Mercurial > repos > devteam > cuffmerge
annotate cuffmerge_wrapper.xml @ 7:4df774d8a900 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 52b81aad3194e02a04ec09eea1aa0c1e9301e942
| author | iuc |
|---|---|
| date | Wed, 23 Oct 2024 22:12:11 +0000 |
| parents | f4bc1b2fc4d4 |
| children |
| rev | line source |
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7
4df774d8a900
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 52b81aad3194e02a04ec09eea1aa0c1e9301e942
iuc
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1 <tool id="cuffmerge" name="Cuffmerge" version="@TOOL_VERSION@.5" profile="@PROFILE@"> |
| 0 | 2 <description>merge together several Cufflinks assemblies</description> |
| 3 <macros> | |
| 4 <import>cuff_macros.xml</import> | |
| 5 </macros> | |
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0ed8b7f6d506
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffmerge commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
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changeset
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6 <expand macro="requirements" /> |
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7a9ca385b471
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"
iuc
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7 <version_command>cuffmerge -v</version_command> |
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7a9ca385b471
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"
iuc
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8 <command detect_errors="aggressive"><![CDATA[ |
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7a9ca385b471
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"
iuc
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9 @CUFFLINKS_LINK_GTF_INPUTS@ |
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4df774d8a900
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 52b81aad3194e02a04ec09eea1aa0c1e9301e942
iuc
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diff
changeset
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10 echo @CUFFLINKS_GTF_INPUTS@ | sed 's/\s\+/\n/g' > assembly_GTF_list.txt && |
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7a9ca385b471
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"
iuc
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11 cuffmerge |
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7a9ca385b471
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"
iuc
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12 -o output |
| 0 | 13 --num-threads="\${GALAXY_SLOTS:-4}" |
| 14 ## Use annotation reference? | |
| 15 #if $annotation.use_ref_annotation == "Yes": | |
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0ed8b7f6d506
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffmerge commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents:
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changeset
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16 -g '${annotation.reference_annotation}' |
| 0 | 17 #end if |
| 18 | |
| 19 ## Use sequence data? | |
| 20 #if $seq_data.use_seq_data == "Yes": | |
| 21 -s | |
| 22 #if $seq_data.seq_source.index_source == "history": | |
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8cedf303be28
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
iuc
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23 '${seq_data.seq_source.ref_file}' |
| 0 | 24 #else: |
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8cedf303be28
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 92be38a0f40ef6d6ccb55999f3eb8bf960e376c8"
iuc
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25 '${seq_data.seq_source.index.fields.path}' |
| 0 | 26 #end if |
| 27 #end if | |
| 28 | |
| 29 --min-isoform-fraction="${min_isoform_fraction}" | |
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7a9ca385b471
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"
iuc
parents:
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diff
changeset
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30 assembly_GTF_list.txt |
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7a9ca385b471
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"
iuc
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31 ]]></command> |
| 0 | 32 <inputs> |
| 33 <expand macro="cufflinks_gtf_inputs" /> | |
| 34 <conditional name="annotation"> | |
| 35 <param name="use_ref_annotation" type="select" label="Use Reference Annotation"> | |
| 36 <option value="No">No</option> | |
| 37 <option value="Yes">Yes</option> | |
| 38 </param> | |
| 39 <when value="Yes"> | |
| 40 <param format="gff3,gtf" name="reference_annotation" type="data" label="Reference Annotation" help="Requires an annotation file in GFF3 or GTF format."/> | |
| 41 </when> | |
| 42 <when value="No"> | |
| 43 </when> | |
| 44 </conditional> | |
| 45 <conditional name="seq_data"> | |
| 46 <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."> | |
| 47 <option value="No">No</option> | |
| 48 <option value="Yes">Yes</option> | |
| 49 </param> | |
| 50 <when value="No"></when> | |
| 51 <when value="Yes"> | |
| 52 <conditional name="seq_source"> | |
| 53 <param name="index_source" type="select" label="Choose the source for the reference list"> | |
| 54 <option value="cached">Locally cached</option> | |
| 55 <option value="history">History</option> | |
| 56 </param> | |
| 57 <when value="cached"> | |
| 58 <param name="index" type="select" label="Using reference genome"> | |
| 59 <options from_data_table="fasta_indexes"> | |
| 60 <filter type="data_meta" ref="inputs" key="dbkey" column="1" /> | |
| 61 <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" /> | |
| 62 </options> | |
| 63 </param> | |
| 64 </when> | |
| 65 <when value="history"> | |
| 66 <param name="ref_file" type="data" format="fasta" label="Using reference file" /> | |
| 67 </when> | |
| 68 </conditional> | |
| 69 </when> | |
| 70 </conditional> | |
| 71 <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" /> | |
| 72 </inputs> | |
| 73 | |
| 74 <outputs> | |
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7a9ca385b471
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"
iuc
parents:
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diff
changeset
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75 <data format="gtf" name="merged_transcripts" label="${tool.name} on ${on_string}: merged transcripts" from_work_dir="output/merged.gtf"/> |
| 0 | 76 </outputs> |
| 77 | |
| 78 <tests> | |
| 79 <!-- | |
| 80 cuffmerge -g cuffcompare_in3.gtf cuffcompare_in1.gtf cuffcompare_in2.gtf | |
| 81 --> | |
| 82 <test> | |
| 83 <param name="inputs" value="cuffcompare_in1.gtf,cuffcompare_in2.gtf" ftype="gtf"/> | |
| 84 <param name="use_ref_annotation" value="Yes"/> | |
| 85 <param name="reference_annotation" value="cuffcompare_in3.gtf" ftype="gtf"/> | |
| 86 <param name="min_isoform_fraction" value="0.08" /> | |
| 87 <param name="use_seq_data" value="No"/> | |
| 88 <!-- oId assignment differ/are non-deterministic --> | |
| 89 <output name="merged_transcripts" file="cuffmerge_out1.gtf" lines_diff="50"/> | |
| 90 </test> | |
| 91 </tests> | |
| 92 | |
| 93 <help> | |
| 94 **Cuffmerge Overview** | |
| 95 | |
| 96 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 | |
| 97 | |
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02f427c3614b
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
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98 .. _Cufflinks: http://cole-trapnell-lab.github.io/cufflinks/ |
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02f427c3614b
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
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99 |
| 0 | 100 ------ |
| 101 | |
| 102 **Know what you are doing** | |
| 103 | |
| 104 .. class:: warningmark | |
| 105 | |
| 106 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. | |
| 107 | |
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02f427c3614b
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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108 .. __: http://cole-trapnell-lab.github.io/cufflinks/cuffmerge/ |
| 0 | 109 |
| 110 ------ | |
| 111 | |
| 112 **Input format** | |
| 113 | |
| 114 Cuffmerge takes Cufflinks' GTF output as input, and optionally can take a "reference" annotation (such as from Ensembl_) | |
| 115 | |
| 116 .. _Ensembl: http://www.ensembl.org | |
| 117 | |
| 118 ------ | |
| 119 | |
| 120 **Outputs** | |
| 121 | |
| 122 Cuffmerge produces the following output files: | |
| 123 | |
| 124 Merged transcripts file: | |
| 125 | |
| 126 Cuffmerge produces a GTF file that contains an assembly that merges together the input assemblies. | |
| 127 </help> | |
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7a9ca385b471
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"
iuc
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128 <expand macro="citations"/> |
| 0 | 129 </tool> |