5
|
1 <tool id="get_chrom_sizes" name="Get Chromosome Sizes" version="2.2">
|
1
|
2 <description>Chromosome sizes are needed for the creation of ribosome profiles. This tool generates a tab delimited chrom.sizes file from an inputted fasta</description>
|
|
3 <command>
|
8
|
4 python $__tool_directory__/calculating_chrom.sizes.py ${refGenomeSource.genomeSource} ${refGenomeSource.genomeSource.input1_file} ${refGenomeSource.genomeSource.input1_builtin} ${input2} ${output1}
|
1
|
5 </command>
|
0
|
6 <inputs>
|
4
|
7 <conditional name="refGenomeSource">
|
|
8 <param name="genomeSource" type="select" label="Will you select a reference from your history or use a built-in FASTA?">
|
|
9 <option value="builtin">Use a built-in FASTA</option>
|
|
10 <option value="history">Use one from the history</option>
|
|
11 </param>
|
|
12 <when value="builtin">
|
6
|
13 <param name="input1_builtin" type="select" label="Select a reference" help="if your reference of interest is not listed - contact RiboGalaxy team">
|
4
|
14 <options from_data_table="builtin_fastas">
|
|
15 <filter type="sort_by" column="2" />
|
|
16 <validator type="no_options" message="No built-ins are available" />
|
|
17 </options>
|
|
18 </param>
|
|
19 </when>
|
|
20 <when value="history">
|
6
|
21 <param name="input1_file" type="data" format="fasta" label="FASTA File" />
|
4
|
22 </when>
|
|
23 </conditional>
|
|
24 <param name="input2" type="select" label="Chromosome Column Prefix (eg. chr)">
|
|
25 <option value="chr">'chr' (required for upload to GWIPS-Viz)</option>
|
|
26 <option value="none" selected='true'>None - do not add a prefix</option>
|
|
27 <option value="manual">Specify you own</option>
|
|
28 </param>
|
3
|
29
|
0
|
30 </inputs>
|
|
31 <outputs>
|
|
32 <data name="output1" format="tabular"/>
|
|
33 </outputs>
|
|
34 <tests>
|
|
35 <test>
|
1
|
36 <param name="input1" value="test.fasta" ftype="fasta" />
|
3
|
37 <param name="input2" value="chr"/>
|
0
|
38 <output name="output1" file="test.fasta.sizes" ftype="tabular" lines_diff="4" />
|
|
39 </test>
|
|
40 </tests>
|
|
41 <help>
|
|
42 **What it does**
|
|
43
|
4
|
44 Creates a chromosome sizes file from a fasta file.
|
0
|
45 </help>
|
|
46 <citations/>
|
|
47 </tool>
|