Mercurial > repos > iuc > nanopolishcomp_eventaligncollapse
comparison eventaligncollapse.xml @ 0:6847a625db4d draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ commit e96954b0926211a1da3292c00aada6d366a2b25d"
author | iuc |
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date | Thu, 30 Apr 2020 05:56:29 -0400 |
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children | ad011fc670d6 |
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1 <?xml version="1.0"?> | |
2 <tool id="nanopolishcomp_eventaligncollapse" name="Eventalign Collapse" version="@TOOL_VERSION@+@WRAPPER_VERSION@"> | |
3 <description>by kmers rather than by event</description> | |
4 <macros> | |
5 <import>macros.xml</import> | |
6 </macros> | |
7 <expand macro="requirements"/> | |
8 <stdio></stdio> | |
9 <version_command>NanopolishComp --version</version_command> | |
10 <command detect_errors="exit_code"><![CDATA[ | |
11 ## initialize | |
12 ## requires a minimum of 3 threads | |
13 threads=\$((3 > \${GALAXY_SLOTS:-3} ? 3 : \${GALAXY_SLOTS:-3})) && | |
14 | |
15 ## run | |
16 NanopolishComp | |
17 Eventalign_collapse | |
18 -i '$i' | |
19 -s | |
20 -r $r | |
21 -f | |
22 #for $current in $f | |
23 $current | |
24 #end for | |
25 -o 'results' | |
26 -p 'out' | |
27 -t \$threads | |
28 -v | |
29 ]]></command> | |
30 <inputs> | |
31 <param argument="-i" type="data" format="tabular" label="Select nanopolish eventalign file"/> | |
32 <param argument="-s" type="boolean" truevalue="-s" falsevalue="" label="Should raw samples be written?" help="You need to run nanopolish eventalign with --sample option to make use of this feature."/> | |
33 <param argument="-r" type="integer" value="0" min="0" label="Set maximum number of reads to parse" help="Use 0 to deactivate this option."/> | |
34 <param argument="-f" type="select" multiple="true" label="Select statistical fields to compute" help="You need to run nanopolish eventalign with --sample option to make use of this feature."> | |
35 <option value="mean" selected="true">Mean</option> | |
36 <option value="std">Std</option> | |
37 <option value="median" selected="true">Median</option> | |
38 <option value="mad">Mad</option> | |
39 <option value="num_signals" selected="true">Number of signals</option> | |
40 </param> | |
41 <param name="out" type="select" multiple="true" label="Select output file(s)" help=""> | |
42 <option value="eventalign_collapse" selected="true">Eventalign Collapse</option> | |
43 <option value="index" selected="true">Index</option> | |
44 <option value="log">Log</option> | |
45 </param> | |
46 </inputs> | |
47 <outputs> | |
48 <data name="out_eventalign_collapse" format="tabular" from_work_dir="results/out_eventalign_collapse.tsv" label="${tool.name} on ${on_string}: Eventalign Collapse"> | |
49 <filter>'eventalign_collapse' in out</filter> | |
50 </data> | |
51 <data name="out_index" format="tabular" from_work_dir="results/out_eventalign_collapse.tsv.idx" label="${tool.name} on ${on_string}: Index"> | |
52 <filter>'index' in out</filter> | |
53 </data> | |
54 <data name="out_log" format="txt" from_work_dir="results/out_eventalign_collapse.log" label="${tool.name} on ${on_string}: log"> | |
55 <filter>'log' in out</filter> | |
56 </data> | |
57 </outputs> | |
58 <tests> | |
59 <!-- #1 default --> | |
60 <test expect_num_outputs="3"> | |
61 <param name="i" value="sample.tsv"/> | |
62 <param name="out" value="eventalign_collapse,index,log"/> | |
63 <output name="out_eventalign_collapse"> | |
64 <assert_contents> | |
65 <has_n_lines n="236"/> | |
66 <has_text_matching expression="ref_pos	ref_kmer"/> | |
67 <has_text_matching expression="22102	GGAAA"/> | |
68 </assert_contents> | |
69 </output> | |
70 <output name="out_index"> | |
71 <assert_contents> | |
72 <has_n_lines n="60"/> | |
73 <has_text_matching expression="ref_id	ref_start"/> | |
74 <has_text_matching expression="chr	22102"/> | |
75 </assert_contents> | |
76 </output> | |
77 <output name="out_log"> | |
78 <assert_contents> | |
79 <has_n_lines n="13"/> | |
80 <has_line line="General options:"/> | |
81 </assert_contents> | |
82 </output> | |
83 </test> | |
84 <!-- #2 --> | |
85 <test expect_num_outputs="2"> | |
86 <param name="i" value="sample.tsv"/> | |
87 <param name="s" value="true"/> | |
88 <param name="r" value="10"/> | |
89 <param name="f" value="mean,std,median,mad,num_signals"/> | |
90 <param name="out" value="eventalign_collapse,index"/> | |
