Mercurial > repos > iuc > medaka_consensus_pipeline

comparison medaka_consensus.xml @ 13:72b5e9dda577 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
author iuc
date Thu, 18 Nov 2021 20:01:28 +0000
parents 8dfe8a52346f
children cb34f00cc10f
comparison
equal deleted inserted replaced
12:0e9e7fcdd543 13:72b5e9dda577
1 <tool id="medaka_consensus_pipeline" name="medaka consensus pipeline" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> 1 <tool id="medaka_consensus_pipeline" name="medaka consensus pipeline" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" 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"/>
53 </data> 53 </data>
54 </outputs> 54 </outputs>
55 <tests> 55 <tests>
56 <!-- #1 default --> 56 <!-- #1 default -->
57 <test expect_num_outputs="3"> 57 <test expect_num_outputs="3">
58 <param name="i" value="basecalls.fastq"/> 58 <param name="i" value="basecalls.fastq.gz"/>
59 <param name="d" value="assembly.fasta"/> 59 <param name="d" value="assembly.fasta"/>
60 <output name="out_consensus"> 60 <output name="out_consensus">
61 <assert_contents> 61 <assert_contents>
62 <has_n_lines n="2"/> 62 <has_n_lines n="2"/>
63 <has_line line=">4"/> 63 <has_line line=">4"/>
69 <has_size value="165503" delta="100"/> 69 <has_size value="165503" delta="100"/>
70 </assert_contents> 70 </assert_contents>
71 </output> 71 </output>
72 <output name="out_calls"> 72 <output name="out_calls">
73 <assert_contents> 73 <assert_contents>
74 <has_size value="343197" delta="100"/> 74 <has_size value="343341" delta="100"/>
75 </assert_contents> 75 </assert_contents>
76 </output> 76 </output>
77 </test> 77 </test>
78 <!-- #2 --> 78 <!-- #2 -->
79 <test expect_num_outputs="5"> 79 <test expect_num_outputs="5">
80 <param name="i" value="basecalls.fastq"/> 80 <param name="i" value="basecalls.fastq.gz"/>
81 <param name="d" value="assembly.fasta"/> 81 <param name="d" value="assembly.fasta"/>
82 <param name="m" value="r941_min_fast_g303"/> 82 <param name="m" value="r941_min_fast_g303"/>
83 <param name="b" value="99"/> 83 <param name="b" value="99"/>
84 <param name="out" value="consensus,probs,calls,log,gaps"/> 84 <param name="out" value="consensus,probs,calls,log,gaps"/>
85 <output name="out_consensus"> 85 <output name="out_consensus">
93 <has_size value="166251" delta="100"/> 93 <has_size value="166251" delta="100"/>
94 </assert_contents> 94 </assert_contents>
95 </output> 95 </output>
96 <output name="out_calls"> 96 <output name="out_calls">
97 <assert_contents> 97 <assert_contents>
98 <has_size value="343197" delta="100"/> 98 <has_size value="343340" delta="100"/>
99 </assert_contents> 99 </assert_contents>
100 </output> 100 </output>
101 <output name="out_log"> 101 <output name="out_log">
102 <assert_contents> 102 <assert_contents>
103 <has_line line="Polished assembly written to results/consensus.fasta, have a nice day."/> 103 <has_line line="Polished assembly written to results/consensus.fasta, have a nice day."/>
117 117
118 @WID@ 118 @WID@
119 119
120 The *medaka_consensus* pipeline performs assembly polishing via neural networks. 120 The *medaka_consensus* pipeline performs assembly polishing via neural networks.
121 121
122 ----
123
124 .. class:: infomark
125
122 **Input** 126 **Input**
123 127
124 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. 128 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.
129
130 ----
131
132 .. class:: infomark
125 133
126 **Output** 134 **Output**
127 135
128 - Consensus polished assembly (FASTA) 136 - Consensus polished assembly (FASTA)
129 - Consensus Probabilities (H5/HDF) 137 - Consensus Probabilities (H5/HDF)
130 - Calls To Draft (BAM) 138 - Calls To Draft (BAM)
131 - Draft To Consensus (chain, TXT) 139 - Draft To Consensus (chain, TXT)
132 - Variants: VCF of changes (VCF) 140 - Variants: VCF of changes (VCF)
133 - Polished: BED file of polished regions (BED) 141 - Polished: BED file of polished regions (BED)
134 142
143 @MODELS@
144
145 ----
146
147 .. class:: infomark
148
135 **References** 149 **References**
136 150
137 @REFERENCES@ 151 @REFERENCES@
138 ]]></help> 152 ]]></help>
139 <expand macro="citations"/> 153 <expand macro="citations"/>