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planemo upload commit c1f0c5ceaac87b6b1db12160a8f5b287635db61b
author yating-l
date Thu, 01 Jun 2017 14:07:15 -0400
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1 <?xml version="1.0"?>
2 <tool id="fa_to_twobit" name="faToTwoBit" version="1.0">
3 <description>Converts a FASTA sequence file into a twoBit file</description>
4
5 <macros>
6 <import>ucsc_macros.xml</import>
7 </macros>
8
9 <expand macro="requirements_twobit" />
10
11 <command detect_errors="exit_code">
12 <![CDATA[
13 faToTwoBit
14 "${fasta_input}" ${no_mask} ${strip_version} "${twobit_output}"
15 ]]>
16 </command>
17 <inputs>
18 <param name="fasta_input" type="data" format="fasta" label="FASTA file" />
19
20 <param name="no_mask" type="boolean" checked="true"
21 truevalue="-noMask" falsevalue=""
22 label="Ignore lower-case masking in fa file"
23 help="-noMask" />
24
25 <param name="strip_version" type="boolean" checked="true"
26 truevalue="-stripVersion" falsevalue=""
27 label="Strip off version number after '.' for GenBank accessions"
28 help="-stripVersion" />
29 </inputs>
30 <outputs>
31 <data name="twobit_output" format="twobit" />
32 </outputs>
33 <tests>
34 <test>
35 <param name="fasta_input" value="KB462401.fa" ftype="fasta" />
36 <output name="twobit_output" file="KB462401.unmasked.2bit" />
37 </test>
38 <test>
39 <param name="fasta_input" value="KB462401.fa" ftype="fasta" />
40 <param name="no_mask" value="" />
41 <output name="twobit_output" file="KB462401.masked.2bit" />
42 </test>
43 <test>
44 <param name="fasta_input" value="KB462401.fa" ftype="fasta" />
45 <param name="strip_version" value="" />
46 <output name="twobit_output" file="KB462401.keepversion.2bit" />
47 </test>
48 </tests>
49 <help>
50 <![CDATA[
51 **What it does**
52
53 faToTwoBit converts a DNA sequence file in FASTA format into a
54 `twoBit Sequence Archive <https://genome.ucsc.edu/goldenpath/help/twoBit.html>`_.
55
56 ]]></help>
57
58 <expand macro="citations" />
59 </tool>