Mercurial > repos > iuc > homer_gtf_to_annotations
diff homer_gtf_to_annotation.xml @ 0:8ebb6520eef4 draft
"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 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/homer_gtf_to_annotation.xml Sun Aug 08 11:04:17 2021 +0000 @@ -0,0 +1,83 @@ +<tool id="homer_gtf_to_annotations" name="Converts GTF to Annotations file for Homer" version="@TOOL_VERSION@+galaxy0" profile="20.05"> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ +## Run parseGTF.pl +parseGTF.pl $gtf_file ann +## Different options +$type +$id +$removeAccVer +$removeEnsemblVer +-annTSSstartOffset $annTSSstartOffset +-annTSSendOffset $annTSSendOffset +-annTTSstartOffset $annTTSstartOffset +-annTTSendOffset $annTTSendOffset +#if $features != 'None': + #set features_space = ' '.join(str($features).split(',')) + -features $features_space +#end if +> annotations.txt && +## Prioritize and add intergenic annotation +assignGenomeAnnotation annotations.txt annotations.txt -prioritize $output > $output_stats + ]]></command> + <inputs> + <param name="gtf_file" type="data" format="gtf,gff,gff3" label="GTF file" help="Must be of datatype "gtf" or "gff" or "gff3""/> + <param name="type" type="select" label="Format of input file"> + <option value="">GTF</option> + <option value="-gff">GFF (treats 9th column as ID)</option> + <option value="-gff3">GFF3 (looks for parent attribute to assign gene name)</option> + </param> + <param name="id" type="select" label="Primary identifier"> + <option value="-tid">Transcript ID</option> + <option value="-gid">Gene ID</option> + </param> + <param name="features" type="select" label="Which feature(s) to use?" multiple="true" display="checkboxes"> + <option value="exon" selected="true">exon</option> + <option value="start_codon" selected="true">start_codon</option> + <option value="stop_codon" selected="true">stop_codon</option> + </param> + <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"/> + <param name="removeEnsemblVer" type="boolean" truevalue="-removeEnsemblVer" falsevalue="" label="Remove 'transcript:' and '_T01' style ids" help="-removeEnsemblVer; Default=False"/> + <param name="annTSSstartOffset" type="integer" value="-1000" label="distance upstream of TSS to start promoter annotation" help="-annTSSstartOffset; Default=-1000"/> + <param name="annTSSendOffset" type="integer" value="100" label="distance upstream/downstream of TSS to end promoter annotation" help="-annTSSendOffset; Default=100"/> + <param name="annTTSstartOffset" type="integer" value="-100" label="distance upstream of TTS to start TTS annotation" help="-annTTSstartOffset; Default=-100"/> + <param name="annTTSendOffset" type="integer" value="1000" label="distance upstream/downstream of TTS to end TTS annotation" help="-annTTSendOffset; Default=1000"/> + </inputs> + <outputs> + <data format="tabular" name="output" label="${tool.name} on ${on_string}: Annotations"/> + <data format="tabular" name="output_stats" label="${tool.name} on ${on_string}: Annotation stats"/> + </outputs> + <tests> + <test> + <!-- simple test with default --> + <param name="gtf_file" value="small.gtf" ftype="gtf"/> + <output name="output" file="annotations_default.txt" ftype="tabular"/> + <output name="output_stats" file="annotations_default_stats.txt" ftype="tabular"/> + </test> + <test> + <!-- simple test with default except no exon_end --> + <param name="gtf_file" value="small.gtf" ftype="gtf"/> + <param name="features" value="exon,start_codon"/> + <output name="output" file="annotations_exon_start.txt" ftype="tabular"/> + <output name="output_stats" file="annotations_exon_start_stats.txt" ftype="tabular"/> + </test> + <test> + <!-- simple test with default smaller TSS TTS --> + <param name="gtf_file" value="small.gtf" ftype="gtf"/> + <param name="annTSSstartOffset" value="-50"/> + <param name="annTSSendOffset" value="50"/> + <param name="annTTSstartOffset" value="-50"/> + <param name="annTTSendOffset" value="50"/> + <output name="output" file="annotations_small_TSSTTS.txt" ftype="tabular"/> + <output name="output_stats" file="annotations_small_TSSTTS_stats.txt" ftype="tabular"/> + </test> + </tests> + <help><![CDATA[ +This tool convert a GTF file to a HOMER-style annotation file compatible with annotatePeaks. +It follows the tutorial proposed here: http://homer.ucsd.edu/homer/ngs/advancedAnnotation.html + ]]></help> + <expand macro="citation"/> +</tool>