Mercurial > repos > iuc > homer_annotatepeaks
diff homer_annotatePeaks.xml @ 0:adab852c8216 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
| author | iuc |
|---|---|
| date | Sun, 08 Aug 2021 11:03:29 +0000 |
| parents | |
| children | fa7c3a74acf2 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/homer_annotatePeaks.xml Sun Aug 08 11:03:29 2021 +0000 @@ -0,0 +1,133 @@ +<tool id="homer_annotatePeaks" name="annotatePeaks" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ +annotatePeaks.pl +## Peak file +'$input' +## Genome +#if $CpG.bool == "true": + #if $CpG.genome.source == 'installed': + '${CpG.genome.all_fasta_source.fields.path}' + #else + '${CpG.genome.fasta}' + #end if + -CpG +#else + none +#end if +#if $gtf_file: + -gtf '$gtf_file' +#end if +#if $ann_file: + -ann '$ann_file' +#end if +> '$output' + ]]></command> + <inputs> + <param name="input" type="data" format="bed,encodepeak,tabular" label="Peak file"/> + <!-- CpG --> + <conditional name="CpG"> + <param name="bool" type="select" label="Do you want to compute CpG/GC content?"> + <option value="true">Yes</option> + <option value="false">No</option> + </param> + <when value="true"> + <conditional name="genome"> + <param name="source" type="select" label="Will you select a reference genome from your history or use a installed genome?"> + <option value="installed">Installed</option> + <option value="history">From History</option> + </param> + <when value="installed"> + <param name="all_fasta_source" type="select" label="Source FASTA Sequence"> + <options from_data_table="all_fasta"> + <filter type="sort_by" column="2"/> + <validator type="no_options" message="No references are available"/> + </options> + </param> + </when> + <when value="history"> + <param name="fasta" type="data" format="fasta" label="Select reference genome"/> + </when> + </conditional> + </when> + <when value="false"/> + </conditional> + <param name="gtf_file" type="data" format="gtf,gff,gff3" optional="True" label="GTF file" help="Must be of datatype "gtf" or "gff" or "gff3"" argument="-gtf"/> + <param name="ann_file" type="data" format="tabular" optional="True" label="Annotation data file for HOMER" help="This file can be generated from gtf with the tool 'Converts GTF to Annotations file for Homer" argument="-ann"/> + </inputs> + <outputs> + <data format="tabular" name="output"/> + </outputs> + <tests> + <test expect_num_outputs="1"> + <!-- first simple test with ann and gtf--> + <param name="input" value="CTCF_peaks.bed" ftype="bed"/> + <conditional name="CpG"> + <param name="bool" value="false"/> + </conditional> + <param name="ann_file" value="annotations_default_simplified.txt" ftype="tabular"/> + <param name="gtf_file" value="small_simplified.gtf" ftype="gtf"/> + <output name="output" file="CTCF_peaks_first.txt" ftype="tabular" compare="diff" lines_diff="2"/> + </test> + <test expect_num_outputs="1"> + <!-- second simple test with ann only--> + <param name="input" value="CTCF_peaks.bed" ftype="bed"/> + <conditional name="CpG"> + <param name="bool" value="false"/> + </conditional> + <param name="ann_file" value="annotations_default.txt" ftype="tabular"/> + <output name="output" file="CTCF_peaks_second.txt" ftype="tabular" compare="diff" lines_diff="2"/> + </test> + <test expect_num_outputs="1"> + <!-- third simple test with gtf only--> + <param name="input" value="CTCF_peaks.bed" ftype="bed"/> + <conditional name="CpG"> + <param name="bool" value="false"/> + </conditional> + <param name="gtf_file" value="small_simplified.gtf" ftype="gtf"/> + <output name="output" file="CTCF_peaks_third.txt" ftype="tabular" compare="diff" lines_diff="2"/> + </test> + <test expect_num_outputs="1"> + <!--test with CpG--> + <param name="input" value="fake_phix_peaks.bed"/> + <conditional name="CpG"> + <param name="bool" value="true"/> + <conditional name="genome"> + <param name="source" value="history"/> + <param name="fasta" value="phiX174.fasta"/> + </conditional> + </conditional> + <output name="output" file="phiXcpg.txt" ftype="tabular" compare="diff" lines_diff="2"/> + </test> + <test expect_num_outputs="1"> + <!--test with CpG from table--> + <param name="input" value="fake_phix_peaks.bed"/> + <conditional name="CpG"> + <param name="bool" value="true"/> + <conditional name="genome"> + <param name="source" value="installed"/> + <param name="all_fasta_source" value="phiX174"/> + </conditional> + </conditional> + <output name="output" file="phiXcpg.txt" ftype="tabular" compare="diff" lines_diff="2"/> + </test> + <test expect_num_outputs="1"> + <!--test with nothing--> + <param name="input" value="fake_phix_peaks.bed"/> + <conditional name="CpG"> + <param name="bool" value="false"/> + </conditional> + <output name="output" file="phiX_nothing.txt" ftype="tabular" compare="diff" lines_diff="2"/> + </test> + </tests> + <help><![CDATA[ +This wrapper allow to annotate peaks with simple annotations with annotatePeaks.pl from HOMER. +The annotation file and the GTF file may seem redundant but: +- the use of gtf file only misses the UTR annotations and does not allow to set the desired offsets for TSS and TTS. +- the use of annotation file only misses the distance to tss and the correspondance between id and classical gene name. + ]]></help> + <expand macro="citation"/> +</tool>