Mercurial > repos > iuc > flair
diff flair_collapse.xml @ 0:5d17cf201540 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
| author | iuc |
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| date | Fri, 27 Nov 2020 18:45:47 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flair_collapse.xml Fri Nov 27 18:45:47 2020 +0000 @@ -0,0 +1,188 @@ +<tool id="flair_collapse" name="FLAIR collapse" version="@TOOL_VERSION@" profile="20.01"> + <description>defines high-confidence isoforms from flair-corrected reads</description> + + <macros> + <import>flair_macros.xml</import> + </macros> + + <expand macro="requirements" /> + <expand macro="version_command" /> + + <command detect_errors="exit_code"><![CDATA[ + +@PREPARE_REF@ + +ln -s '$input_query' query.bed && + +flair.py collapse + +########### +## Input ## +########### + +-q query.bed +-r '$input_reads' +-g reference.fa +-f '$input_gtf' + +#if $input_promotors: + -p '$input_promotors' +#end if + +######################## +## Additional Options ## +######################## + +-w $additional_options.window +-s $additional_options.support +$additional_options.stringent + +#if str($additional_options.select_uniqueness): + -n str($additional_options.select_uniqueness) +#end if + +$additional_options.isoform +--max_ends $additional_options.maxends +$additional_options.trustends + +#if str($additional_options.select_filter): + -e str($additional_options.select_filter) +#end if + +######### +## END ## +######### + + ]]></command> + <inputs> + <param name="input_query" argument="-q" type="data" format="bed" label="Corrected Reads as BED file"/> + <param name="input_reads" argument="-r" type="data" format="fasta,fastq" label="FASTA/FASTQ file of raw reads"/> + <expand macro="reference_interface" /> + <param name="input_gtf" argument="-f" type="data" format="gtf" label="GTF annotation file"/> + <param name="input_promotors" optional="true" argument="-p" type="data" format="bed" label="Promotor BED file to identify full-length reads" /> + + <!-- Additional Options --> + <section name="additional_options" title="Additional Options"> + <param name="window" argument="-w" type="integer" min="1" value="100" label="Window Size" help="Window size for comparing TSS/TES (Default=100)" /> + <param name="support" argument="-s" type="integer" min="1" value="3" label="Supporting Reads" help="Minimum number of supporting reads for an isoform (Default=3)" /> + <param name="stringent" argument="--stringent" type="boolean" checked="false" truevalue="--stringent" falsevalue="" label="Use Stringent Mode" help="Specify if all supporting reads need to be full-length (80% coverage and spanning 25 bp of the first and last exons) (Default=false)"/> + <param name="select_uniqueness" argument="-n" type="select" label="Choose the TSS/TES for each unique set of splice junction." > + <option value="" selected="true">No Selection</option> + <option value="none">Best TSSs/TESs</option> + <option value="longest">Single TSS/TES chosen to maximize length</option> + <option value="best_only">Single most supported TSS/TES used in conjunction chosen</option> + </param> + <param name="isoform" argument="-i" type="boolean" checked="false" truevalue="-i" falsevalue="" label="Use Isoform Mode" help="TSS/TES for each isoform will be determined from supporting reads for individual isoforms (Default=false)"/> + <param name="maxends" argument="--max_ends" type="integer" min="0" value="2" label="Maximum Number of TSS/TES picked per isoform" help="(Default=2)" /> + <param name="trustends" argument="--trust_ends" type="boolean" checked="false" truevalue="--trust_ends" falsevalue="" label="Reads are generated from a long read method with minimal fragmentation?" /> + <param name="select_filter" argument="-e" type="select" label="Filter for isoforms." > + <option value="" selected="true">No Filter</option> + <option value="nosubset">Any