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comparison aacoverage.xml @ 0:71976cfc9022 draft

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planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
author nml
date Mon, 04 Dec 2017 10:25:26 -0500
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1 <tool id="aacoverage" name="Amino Acid Coverage" version="0.1.0">
2 <description>Builds an aa census and returns its coverage</description>
3 <requirements>
4 <requirement type="package" version="0.2.2">quasitools</requirement>
5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[
7
8 ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai &&
9
10 quasitools aacoverage $input_bam $ref_file $input_genes -o output.csv
11
12 ]]></command>
13 <inputs>
14 <param name="input_bam" type="data" format="bam" optional="false" label="Bam file" />
15 <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" />
16 <param name="input_genes" type="data" format="bed" optional="false" label="Gene file" />
17 </inputs>
18 <outputs>
19 <data format="csv" name="output" from_work_dir="output.csv" />
20 </outputs>
21 <tests>
22 <test>
23 <param name="input_bam" value="align.bam" />
24 <param name="ref_file" value="hxb2_pol.fas" />
25 <param name="input_genes" ftype="bed" value="hxb2_pol.bed" />
26 <output name="output" >
27 <assert_contents>
28 <has_text text="frame: 0" />
29 <has_text text="1,0" />
30 <has_text text="948,1" />
31 </assert_contents>
32 </output>
33 </test>
34 </tests>
35 <help><![CDATA[
36
37 Amino Acid Coverage
38 ===================
39
40 Builds an amino acid census and returns its coverage.
41
42 **Output**
43
44 A file with one entry per line with the AA position and the coverage at the position.
45
46 ]]></help>
47 <citations>
48 </citations>
49 </tool>