91 <output name="out_eventalign_collapse"> | |
92 <assert_contents> | |
93 <has_n_lines n="236"/> | |
94 <has_text_matching expression="ref_pos	ref_kmer"/> | |
95 <has_text_matching expression="22102	GGAAA"/> | |
96 </assert_contents> | |
97 </output> | |
98 <output name="out_index"> | |
99 <assert_contents> | |
100 <has_n_lines n="60"/> | |
101 <has_text_matching expression="ref_id	ref_start"/> | |
102 <has_text_matching expression="chr	22102"/> | |
103 </assert_contents> | |
104 </output> | |
105 </test> | |
106 </tests> | |
107 <help><![CDATA[ | |
108 .. class:: infomark | |
109 | |
110 **What it does** | |
111 | |
112 @WID@ | |
113 | |
114 Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. | |
115 | |
116 **Input** | |
117 | |
118 A nanopolish eventalign tabular output file. | |
119 | |
120 **Output** | |
121 | |
122 Contrary to nanopolish eventalign output text file, in Eventalign_collapse the reads are separated by a hashtag headers containing the read_id and ref_id. This reduces the redundancy and makes it easier to find the start and end of a read. | |
123 | |
124 :: | |
125 | |
126 Example : #7ef1d7b9-5824-4382-b23b-78d82c07ebbd YHR055C. | |
127 | |
128 The main data file contains the following fields: | |
129 | |
130 - ref_pos: Reference sequence ID (contig). | |
131 - ref_kmer: Sequence of the reference kmers. | |
132 - -num_events: Number of events for this kmer before collapsing. | |
133 - dwell_time: dwell time for this kmer in seconds | |
134 - NNNNN_dwell_time: dwell time of events for this kmers with a model sequence "NNNNN" (events ignored by nanopolish HMM). | |
135 - mismatch_dwell_time: dwell time of events for this kmers with a model sequence different from the reference kmer | |
136 - start_idx: Only if nanopolish eventalign called with --signal_idx. Start coordinate on original raw signal in fast5 file | |
137 - end_idx: Only if nanopolish eventalign called with --signal_idx. End coordinate on original raw signal in fast5 file | |
138 - mean: Only if nanopolish eventalign called with --samples. Mean of the normalised signal values provided by Nanopolish eventalign | |
139 - median: Only if nanopolish eventalign called with --samples. Median of the normalised signal values provided by Nanopolish eventalign | |
140 - std: Only if nanopolish eventalign called with --samples. Standard deviation of the normalised signal values provided by Nanopolish eventalign | |
141 - mad: Only if nanopolish eventalign called with --samples. Median absolute deviation of the normalised signal values provided by Nanopolish eventalign | |
142 - num_signals: Only if nanopolish eventalign called with --samples. Number of raw signal points. | |
143 - samples: Only if nanopolish eventalign called with --samples and Eventalign_collapse called with --write_samples. List of normalised signal intensity values for this kmer | |
144 | |
145 In addition Eventalign_collapse also generates an useful index file containing reads level information. It contains the following fields: | |
146 | |
147 - read_id: Name or index of the read | |
148 - ref_id: Name of the reference sequence the read was aligned on (contig) | |
149 - ref_start: Start coordinate of the alignment on the reference sequence | |
150 - ref_end: End coordinate of the alignment on the reference sequence | |
151 - dwell_time: Cumulative dwell time in seconds for the entire resquiggled sequence | |
152 - kmers: Overall number of resquiggled kmers | |
153 - NNNNN_kmers: Number of resquiggled kmers containing at least 1 event for which the model sequence was "NNNNN" | |
154 - mismatching_kmers: Number of resquiggled kmers containing at least 1 event for which the model sequence diverged from the reference sequence | |
155 - missing_kmers: Number of skipped/missing reference positions in nanopolish output | |
156 - byte_offset: Number of characters before the start of the sequence in the main output file. This can be used in conjunction with file.seek() to directly access the start of a read. An example is provided in the Usage notebook. | |
157 - byte_len: Length of characters after byte_offset to the end of the read, excluding the last newline. This can be used in conjunction with read() to read all the text chunk corresponding to the read. | |
158 | |
159 .. class:: infomark | |
160 | |
161 **References** | |
162 | |
163 @REFERENCES@ | |
164 ]]></help> | |
165 <expand macro="citations"/> | |
166 </tool> |