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comparison medaka_consensus.xml @ 0:eecb8c891134 draft

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"planemo upload for repository https://github.com/public-health-bioinformatics/galaxytools/tree/master/tools/medaka commit 54b753ab7f1805cdef74b8eac46cbe4fa039c9b6-dirty"
author dfornika
date Wed, 11 Mar 2020 00:48:06 +0000
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-1:000000000000 0:eecb8c891134
1 <tool id="medaka_consensus" name="medaka_consensus" version="@VERSION@" profile="19.01">
2 <description>Creates a consensus sequence from an alignment generated from nanopore sequence data</description>
3 <macros>
4 <token name="@VERSION@">0.11.5</token>
5 </macros>
6 <requirements>
7 <requirement type="package" version="@VERSION@">medaka</requirement>
8 <requirement type="package" version="1.9">samtools</requirement>
9 </requirements>
10 <version_command>medaka --version</version_command>
11 <command detect_errors="exit_code"><![CDATA[
12 ln -s '${input_alignment}' alignment.bam &&
13 samtools index alignment.bam &&
14 medaka consensus
15 --threads \${GALAXY_SLOTS:-4}
16 --model '${model}'
17 alignment.bam
18 '${consensus_hdf}'
19 > '${log}'
20 ]]></command>
21 <inputs>
22 <param name="input_alignment" type="data" format="bam" label="Input Alignment"/>
23 <param name="model" type="select" label="Model">
24 <option value="r941_min_fast_g303">r941_min_fast_g303</option>
25 <option value="r941_min_high_g303" selected="True">r941_min_high_g303</option>
26 <option value="r941_min_high_g330">r941_min_high_g330</option>
27 <option value="r941_min_high_g344">r941_min_high_g344</option>
28 <option value="r941_prom_fast_g303">r941_prom_fast_g303</option>
29 <option value="r941_prom_high_g303">r941_prom_high_g303</option>
30 <option value="r941_prom_high_g344">r941_prom_high_g344</option>
31 <option value="r941_prom_high_g330">r941_prom_high_g330</option>
32 <option value="r10_min_high_g303">r10_min_high_g303</option>
33 <option value="r10_min_high_g340">r10_min_high_g340</option>
34 <option value="r103_min_high_g345">r103_min_high_g345</option>
35 <option value="r941_prom_snp_g303">r941_prom_snp_g303</option>
36 <option value="r941_prom_variant_g303">r941_prom_variant_g303</option>
37 <option value="r941_min_high_g340_rle">r941_min_high_g340_rle</option>
38 </param>
39 </inputs>
40 <outputs>
41 <data name="consensus_hdf" format="binary" label="${tool.name} on ${on_string}: consensus hdf" />
42 <data name="log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="log.txt"/>
43 </outputs>
44 <tests>
45 </tests>
46 <help><![CDATA[
47 ]]></help>
48 </tool>