isoforms that are a proper set of another isoform are removed</option> + <option value="default">Subset isoforms are removed based on support</option> + <option value="comprehensive">Default set + all subset isoforms</option> + <option value="ginormous">Comprehensive set + single exon subset isoforms</option> + </param> + <param name="mapq" argument="--quality" type="integer" min="0" value="1" label="Minimum MAPQ of read assignment to an isoform" help="(Default=1)" /> + </section> + + <section name="additional_outputs" title="Output Options"> + <param name="out_format" type="select" multiple="true" optional="true" display="checkboxes" label="Data types"> + <option value="bed">BED</option> + <option value="fasta">FASTA</option> + </param> + </section> + </inputs> + + <outputs> + <data name="outfile_isoforms_gtf" from_work_dir="flair.collapse.isoforms.gtf" format="gtf" label="${tool.name} on ${on_string}: Isoforms GTF" /> + <data name="outfile_isoforms_bed" from_work_dir="flair.collapse.isoforms.bed" format="bed" label="${tool.name} on ${on_string}: Isoforms BED"> + <filter>additional_outputs['out_format'] and 'bed' in additional_outputs['out_format']</filter> + </data> + <data name="outfile_isoforms_fasta" from_work_dir="flair.collapse.isoforms.fa" format="fasta" label="${tool.name} on ${on_string}: Isoforms FASTA"> + <filter>additional_outputs['out_format'] and 'fasta' in additional_outputs['out_format']</filter> + </data> + </outputs> + + <tests> + <test expect_num_outputs="3"> + <param name="input_query" ftype="bed" value="flair_all_corrected.bed" /> + <param name="input_reads" ftype="fastq.gz" value="chrM.fastq.gz" /> + <param name="ref_selector_genome" value="history" /> + <param name="reffile" ftype="fasta" value="chrM.fa" /> + <param name="input_gtf" ftype="gtf" value="UCSC_Main_on_Human_knownGene_region_chrM.gtf" /> + <param name="out_format" value="bed,fasta" /> + <output name="outfile_isoforms_gtf" ftype="gtf" file="flair.collapse.isoforms.gtf" /> + <output name="outfile_isoforms_bed" ftype="bed" file="flair.collapse.isoforms.bed" /> + <output name="outfile_isoforms_fasta" ftype="fasta" file="flair.collapse.isoforms.fa" /> + </test> + <!-- Test with cached genome --> + <test expect_num_outputs="3"> + <param name="input_query" ftype="bed" value="flair_all_corrected.bed" /> + <param name="input_reads" ftype="fastq.gz" value="chrM.fastq.gz" /> + <param name="ref_selector_genome" value="cached" /> + <param name="reffile" value="chrM" /> + <param name="input_gtf" ftype="gtf" value="UCSC_Main_on_Human_knownGene_region_chrM.gtf" /> + <param name="out_format" value="bed,fasta" /> + <output name="outfile_isoforms_gtf" ftype="gtf" file="flair.collapse.isoforms.gtf" /> + <output name="outfile_isoforms_bed" ftype="bed" file="flair.collapse.isoforms.bed" /> + <output name="outfile_isoforms_fasta" ftype="fasta" file="flair.collapse.isoforms.fa" /> + </test> + </tests> + <help><![CDATA[ + +.. class:: infomark + +**What it does** + +------------------- + +@description@ + +**flair collapse** +Defines high-confidence isoforms from corrected reads. + +------------------- + +**Inputs** + +------------------- + +(1) Corrected Reads as Bed12 File. +(2) FASTA/FASTQ file of raw reads. All raw read fastq/fasta files should be concatenated into a single file. +(3) FASTA of Reference Genome. +(4) GTF annotation file. +(5) Promoter regions bed file to identify full-length reads. + +----------- + +**Outputs** + +----------- + +Outputs the high-confidence isoforms in several formats: +(1) bed, +(2) gtf, +(3) FASTA. + +-------------------- + +**More Information** + +-------------------- + +See the excellent `FLAIR documentation`_ + +.. _`FLAIR documentation`: https://github.com/BrooksLabUCSC/flair + + +-------------------- + +**Galaxy Wrapper Development** + +-------------------- + +@citation@ + + ]]></help> + <expand macro="citations" /> +</tool>