Mercurial > repos > iuc > nanopolishcomp_eventaligncollapse

comparison eventaligncollapse.xml @ 0:2f4e5f252d6a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ commit e96954b0926211a1da3292c00aada6d366a2b25d"
author iuc
date Thu, 30 Apr 2020 09:55:36 +0000
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-1:000000000000 0:2f4e5f252d6a
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&#009;ref_kmer"/>
67 <has_text_matching expression="22102&#009;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&#009;ref_start"/>
74 <has_text_matching expression="chr&#009;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&#009;ref_kmer"/>
95 <has_text_matching expression="22102&#009;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&#009;ref_start"/>
102 <has_text_matching expression="chr&#009;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>