Mercurial > repos > iuc > medaka_consensus_pipeline

comparison medaka_consensus.xml @ 0:ef94bace3a3c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
author iuc
date Sat, 23 May 2020 13:38:26 -0400
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children 551f8c9bc4cf
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-1:000000000000 0:ef94bace3a3c
1 <tool id="medaka_consensus_pipeline" name="medaka: Consensus pipeline" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
2 <description>Assembly polishing via neural networks</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="version_command"/>
8 <command detect_errors="exit_code"><![CDATA[
9 medaka_consensus
10 ## optional
11 -m '${m}'
12 -b $b
13 -o 'results'
14 #if 'draft' in str($out).split(',') or 'variants' in str($out).split(',') or 'polished' in str($out).split(',')
15 -v
16 #end if
17 -t \${GALAXY_SLOTS:-4}
18 ## required
19 -i '$i'
20 -d '$d'
21
22 |& tee 'log.txt'
23 #if 'variants' in str($out).split(',')
24 && bgzip -d 'results/variants.vcf.gz'
25 #end if
26 ]]></command>
27 <inputs>
28 <param argument="-i" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz,fasta,fasta.gz" label="Select basecalls"/>
29 <param argument="-d" type="data" format="fasta,fasta.gz" label="Select assembly" help="The input assembly should be preprocessed with racon."/>
30 <expand macro="model"/>
31 <expand macro="b"/>
32 <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)" help="'Draft To Consensus', 'Variants' and 'Polished regions in draft coordinates' are generated using the parameter -v.">
33 <option value="consensus" selected="true">Consensus</option>
34 <option value="probs" selected="true">Consensus probabilities</option>
35 <option value="calls" selected="true">Calls to draft</option>
36 <option value="draft">Draft to consensus</option>
37 <option value="variants">Variants</option>
38 <option value="polished">Polished regions in draft coordinates</option>
39 <option value="log">Log</option>
40 </param>
41 </inputs>
42 <outputs>
43 <!-- standard -->
44 <data name="out_consensus" format="fasta" from_work_dir="results/consensus.fasta" label="${tool.name} on ${on_string}: Consensus">
45 <filter>'consensus' in out</filter>
46 </data>
47 <data name="out_probs" format="h5" from_work_dir="results/consensus_probs.hdf" label="${tool.name} on ${on_string}: Consensus probabilities">
48 <filter>'probs' in out</filter>
49 </data>
50 <data name="out_calls" format="bam" from_work_dir="results/calls_to_draft.bam" label="${tool.name} on ${on_string}: Calls to draft">
51 <filter>'calls' in out</filter>
52 </data>
53 <!-- optional with parameter -v -->
54 <data name="out_draft" format="txt" from_work_dir="results/draft_to_consensus.chain" label="${tool.name} on ${on_string}: Draft to consensus">
55 <filter>'draft' in out</filter>
56 </data>
57 <data name="out_variants" format="vcf" from_work_dir="results/variants.vcf" label="${tool.name} on ${on_string}: Variants">
58 <filter>'variants' in out</filter>
59 </data>
60 <data name="out_polished" format="bed" from_work_dir="results/polished_regions_in_draft_coords.bed" label="${tool.name} on ${on_string}: Polished regions in Draft">
61 <filter>'polished' in out</filter>
62 </data>
63 <!-- optional -->
64 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="log.txt">
65 <filter>'log' in out</filter>
66 </data>
67 </outputs>
68 <tests>
69 <!-- #1 default -->
70 <test expect_num_outputs="3">
71 <param name="i" value="basecalls.fastq"/>
72 <param name="d" value="assembly.fasta"/>
73 <output name="out_consensus">
74 <assert_contents>
75 <has_n_lines n="2"/>
76 <has_line line=">4_segment0 4:1.0-3792.0"/>
77 <has_text_matching expression=".+GTCAGAATCGCGTTCAGCGCGTTTCAGCGGTGCGTACAATT.+"/>
78 </assert_contents>
79 </output>
80 <output name="out_probs">
81 <assert_contents>
82 <has_size value="194782" delta="100"/>
83 </assert_contents>
84 </output>
85 <output name="out_calls">
86 <assert_contents>
87 <has_size value="533139" delta="100"/>
88 </assert_contents>
89 </output>
90 </test>
91 <!-- #2 -->
92 <test expect_num_outputs="7">
93 <param name="i" value="basecalls.fastq"/>
94 <param name="d" value="assembly.fasta"/>
95 <param name="m" value="r941_min_fast_g303"/>
96 <param name="b" value="99"/>
97 <param name="out" value="consensus,probs,calls,draft,variants,polished,log"/>
98 <output name="out_consensus">
99 <assert_contents>
100 <has_n_lines n="65"/>
101 <has_line line=">4 length=3792 depth=114.52x circular=true"/>
102 <has_line line="CATCTCTTT"/>
103 </assert_contents>
104 </output>
105 <output name="out_probs">
106 <assert_contents>
107 <has_size value="192710" delta="100"/>
108 </assert_contents>
109 </output>
110 <output name="out_calls">
111 <assert_contents>
112 <has_size value="533163" delta="100"/>
113 </assert_contents>
114 </output>
115 <output name="out_draft">
116 <assert_contents>
117 <has_n_lines n="6"/>
118 <has_line line="chain 3789 4 3792 + 0 3792 4 3789 + 0 3789 1"/>
119 <has_line line="1204"/>
120 </assert_contents>
121 </output>
122 <output name="out_polished">
123 <assert_contents>
124 <has_size value="9"/>
125 </assert_contents>
126 </output>
127 <output name="out_variants">
128 <assert_contents>
129 <has_n_lines n="9"/>
130 <has_line line="##fileformat=VCFv4.1"/>
131 <has_text_matching expression="4&#009;.+"/>
132 </assert_contents>
133 </output>
134 <output name="out_log">
135 <assert_contents>
136 <has_line line="Polished assembly written to results/consensus.fasta, have a nice day."/>
137 </assert_contents>
138 </output>
139 </test>
140 </tests>
141 <help><![CDATA[
142 .. class:: infomark
143
144 **What it does**
145
146 @WID@
147
148 The *medaka_consensus* pipeline performs assembly polishing via neural networks.
149
150 **Input**
151
152 An *assembly* in .fasta format and *basecalls* in .fasta or .fastq format are required. See `Creating a Draft Assembly <https://nanoporetech.github.io/medaka/walkthrough.html#basecalling-and-draft-assembly>`_ for a detailed example of one method of obtaining these.
153
154 **Output**
155
156 - Consensus polished assembly (FASTA)
157 - Consensus Probabilities (H5/HDF)
158 - Calls To Draft (BAM)
159 - Draft To Consensus (chain, TXT)
160 - Variants: VCF of changes (VCF)
161 - Polished: BED file of polished regions (BED)
162
163 **References**
164
165 @REFERENCES@
166 ]]></help>
167 <expand macro="citations"/>
168 </tool>