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comparison augur_align.xml @ 1:892c6690a1e8 draft default tip

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planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
author dfornika
date Mon, 08 Apr 2019 13:27:08 -0400
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0:20ad934c5536 1:892c6690a1e8
1 <tool id="augur_align" name="augur align" version="@TOOL_VERSION@+galaxy0">
2 <description></description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">augur</requirement>
8 </requirements>
9 <version_command>augur --version</version_command>
10 <command detect_errors="exit_code"><![CDATA[
11 augur align
12 --nthreads \${GALAXY_SLOTS:-1}
13 --sequences '$sequences'
14 --reference-sequence '$reference_sequence'
15 $fill_gaps
16 --output 'output'
17 ]]></command>
18 <inputs>
19 <param name="sequences" type="data" format="fasta" label="Sequences"/>
20 <param name="reference_sequence" type="data" format="fasta" label="Reference Sequence"/>
21 <param name="fill_gaps" type="boolean" checked="false" truevalue="--fill-gaps" falsevalue="" label="Fill Gaps"/>
22 </inputs>
23 <outputs>
24 <data name="pre_aligner_output" format="fasta" >
25 <discover_datasets pattern="output.pre_aligner.fasta" format="fasta" visible="true" />
26 </data>
27 <data name="post_aligner_output" format="fasta" >
28 <discover_datasets pattern="output.post_aligner.fasta" format="fasta" visible="true" />
29 </data>
30 <data name="log" format="text" >
31 <discover_datasets pattern="*.log" format="text" visible="true" />
32 </data>
33 </outputs>
34 <tests>
35 <test>
36 <param name="sequences" value="augur_align_test_0_sequences.input.fasta" />
37 <param name="reference_sequence" value="augur_align_test_0_reference_sequence.input.fasta" />
38 <param name="fill_gaps" value="false" />
39 <output name="pre_aligner_output" file="augur_align_test_0_pre_aligner_output.output.fasta" />
40 <output name="post_aligner_output" file="augur_align_test_0_post_aligner_output.output.fasta" />
41 </test>
42 </tests>
43 <help><![CDATA[
44 Align multiple sequences from FASTA or VCF.
45 ]]></help>
46 <expand macro="citations" />
47 </tool>