Mercurial > repos > devteam > cuffmerge
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author | devteam |
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date | Fri, 19 Dec 2014 11:59:06 -0500 |
parents | 424d49834830 |
children | 1707a530e598 |
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<tool id="cuffmerge" name="Cuffmerge" version="@VERSION@.0"> <description>merge together several Cufflinks assemblies</description> <expand macro="requirements" /> <expand macro="stdio" /> <macros> <import>cuff_macros.xml</import> </macros> <command interpreter="python"> cuffmerge_wrapper.py --num-threads="\${GALAXY_SLOTS:-4}" ## Use annotation reference? #if $annotation.use_ref_annotation == "Yes": -g "${annotation.reference_annotation}" #end if ## Use sequence data? #if $seq_data.use_seq_data == "Yes": -s #if $seq_data.seq_source.index_source == "history": --ref_file="${seq_data.seq_source.ref_file}" #else: --index="${seq_data.seq_source.index.fields.path}" #end if #end if --min-isoform-fraction="${min_isoform_fraction}" ## Outputs. --merged-transcripts="${merged_transcripts}" @CUFFLINKS_GTF_INPUTS@ </command> <inputs> <expand macro="cufflinks_gtf_inputs" /> <conditional name="annotation"> <param name="use_ref_annotation" type="select" label="Use Reference Annotation"> <option value="No">No</option> <option value="Yes">Yes</option> </param> <when value="Yes"> <param format="gff3,gtf" name="reference_annotation" type="data" label="Reference Annotation" help="Requires an annotation file in GFF3 or GTF format."/> </when> <when value="No"> </when> </conditional> <conditional name="seq_data"> <param name="use_seq_data" type="select" label="Use Sequence Data" help="Use sequence data for some optional classification functions, including the addition of the p_id attribute required by Cuffdiff."> <option value="No">No</option> <option value="Yes">Yes</option> </param> <when value="No"></when> <when value="Yes"> <conditional name="seq_source"> <param name="index_source" type="select" label="Choose the source for the reference list"> <option value="cached">Locally cached</option> <option value="history">History</option> </param> <when value="cached"> <param name="index" type="select" label="Using reference genome"> <options from_data_table="fasta_indexes"> <filter type="data_meta" ref="inputs" key="dbkey" column="1" /> <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" /> </options> </param> </when> <when value="history"> <param name="ref_file" type="data" format="fasta" label="Using reference file" /> </when> </conditional> </when> </conditional> <param name="min_isoform_fraction" type="float" min="0" max="1" value="0.05" label="Minimum isoform fraction" help="Discard isoforms with abundance below this value" /> </inputs> <outputs> <data format="gtf" name="merged_transcripts" label="${tool.name} on ${on_string}: merged transcripts"/> </outputs> <tests> <!-- cuffmerge -g cuffcompare_in3.gtf cuffcompare_in1.gtf cuffcompare_in2.gtf --> <test> <param name="inputs" value="cuffcompare_in1.gtf,cuffcompare_in2.gtf" ftype="gtf"/> <param name="use_ref_annotation" value="Yes"/> <param name="reference_annotation" value="cuffcompare_in3.gtf" ftype="gtf"/> <param name="min_isoform_fraction" value="0.08" /> <param name="use_seq_data" value="No"/> <!-- oId assignment differ/are non-deterministic --> <output name="merged_transcripts" file="cuffmerge_out1.gtf" lines_diff="50"/> </test> </tests> <help> **Cuffmerge Overview** Cuffmerge is part of Cufflinks_. Please cite: Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L. Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms. Nature Biotechnology doi:10.1038/nbt.1621 .. _Cufflinks: http://cole-trapnell-lab.github.io/cufflinks/ ------ **Know what you are doing** .. class:: warningmark There is no such thing (yet) as an automated gearshift in expression analysis. It is all like stick-shift driving in San Francisco. In other words, running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy. .. __: http://cole-trapnell-lab.github.io/cufflinks/cuffmerge/ ------ **Input format** Cuffmerge takes Cufflinks' GTF output as input, and optionally can take a "reference" annotation (such as from Ensembl_) .. _Ensembl: http://www.ensembl.org ------ **Outputs** Cuffmerge produces the following output files: Merged transcripts file: Cuffmerge produces a GTF file that contains an assembly that merges together the input assemblies. </help> <citations> <citation type="doi">10.1038/nbt.1621</citation> </citations> </tool>