Mercurial > repos > devteam > cuffmerge
annotate cuffmerge_wrapper.xml @ 1:02f427c3614b draft
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
| author | devteam |
|---|---|
| date | Tue, 13 Oct 2015 12:38:05 -0400 |
| parents | e556721b9872 |
| children | 0ed8b7f6d506 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="cuffmerge" name="Cuffmerge" version="@VERSION@.0"> |
| 2 <description>merge together several Cufflinks assemblies</description> | |
| 3 <expand macro="requirements" /> | |
| 4 <expand macro="stdio" /> | |
| 5 <macros> | |
| 6 <import>cuff_macros.xml</import> | |
| 7 </macros> | |
| 8 <command interpreter="python"> | |
| 9 cuffmerge_wrapper.py | |
| 10 --num-threads="\${GALAXY_SLOTS:-4}" | |
| 11 | |
| 12 ## Use annotation reference? | |
| 13 #if $annotation.use_ref_annotation == "Yes": | |
| 14 -g "${annotation.reference_annotation}" | |
| 15 #end if | |
| 16 | |
| 17 ## Use sequence data? | |
| 18 #if $seq_data.use_seq_data == "Yes": | |
| 19 -s | |
| 20 #if $seq_data.seq_source.index_source == "history": | |
| 21 --ref_file="${seq_data.seq_source.ref_file}" | |
| 22 #else: | |
| 23 --index="${seq_data.seq_source.index.fields.path}" | |
| 24 #end if | |
| 25 #end if | |
| 26 | |
| 27 --min-isoform-fraction="${min_isoform_fraction}" | |
| 28 | |
| 29 ## Outputs. | |
| 30 --merged-transcripts="${merged_transcripts}" | |
| 31 | |
| 32 @CUFFLINKS_GTF_INPUTS@ | |
| 33 </command> | |
| 34 <inputs> | |
| 35 <expand macro="cufflinks_gtf_inputs" /> | |
| 36 <conditional name="annotation"> | |
| 37 <param name="use_ref_annotation" type="select" label="Use Reference Annotation"> | |
| 38 <option value="No">No</option> | |
| 39 <option value="Yes">Yes</option> | |
| 40 </param> | |
| 41 <when value="Yes"> | |
| 42 <param format="gff3,gtf" name="reference_annotation" type="data" label="Reference Annotation" help="Requires an annotation file in GFF3 or GTF format."/> | |
| 43 </when> | |
| 44 <when value="No"> | |
| 45 </when> | |
| 46 </conditional> | |
| 47 <conditional name="seq_data"> | |
| 48 <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."> | |
| 49 <option value="No">No</option> | |
| 50 <option value="Yes">Yes</option> | |
| 51 </param> | |
| 52 <when value="No"></when> | |
| 53 <when value="Yes"> | |
| 54 <conditional name="seq_source"> | |
| 55 <param name="index_source" type="select" label="Choose the source for the reference list"> | |
| 56 <option value="cached">Locally cached</option> | |
| 57 <option value="history">History</option> | |
| 58 </param> | |
| 59 <when value="cached"> | |
| 60 <param name="index" type="select" label="Using reference genome"> | |
| 61 <options from_data_table="fasta_indexes"> | |
| 62 <filter type="data_meta" ref="inputs" key="dbkey" column="1" /> | |
| 63 <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" /> | |
| 64 </options> | |
| 65 </param> | |
| 66 </when> | |
| 67 <when value="history"> | |
| 68 <param name="ref_file" type="data" format="fasta" label="Using reference file" /> | |
| 69 </when> | |
| 70 </conditional> | |
| 71 </when> | |
| 72 </conditional> | |
| 73 <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" /> | |
| 74 </inputs> | |
| 75 | |
| 76 <outputs> | |
| 77 <data format="gtf" name="merged_transcripts" label="${tool.name} on ${on_string}: merged transcripts"/> | |
| 78 </outputs> | |
| 79 | |
| 80 <tests> | |
| 81 <!-- | |
| 82 cuffmerge -g cuffcompare_in3.gtf cuffcompare_in1.gtf cuffcompare_in2.gtf | |
| 83 --> | |
| 84 <test> | |
| 85 <param name="inputs" value="cuffcompare_in1.gtf,cuffcompare_in2.gtf" ftype="gtf"/> | |
| 86 <param name="use_ref_annotation" value="Yes"/> | |
| 87 <param name="reference_annotation" value="cuffcompare_in3.gtf" ftype="gtf"/> | |
| 88 <param name="min_isoform_fraction" value="0.08" /> | |
| 89 <param name="use_seq_data" value="No"/> | |
| 90 <!-- oId assignment differ/are non-deterministic --> | |
| 91 <output name="merged_transcripts" file="cuffmerge_out1.gtf" lines_diff="50"/> | |
| 92 </test> | |
| 93 </tests> | |
| 94 | |
| 95 <help> | |
| 96 **Cuffmerge Overview** | |
| 97 | |
| 98 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 | |
| 99 | |
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02f427c3614b
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
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100 .. _Cufflinks: http://cole-trapnell-lab.github.io/cufflinks/ |
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02f427c3614b
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
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101 |
| 0 | 102 ------ |
| 103 | |
| 104 **Know what you are doing** | |
| 105 | |
| 106 .. class:: warningmark | |
| 107 | |
| 108 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. | |
| 109 | |
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02f427c3614b
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
0
diff
changeset
|
110 .. __: http://cole-trapnell-lab.github.io/cufflinks/cuffmerge/ |
| 0 | 111 |
| 112 ------ | |
| 113 | |
| 114 **Input format** | |
| 115 | |
| 116 Cuffmerge takes Cufflinks' GTF output as input, and optionally can take a "reference" annotation (such as from Ensembl_) | |
| 117 | |
| 118 .. _Ensembl: http://www.ensembl.org | |
| 119 | |
| 120 ------ | |
| 121 | |
| 122 **Outputs** | |
| 123 | |
| 124 Cuffmerge produces the following output files: | |
| 125 | |
| 126 Merged transcripts file: | |
| 127 | |
| 128 Cuffmerge produces a GTF file that contains an assembly that merges together the input assemblies. | |
| 129 </help> | |
| 130 <citations> | |
| 131 <citation type="doi">10.1038/nbt.1621</citation> | |
| 132 </citations> | |
| 133 </tool> |