Mercurial > repos > devteam > tophat2
annotate tophat_macros.xml @ 5:8d4074c9c2d8 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2 commit 9f1003eecdf81dc46af598617c8a1042c9d9eb8c
| author | devteam |
|---|---|
| date | Sun, 01 Jan 2017 07:12:48 -0500 |
| parents | d1009ebd6f15 |
| children |
| rev | line source |
|---|---|
| 0 | 1 <macros> |
| 2 <macro name="refGenomeSourceConditional"> | |
| 3 <conditional name="refGenomeSource"> | |
| 4 <param name="genomeSource" type="select" label="Use a built in reference genome or own from your history" help="Built-ins genomes were created using default options"> | |
| 5 <option value="indexed" selected="True">Use a built-in genome</option> | |
| 6 <option value="history">Use a genome from history</option> | |
| 7 </param> | |
| 8 <when value="indexed"> | |
| 9 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> | |
| 10 <yield /> | |
| 11 </param> | |
| 12 </when> | |
| 13 <when value="history"> | |
| 14 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" /> | |
| 15 </when> <!-- history --> | |
| 16 </conditional> <!-- refGenomeSource --> | |
| 17 </macro> | |
| 18 <macro name="indel_searchConditional"> | |
| 19 <conditional name="indel_search"> | |
| 20 <param name="allow_indel_search" type="select" label="Allow indel search"> | |
| 21 <option value="Yes">Yes</option> | |
| 22 <option value="No">No</option> | |
| 23 </param> | |
| 24 <when value="No"/> | |
| 25 <when value="Yes"> | |
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0d9d5dede10b
planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
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26 <param name="max_insertion_length" type="integer" value="3" label="Max insertion length." help="--max-insertion-length; The maximum insertion length. The default is 3." /> |
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0d9d5dede10b
planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
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27 <param name="max_deletion_length" type="integer" value="3" label="Max deletion length." help="--max-deletion-length; The maximum deletion length. The default is 3." /> |
| 0 | 28 </when> |
| 29 </conditional> | |
| 30 </macro> | |
| 31 <macro name="own_junctionsConditional"> | |
| 32 <conditional name="own_junctions"> | |
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0d9d5dede10b
planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
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33 <param name="use_junctions" type="select" label="Do you want to supply your own junction data" help="The options below allow you validate your own list of known transcripts or junctions with your RNA-Seq data. Note that the chromosome names in the files provided with the options below must match the names in the Bowtie index."> |
| 0 | 34 <option value="No">No</option> |
| 35 <option value="Yes">Yes</option> | |
| 36 </param> | |
| 37 <when value="Yes"> | |
| 38 <conditional name="gene_model_ann"> | |
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d1009ebd6f15
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2 commit d930385294c447acf3d18e3a8efbe5dbea524b5d
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39 <param name="use_annotations" type="select" label="Use Gene Annotation Model" help="-G/--GTF; TopHat with a set of gene model annotations and/or known transcripts, as a GTF 2.2 or GFF3 formatted file. If this option is provided, TopHat will first extract the transcript sequences and use Bowtie to align reads to this virtual transcriptome first. Only the reads that do not fully map to the transcriptome will then be mapped on the genome. The reads that did map on the transcriptome will be converted to genomic mappings (spliced as needed) and merged with the novel mappings and junctions in the final tophat output. Please note that the values in the first column of the provided GTF/GFF file (column which indicates the chromosome or contig on which the feature is located), must match the name of the reference sequence in the Bowtie index you are using with TopHat."> |
| 0 | 40 <option value="No">No</option> |
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d1009ebd6f15
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2 commit d930385294c447acf3d18e3a8efbe5dbea524b5d
devteam
parents:
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diff
changeset
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41 <option value="indexed">Use a built-in gene annotation</option> |
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d1009ebd6f15
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2 commit d930385294c447acf3d18e3a8efbe5dbea524b5d
devteam
parents:
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diff
changeset
|
42 <option value="history">Use a gene annotation from history</option> |
| 0 | 43 </param> |
| 44 <when value="No" /> | |
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d1009ebd6f15
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2 commit d930385294c447acf3d18e3a8efbe5dbea524b5d
devteam
parents:
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diff
changeset
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45 <when value="indexed"> |
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d1009ebd6f15
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2 commit d930385294c447acf3d18e3a8efbe5dbea524b5d
devteam
parents:
1
diff
changeset
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46 <param format="gtf,gff3" name="gene_annotation_model" type="select" label="Gene Model Annotations"> |
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d1009ebd6f15
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2 commit d930385294c447acf3d18e3a8efbe5dbea524b5d
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parents:
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diff
changeset
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47 <options from_data_table="gff_gene_annotations"/> |
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d1009ebd6f15
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2 commit d930385294c447acf3d18e3a8efbe5dbea524b5d
devteam
parents:
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diff
changeset
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48 </param> |
| 0 | 49 </when> |
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4
d1009ebd6f15
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2 commit d930385294c447acf3d18e3a8efbe5dbea524b5d
devteam
parents:
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diff
changeset
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50 <when value="history"> |
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d1009ebd6f15
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2 commit d930385294c447acf3d18e3a8efbe5dbea524b5d
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parents:
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diff
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51 <param format="gtf,gff3" name="gene_annotation_model" type="data" label="Gene Model Annotations" metadata_name="dbkey" /> |
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d1009ebd6f15
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2 commit d930385294c447acf3d18e3a8efbe5dbea524b5d
devteam
parents:
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diff
changeset
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52 </when> |
| 0 | 53 </conditional> |
| 54 <expand macro="raw_juncsConditional" /> | |
| 55 <expand macro="no_novel_juncsParam" /> | |
| 56 </when> | |
| 57 <when value="No" /> | |
| 58 </conditional> <!-- /own_junctions --> | |
| 59 </macro> | |
| 60 <macro name="raw_juncsConditional"> | |
| 61 <conditional name="raw_juncs"> | |
| 62 <param name="use_juncs" type="select" label="Use Raw Junctions"> | |
| 63 <option value="No">No</option> | |
| 64 <option value="Yes">Yes</option> | |
| 65 </param> | |
| 66 <when value="No" /> | |
| 67 <when value="Yes"> | |
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1
0d9d5dede10b
planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
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diff
changeset
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68 <param format="interval" name="raw_juncs" type="data" label="Raw Junctions" help="-j/--raw-juncs; Supply TopHat with a list of raw junctions. Junctions are specified one per line, in a tab-delimited format. Records look like: [chrom] [left] [right] [+/-] left and right are zero-based coordinates, and specify the last character of the left sequenced to be spliced to the first character of the right sequence, inclusive."/> |
| 0 | 69 </when> |
| 70 </conditional> | |
| 71 </macro> | |
| 72 <macro name="no_novel_juncsParam"> | |
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0d9d5dede10b
planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
0
diff
changeset
|
73 <param name="no_novel_juncs" type="select" label="Only look for supplied junctions" help="--no-novel-juncs; Only look for reads across junctions indicated in the supplied GFF or junctions file."> |
| 0 | 74 <option value="No">No</option> |
| 75 <option value="Yes">Yes</option> | |
| 76 </param> | |
| 77 </macro> | |
| 78 </macros> |