Mercurial > repos > mvdbeek > r_goseq_1_22_0
comparison get_length_and_gc_content.xml @ 1:3ab168143b69 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
author | mvdbeek |
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date | Thu, 25 Feb 2016 05:26:51 -0500 |
parents | |
children | a6198fc1116f |
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0:fe71b97cc1a5 | 1:3ab168143b69 |
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1 <tool id="length_and_gc_content" name="gene length and gc content from gtf file" version="0.1.0"> | |
2 <description /> | |
3 <requirements> | |
4 <requirement type="package" version="3.2.1">R</requirement> | |
5 <requirement type="package" version="1.22.0">goseq</requirement> | |
6 </requirements> | |
7 <command interpreter="Rscript"> | |
8 get_length_and_gc_content.r --gtf "$gtf" | |
9 --fasta "$fasta" | |
10 --output "output" | |
11 </command> | |
12 <inputs> | |
13 <param help="The GTF must match the FASTA file" label="GTF file for length and GC calculation" name="gtf" type="data" /> | |
14 <conditional name="fastaSource"> | |
15 <param help="choose history if you don't see the correct genome fasta" label="Select a reference fasta from your history or use a built-in fasta?" name="genomeSource" type="select"> | |
16 <option value="indexed">Use a built-in fasta</option> | |
17 <option value="history">Use fasta from history</option> | |
18 </param> | |
19 <when value="indexed"> | |
20 <param help="Select the fasta file from a list of pre-installed genomes" label="Select a fasta sequence" name="fasta" type="select"> | |
21 <options from_data_table="all_fasta"/> | |
22 </param> | |
23 </when> | |
24 <when value="history"> | |
25 <param format="fasta" label="Select a fasta file, to serve as index reference" name="fasta" type="data" /> | |
26 </when> | |
27 </conditional> | |
28 </inputs> | |
29 <outputs> | |
30 <data format="tabular" label="length and gc content" name="output" /> | |
31 </outputs> | |
32 <tests> | |
33 <test> | |
34 </test> | |
35 </tests> | |
36 <help> | |
37 | |
38 **What it does** | |
39 | |
40 Returns a tabular file with gene name, length and GC content, based on a supplied GTF and a FASTA file. | |
41 | |
42 | |
43 </help> | |
44 <citations> | |
45 </citations> | |
46 </tool> |