|
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">
|
|
|
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>
|
