Mercurial > repos > iuc > medaka_consensus_pipeline
comparison medaka_consensus.xml @ 10:1ca4ce7241fd draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13"
author | iuc |
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date | Thu, 22 Apr 2021 20:25:13 +0000 |
parents | a1b70f038b4a |
children | 8dfe8a52346f |
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9:a7228a7ea146 | 10:1ca4ce7241fd |
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1 <tool id="medaka_consensus_pipeline" name="medaka consensus pipeline" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@"> | 1 <tool id="medaka_consensus_pipeline" name="medaka consensus pipeline" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> |
2 <description>Assembly polishing via neural networks</description> | 2 <description>Assembly polishing via neural networks</description> |
3 <macros> | 3 <macros> |
4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro="requirements"/> | 6 <expand macro="requirements"/> |
9 medaka_consensus | 9 medaka_consensus |
10 ## optional | 10 ## optional |
11 -m ${m} | 11 -m ${m} |
12 -b $b | 12 -b $b |
13 -o results | 13 -o results |
14 #if 'draft' in str($out).split(',') or 'variants' in str($out).split(',') or 'polished' in str($out).split(',') | |
15 -v | |
16 #end if | |
17 -t \${GALAXY_SLOTS:-4} | 14 -t \${GALAXY_SLOTS:-4} |
18 ## required | 15 ## required |
19 -i '$i' | 16 -i '$i' |
20 -d '$d' | 17 -d '$d' |
21 | 18 |
24 <inputs> | 21 <inputs> |
25 <param argument="-i" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz,fasta,fasta.gz" label="Select basecalls"/> | 22 <param argument="-i" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz,fasta,fasta.gz" label="Select basecalls"/> |
26 <param argument="-d" type="data" format="fasta,fasta.gz" label="Select assembly" help="The input assembly should be preprocessed with racon."/> | 23 <param argument="-d" type="data" format="fasta,fasta.gz" label="Select assembly" help="The input assembly should be preprocessed with racon."/> |
27 <expand macro="model"/> | 24 <expand macro="model"/> |
28 <expand macro="b"/> | 25 <expand macro="b"/> |
26 <param argument="-g" type="boolean" truevalue="-g" falsevalue="" label="Don't fill gaps in consensus with draft sequence?" checked="false" /> | |
29 <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."> | 27 <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."> |
30 <option value="consensus" selected="true">Consensus</option> | 28 <option value="consensus" selected="true">Consensus</option> |
31 <option value="probs" selected="true">Consensus probabilities</option> | 29 <option value="probs" selected="true">Consensus probabilities</option> |
32 <option value="calls" selected="true">Calls to draft</option> | 30 <option value="calls" selected="true">Calls to draft</option> |
33 <option value="draft">Draft to consensus</option> | |
34 <option value="variants">Variants</option> | |
35 <option value="polished">Polished regions in draft coordinates</option> | |
36 <option value="log">Log</option> | 31 <option value="log">Log</option> |
32 <option value="gaps">Gap regions in draft</option> | |
37 </param> | 33 </param> |
38 </inputs> | 34 </inputs> |
39 <outputs> | 35 <outputs> |
40 <!-- standard --> | 36 <!-- standard --> |
41 <data name="out_consensus" format="fasta" from_work_dir="results/consensus.fasta" label="${tool.name} on ${on_string}: Consensus"> | 37 <data name="out_consensus" format="fasta" from_work_dir="results/consensus.fasta" label="${tool.name} on ${on_string}: Consensus"> |
45 <filter>'probs' in out</filter> | 41 <filter>'probs' in out</filter> |
46 </data> | 42 </data> |
47 <data name="out_calls" format="bam" from_work_dir="results/calls_to_draft.bam" label="${tool.name} on ${on_string}: Calls to draft"> | 43 <data name="out_calls" format="bam" from_work_dir="results/calls_to_draft.bam" label="${tool.name} on ${on_string}: Calls to draft"> |
48 <filter>'calls' in out</filter> | 44 <filter>'calls' in out</filter> |
49 </data> | 45 </data> |
50 <!-- optional with parameter -v --> | 46 <data name="out_gaps" format="bed" from_work_dir="results/consensus.fasta.gaps_in_draft_coords.bed" label="${tool.name} on ${on_string}: Gaps in draft"> |
51 <data name="out_draft" format="txt" from_work_dir="results/draft_to_consensus.chain" label="${tool.name} on ${on_string}: Draft to consensus"> | 47 <filter>'gaps' in out</filter> |
52 <filter>'draft' in out</filter> | |
53 </data> | |
