options
10 $type
11 $id
12 $removeAccVer
13 $removeEnsemblVer
14 -annTSSstartOffset $annTSSstartOffset
15 -annTSSendOffset $annTSSendOffset
16 -annTTSstartOffset $annTTSstartOffset
17 -annTTSendOffset $annTTSendOffset
18 #if $features != 'None':
19 #set features_space = ' '.join(str($features).split(','))
20 -features $features_space
21 #end if
22 > annotations.txt &&
23 ## Prioritize and add intergenic annotation
24 assignGenomeAnnotation annotations.txt annotations.txt -prioritize $output > $output_stats
25 ]]></command>
26 <inputs>
27 <param name="gtf_file" type="data" format="gtf,gff,gff3" label="GTF file" help="Must be of datatype &quot;gtf&quot; or &quot;gff&quot; or &quot;gff3&quot;"/>
28 <param name="type" type="select" label="Format of input file">
29 <option value="">GTF</option>
30 <option value="-gff">GFF (treats 9th column as ID)</option>
31 <option value="-gff3">GFF3 (looks for parent attribute to assign gene name)</option>
32 </param>
33 <param name="id" type="select" label="Primary identifier">
34 <option value="-tid">Transcript ID</option>
35 <option value="-gid">Gene ID</option>
36 </param>
37 <param name="features" type="select" label="Which feature(s) to use?" multiple="true" display="checkboxes">
38 <option value="exon" selected="true">exon</option>
39 <option value="start_codon" selected="true">start_codon</option>
40 <option value="stop_codon" selected="true">stop_codon</option>
41 </param>
42 <param name="removeAccVer" type="boolean" truevalue="-removeAccVer" falsevalue="" label="Remove any .1, .2, etc. at end of accession numbers, i.e. AT1G01040.2" help="-removeAccVer; Default=False"/>
43 <param name="removeEnsemblVer" type="boolean" truevalue="-removeEnsemblVer" falsevalue="" label="Remove 'transcript:' and '_T01' style ids" help="-removeEnsemblVer; Default=False"/>
44 <param name="annTSSstartOffset" type="integer" value="-1000" label="distance upstream of TSS to start promoter annotation" help="-annTSSstartOffset; Default=-1000"/>
45 <param name="annTSSendOffset" type="integer" value="100" label="distance upstream/downstream of TSS to end promoter annotation" help="-annTSSendOffset; Default=100"/>
46 <param name="annTTSstartOffset" type="integer" value="-100" label="distance upstream of TTS to start TTS annotation" help="-annTTSstartOffset; Default=-100"/>
47 <param name="annTTSendOffset" type="integer" value="1000" label="distance upstream/downstream of TTS to end TTS annotation" help="-annTTSendOffset; Default=1000"/>
48 </inputs>
49 <outputs>
50 <data format="tabular" name="output" label="${tool.name} on ${on_string}: Annotations"/>
51 <data format="tabular" name="output_stats" label="${tool.name} on ${on_string}: Annotation stats"/>
52 </outputs>
53 <tests>
54 <test>
55 <!-- simple test with default -->
56 <param name="gtf_file" value="small.gtf" ftype="gtf"/>
57 <output name="output" file="annotations_default.txt" ftype="tabular"/>
58 <output name="output_stats" file="annotations_default_stats.txt" ftype="tabular"/>
59 </test>
60 <test>
61 <!-- simple test with default except no exon_end -->
62 <param name="gtf_file" value="small.gtf" ftype="gtf"/>
63 <param name="features" value="exon,start_codon"/>
64 <output name="output" file="annotations_exon_start.txt" ftype="tabular"/>
65 <output name="output_stats" file="annotations_exon_start_stats.txt" ftype="tabular"/>
66 </test>
67 <test>
68 <!-- simple test with default smaller TSS TTS -->
69 <param name="gtf_file" value="small.gtf" ftype="gtf"/>
70 <param name="annTSSstartOffset" value="-50"/>
71 <param name="annTSSendOffset" value="50"/>
72 <param name="annTTSstartOffset" value="-50"/>
73 <param name="annTTSendOffset" value="50"/>
74 <output name="output" file="annotations_small_TSSTTS.txt" ftype="tabular"/>
75 <output name="output_stats" file="annotations_small_TSSTTS_stats.txt" ftype="tabular"/>
76 </test>
77 </tests>
78 <help><![CDATA[
79 This tool convert a GTF file to a HOMER-style annotation file compatible with annotatePeaks.
80 It follows the tutorial proposed here: http://homer.ucsd.edu/homer/ngs/advancedAnnotation.html
81 ]]></help>
82 <expand macro="citation"/>
83 </tool>