Mercurial > repos > devteam > cuffmerge
annotate cuffmerge_wrapper.xml @ 2:5b285b6e4ee3
Update to the new data table specification.
| author | Dave Bouvier <dave@bx.psu.edu> |
|---|---|
| date | Wed, 04 Dec 2013 13:24:59 -0500 |
| parents | dbbd37e013aa |
| children | 68eaaae05c51 |
| rev | line source |
|---|---|
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5b285b6e4ee3
Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
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1 <tool id="cuffmerge" name="Cuffmerge" version="0.0.6"> |
| 0 | 2 <!-- Wrapper supports Cuffmerge versions 1.3 and newer --> |
| 3 <description>merge together several Cufflinks assemblies</description> | |
| 4 <requirements> | |
| 5 <requirement type="package" version="2.1.1">cufflinks</requirement> | |
| 6 </requirements> | |
| 7 <command interpreter="python"> | |
| 8 cuffmerge_wrapper.py | |
| 9 | |
| 10 --num-threads="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: | |
|
2
5b285b6e4ee3
Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
23 --index=${bias_correction.seq_source.index.fields.path} |
| 0 | 24 #end if |
| 25 #end if | |
| 26 | |
| 27 ## Outputs. | |
| 28 --merged-transcripts=${merged_transcripts} | |
| 29 | |
| 30 ## Inputs. | |
| 31 ${first_input} | |
| 32 #for $input_file in $input_files: | |
| 33 ${input_file.additional_input} | |
| 34 #end for | |
| 35 | |
| 36 </command> | |
| 37 <inputs> | |
| 38 <param format="gtf" name="first_input" type="data" label="GTF file produced by Cufflinks" help=""/> | |
| 39 <repeat name="input_files" title="Additional GTF Input Files"> | |
| 40 <param format="gtf" name="additional_input" type="data" label="GTF file produced by Cufflinks" help=""/> | |
| 41 </repeat> | |
| 42 <conditional name="annotation"> | |
| 43 <param name="use_ref_annotation" type="select" label="Use Reference Annotation"> | |
| 44 <option value="No">No</option> | |
| 45 <option value="Yes">Yes</option> | |
| 46 </param> | |
| 47 <when value="Yes"> | |
| 48 <param format="gff3,gtf" name="reference_annotation" type="data" label="Reference Annotation" help="Requires an annotation file in GFF3 or GTF format."/> | |
| 49 </when> | |
| 50 <when value="No"> | |
| 51 </when> | |
| 52 </conditional> | |
| 53 <conditional name="seq_data"> | |
| 54 <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."> | |
| 55 <option value="No">No</option> | |
| 56 <option value="Yes">Yes</option> | |
| 57 </param> | |
| 58 <when value="No"></when> | |
| 59 <when value="Yes"> | |
| 60 <conditional name="seq_source"> | |
| 61 <param name="index_source" type="select" label="Choose the source for the reference list"> | |
| 62 <option value="cached">Locally cached</option> | |
| 63 <option value="history">History</option> | |
| 64 </param> | |
|
2
5b285b6e4ee3
Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
65 <when value="cached"> |
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5b285b6e4ee3
Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
66 <param name="index" type="select" label="Using reference genome"> |
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5b285b6e4ee3
Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
67 <options from_data_table="fasta_indexes"> |
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5b285b6e4ee3
Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
68 <filter type="data_meta" ref="input" key="dbkey" column="1" /> |
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5b285b6e4ee3
Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
69 <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" /> |
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5b285b6e4ee3
Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
70 </options> |
|
5b285b6e4ee3
Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
71 </param> |
|
5b285b6e4ee3
Update to the new data table specification.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
72 </when> |
| 0 | 73 <when value="history"> |
| 74 <param name="ref_file" type="data" format="fasta" label="Using reference file" /> | |
| 75 </when> | |
| 76 </conditional> | |
| 77 </when> | |
| 78 </conditional> | |
| 79 </inputs> | |
| 80 | |
| 81 <outputs> | |
| 82 <data format="gtf" name="merged_transcripts" label="${tool.name} on ${on_string}: merged transcripts"/> | |
| 83 </outputs> | |
| 84 | |
| 85 <tests> | |
| 86 <!-- | |
| 87 cuffmerge -g cuffcompare_in3.gtf cuffcompare_in1.gtf cuffcompare_in2.gtf | |
| 88 --> | |
| 89 <test> | |
| 90 <param name="first_input" value="cuffcompare_in1.gtf" ftype="gtf"/> | |
| 91 <param name="additional_input" value="cuffcompare_in2.gtf" ftype="gtf"/> | |
| 92 <param name="use_ref_annotation" value="Yes"/> | |
| 93 <param name="reference_annotation" value="cuffcompare_in3.gtf" ftype="gtf"/> | |
| 94 <param name="use_seq_data" value="No"/> | |
| 95 <!-- oId assignment differ/are non-deterministic --> | |
| 96 <output name="merged_transcripts" file="cuffmerge_out1.gtf" lines_diff="50"/> | |
| 97 </test> | |
| 98 </tests> | |
| 99 | |
| 100 <help> | |
| 101 **Cuffmerge Overview** | |
| 102 | |
| 103 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 | |
| 104 | |
| 105 .. _Cufflinks: http://cufflinks.cbcb.umd.edu/ | |
| 106 | |
| 107 ------ | |
| 108 | |
| 109 **Know what you are doing** | |
| 110 | |
| 111 .. class:: warningmark | |
| 112 | |
| 113 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. | |
| 114 | |
| 115 .. __: http://cufflinks.cbcb.umd.edu/manual.html#cuffmerge | |
| 116 | |
| 117 ------ | |
| 118 | |
| 119 **Input format** | |
| 120 | |
| 121 Cuffmerge takes Cufflinks' GTF output as input, and optionally can take a "reference" annotation (such as from Ensembl_) | |
| 122 | |
| 123 .. _Ensembl: http://www.ensembl.org | |
| 124 | |
| 125 ------ | |
| 126 | |
| 127 **Outputs** | |
| 128 | |
| 129 Cuffmerge produces the following output files: | |
| 130 | |
| 131 Merged transcripts file: | |
| 132 | |
| 133 Cuffmerge produces a GTF file that contains an assembly that merges together the input assemblies. </help> | |
| 134 </tool> |