54 <data name="out_variants" format="vcf_bgzip" from_work_dir="results/variants.vcf.gz" label="${tool.name} on ${on_string}: Variants"> | |
55 <filter>'variants' in out</filter> | |
56 </data> | |
57 <data name="out_polished" format="bed" from_work_dir="results/polished_regions_in_draft_coords.bed" label="${tool.name} on ${on_string}: Polished regions in Draft"> | |
58 <filter>'polished' in out</filter> | |
59 </data> | 48 </data> |
60 <!-- optional --> | 49 <!-- optional --> |
61 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log"> | 50 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log"> |
62 <filter>'log' in out</filter> | 51 <filter>'log' in out</filter> |
63 </data> | 52 </data> |
68 <param name="i" value="basecalls.fastq"/> | 57 <param name="i" value="basecalls.fastq"/> |
69 <param name="d" value="assembly.fasta"/> | 58 <param name="d" value="assembly.fasta"/> |
70 <output name="out_consensus"> | 59 <output name="out_consensus"> |
71 <assert_contents> | 60 <assert_contents> |
72 <has_n_lines n="2"/> | 61 <has_n_lines n="2"/> |
73 <has_line line=">4_segment0 4:1.0-3792.0"/> | 62 <has_line line=">4"/> |
74 <has_text_matching expression=".+GTCAGAATCGCGTTCAGCGCGTTTCAGCGGTGCGTACAATT.+"/> | 63 <has_text_matching expression=".+GTCAGAATCGCGTTCAGCGCGTTTCAGCGGTGCGTACAATT.+"/> |
75 </assert_contents> | 64 </assert_contents> |
76 </output> | 65 </output> |
77 <output name="out_probs"> | 66 <output name="out_probs"> |
78 <assert_contents> | 67 <assert_contents> |
79 <has_size value="165271" delta="100"/> | 68 <has_size value="165503" delta="100"/> |
80 </assert_contents> | 69 </assert_contents> |
81 </output> | 70 </output> |
82 <output name="out_calls"> | 71 <output name="out_calls"> |
83 <assert_contents> | 72 <assert_contents> |
84 <has_size value="343197" delta="100"/> | 73 <has_size value="343197" delta="100"/> |
85 </assert_contents> | 74 </assert_contents> |
86 </output> | 75 </output> |
87 </test> | 76 </test> |
88 <!-- #2 --> | 77 <!-- #2 --> |
89 <test expect_num_outputs="7"> | 78 <test expect_num_outputs="5"> |
90 <param name="i" value="basecalls.fastq"/> | 79 <param name="i" value="basecalls.fastq"/> |
91 <param name="d" value="assembly.fasta"/> | 80 <param name="d" value="assembly.fasta"/> |
92 <param name="m" value="r941_min_fast_g303"/> | 81 <param name="m" value="r941_min_fast_g303"/> |
93 <param name="b" value="99"/> | 82 <param name="b" value="99"/> |
94 <param name="out" value="consensus,probs,calls,draft,variants,polished,log"/> | 83 <param name="out" value="consensus,probs,calls,log,gaps"/> |
95 <output name="out_consensus"> | 84 <output name="out_consensus"> |
96 <assert_contents> | 85 <assert_contents> |
97 <has_n_lines n="65"/> | 86 <has_n_lines n="2"/> |
98 <has_line line=">4 length=3792 depth=114.52x circular=true"/> | 87 <has_line line=">4"/> <!-- Replace test --> |
99 <has_line line="ATCTCTTT"/> | |
100 </assert_contents> | 88 </assert_contents> |
101 </output> | 89 </output> |
102 <output name="out_probs"> | 90 <output name="out_probs"> |
103 <assert_contents> | 91 <assert_contents> |
104 <has_size value="166251" delta="100"/> | 92 <has_size value="166251" delta="100"/> |
107 <output name="out_calls"> | 95 <output name="out_calls"> |
108 <assert_contents> | 96 <assert_contents> |
109 <has_size value="343197" delta="100"/> | 97 <has_size value="343197" delta="100"/> |
110 </assert_contents> | 98 </assert_contents> |
111 </output> | 99 </output> |
112 <output name="out_draft"> | |
113 <assert_contents> | |
114 <has_line line="chain 3788 4 3792 + 0 3792 4 3788 + 0 3788 1"/> | |
115 <has_line line="1409 1 0"/> | |
116 <has_line line="440 1 0"/> | |
117 <has_line line="736 1 0"/> | |
118 <has_line line="853 1 0"/> | |
119 <has_line line="350"/> | |
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" file="variants.vcf.gz" decompress="true"/> | |
128 <output name="out_log"> | 100 <output name="out_log"> |
129 <assert_contents> | 101 <assert_contents> |
130 <has_line line="Polished assembly written to results/consensus.fasta, have a nice day."/> | 102 <has_line line="Polished assembly written to results/consensus.fasta, have a nice day."/> |
103 </assert_contents> | |
104 </output> | |
105 <output name="out_gaps"> | |
106 <assert_contents> | |
107 <has_size value="0" delta="0"/> | |
131 </assert_contents> | 108 </assert_contents> |
132 </output> | 109 </output> |
133 </test> | 110 </test> |
134 </tests> | 111 </tests> |
135 <help><![CDATA[ | 112 <help><![CDATA[ |