Mercurial > repos > devteam > tophat2
comparison tophat_macros.xml @ 0:ffa30bedbee3
Imported from capsule None
| author | devteam |
|---|---|
| date | Mon, 27 Jan 2014 09:26:57 -0500 |
| parents | |
| children | 5c5517d2a9e9 |
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| -1:000000000000 | 0:ffa30bedbee3 |
|---|---|
| 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"> | |
| 26 <param name="max_insertion_length" type="integer" value="3" label="Max insertion length." help="The maximum insertion length." /> | |
| 27 <param name="max_deletion_length" type="integer" value="3" label="Max deletion length." help="The maximum deletion length." /> | |
| 28 </when> | |
| 29 </conditional> | |
| 30 </macro> | |
| 31 <macro name="own_junctionsConditional"> | |
| 32 <conditional name="own_junctions"> | |
| 33 <param name="use_junctions" type="select" label="Use Own Junctions"> | |
| 34 <option value="No">No</option> | |
| 35 <option value="Yes">Yes</option> | |
| 36 </param> | |
| 37 <when value="Yes"> | |
| 38 <conditional name="gene_model_ann"> | |
| 39 <param name="use_annotations" type="select" label="Use Gene Annotation Model"> | |
| 40 <option value="No">No</option> | |
| 41 <option value="Yes">Yes</option> | |
| 42 </param> | |
| 43 <when value="No" /> | |
| 44 <when value="Yes"> | |
| 45 <param format="gtf,gff3" name="gene_annotation_model" type="data" label="Gene Model Annotations" help="TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping."/> | |
| 46 </when> | |
| 47 </conditional> | |
| 48 <expand macro="raw_juncsConditional" /> | |
| 49 <expand macro="no_novel_juncsParam" /> | |
| 50 </when> | |
| 51 <when value="No" /> | |
| 52 </conditional> <!-- /own_junctions --> | |
| 53 </macro> | |
| 54 <macro name="raw_juncsConditional"> | |
| 55 <conditional name="raw_juncs"> | |
| 56 <param name="use_juncs" type="select" label="Use Raw Junctions"> | |
| 57 <option value="No">No</option> | |
| 58 <option value="Yes">Yes</option> | |
| 59 </param> | |
| 60 <when value="No" /> | |
| 61 <when value="Yes"> | |
| 62 <param format="interval" name="raw_juncs" type="data" label="Raw Junctions" help="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."/> | |
| 63 </when> | |
| 64 </conditional> | |
| 65 </macro> | |
| 66 <macro name="no_novel_juncsParam"> | |
| 67 <param name="no_novel_juncs" type="select" label="Only look for supplied junctions"> | |
| 68 <option value="No">No</option> | |
| 69 <option value="Yes">Yes</option> | |
| 70 </param> | |
| 71 </macro> | |
| 72 </macros> |