annotate eventaligncollapse.xml @ 0:6847a625db4d draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ commit e96954b0926211a1da3292c00aada6d366a2b25d"
author iuc
date Thu, 30 Apr 2020 05:56:29 -0400
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children ad011fc670d6
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 <?xml version="1.0"?>
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2 <tool id="nanopolishcomp_eventaligncollapse" name="Eventalign Collapse" version="@TOOL_VERSION@+@WRAPPER_VERSION@">
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3 <description>by kmers rather than by event</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <stdio></stdio>
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9 <version_command>NanopolishComp --version</version_command>
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10 <command detect_errors="exit_code"><![CDATA[
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11 ## initialize
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12 ## requires a minimum of 3 threads
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13 threads=\$((3 > \${GALAXY_SLOTS:-3} ? 3 : \${GALAXY_SLOTS:-3})) &&
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14
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15 ## run
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16 NanopolishComp
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17 Eventalign_collapse
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18 -i '$i'
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19 -s
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20 -r $r
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21 -f
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22 #for $current in $f
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23 $current
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24 #end for
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25 -o 'results'
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26 -p 'out'
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27 -t \$threads
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28 -v
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29 ]]></command>
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30 <inputs>
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31 <param argument="-i" type="data" format="tabular" label="Select nanopolish eventalign file"/>
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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."/>
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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."/>
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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.">
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35 <option value="mean" selected="true">Mean</option>
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36 <option value="std">Std</option>
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37 <option value="median" selected="true">Median</option>
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38 <option value="mad">Mad</option>
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39 <option value="num_signals" selected="true">Number of signals</option>
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40 </param>
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41 <param name="out" type="select" multiple="true" label="Select output file(s)" help="">
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42 <option value="eventalign_collapse" selected="true">Eventalign Collapse</option>
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43 <option value="index" selected="true">Index</option>
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44 <option value="log">Log</option>
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45 </param>
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46 </inputs>
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47 <outputs>
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48 <data name="out_eventalign_collapse" format="tabular" from_work_dir="results/out_eventalign_collapse.tsv" label="${tool.name} on ${on_string}: Eventalign Collapse">
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49 <filter>'eventalign_collapse' in out</filter>
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50 </data>
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51 <data name="out_index" format="tabular" from_work_dir="results/out_eventalign_collapse.tsv.idx" label="${tool.name} on ${on_string}: Index">
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52 <filter>'index' in out</filter>
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53 </data>
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54 <data name="out_log" format="txt" from_work_dir="results/out_eventalign_collapse.log" label="${tool.name} on ${on_string}: log">
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55 <filter>'log' in out</filter>
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56 </data>
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57 </outputs>
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58 <tests>
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59 <!-- #1 default -->
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60 <test expect_num_outputs="3">
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61 <param name="i" value="sample.tsv"/>
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62 <param name="out" value="eventalign_collapse,index,log"/>
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63 <output name="out_eventalign_collapse">
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64 <assert_contents>
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65 <has_n_lines n="236"/>
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66 <has_text_matching expression="ref_pos&#009;ref_kmer"/>
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67 <has_text_matching expression="22102&#009;GGAAA"/>
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68 </assert_contents>
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69 </output>
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70 <output name="out_index">
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71 <assert_contents>
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72 <has_n_lines n="60"/>
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73 <has_text_matching expression="ref_id&#009;ref_start"/>
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74 <has_text_matching expression="chr&#009;22102"/>
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75 </assert_contents>
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76 </output>
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77 <output name="out_log">
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78 <assert_contents>
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79 <has_n_lines n="13"/>
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80 <has_line line="General options:"/>
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81 </assert_contents>
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82 </output>
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83 </test>
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84 <!-- #2 -->
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85 <test expect_num_outputs="2">
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86 <param name="i" value="sample.tsv"/>
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87 <param name="s" value="true"/>
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88 <param name="r" value="10"/>
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89 <param name="f" value="mean,std,median,mad,num_signals"/>
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90 <param name="out" value="eventalign_collapse,index"/>
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91 <output name="out_eventalign_collapse">
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92 <assert_contents>
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93 <has_n_lines n="236"/>
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94 <has_text_matching expression="ref_pos&#009;ref_kmer"/>
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95 <has_text_matching expression="22102&#009;GGAAA"/>
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96 </assert_contents>
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97 </output>
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98 <output name="out_index">
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99 <assert_contents>
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100 <has_n_lines n="60"/>
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101 <has_text_matching expression="ref_id&#009;ref_start"/>
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102 <has_text_matching expression="chr&#009;22102"/>
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103 </assert_contents>
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104 </output>
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105 </test>
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106 </tests>
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107 <help><![CDATA[
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108 .. class:: infomark
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109
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110 **What it does**
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111
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112 @WID@
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113
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114 Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event.
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115
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116 **Input**
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117
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118 A nanopolish eventalign tabular output file.
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119
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120 **Output**
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121
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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.
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123
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124 ::
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125
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126 Example : #7ef1d7b9-5824-4382-b23b-78d82c07ebbd YHR055C.
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127
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128 The main data file contains the following fields:
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129
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130 - ref_pos: Reference sequence ID (contig).
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131 - ref_kmer: Sequence of the reference kmers.
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132 - -num_events: Number of events for this kmer before collapsing.
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133 - dwell_time: dwell time for this kmer in seconds
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134 - NNNNN_dwell_time: dwell time of events for this kmers with a model sequence "NNNNN" (events ignored by nanopolish HMM).
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135 - mismatch_dwell_time: dwell time of events for this kmers with a model sequence different from the reference kmer
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136 - start_idx: Only if nanopolish eventalign called with --signal_idx. Start coordinate on original raw signal in fast5 file
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137 - end_idx: Only if nanopolish eventalign called with --signal_idx. End coordinate on original raw signal in fast5 file
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138 - mean: Only if nanopolish eventalign called with --samples. Mean of the normalised signal values provided by Nanopolish eventalign
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139 - median: Only if nanopolish eventalign called with --samples. Median of the normalised signal values provided by Nanopolish eventalign
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140 - std: Only if nanopolish eventalign called with --samples. Standard deviation of the normalised signal values provided by Nanopolish eventalign
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141 - mad: Only if nanopolish eventalign called with --samples. Median absolute deviation of the normalised signal values provided by Nanopolish eventalign
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142 - num_signals: Only if nanopolish eventalign called with --samples. Number of raw signal points.
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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
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144
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145 In addition Eventalign_collapse also generates an useful index file containing reads level information. It contains the following fields:
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146
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147 - read_id: Name or index of the read
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148 - ref_id: Name of the reference sequence the read was aligned on (contig)
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149 - ref_start: Start coordinate of the alignment on the reference sequence
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150 - ref_end: End coordinate of the alignment on the reference sequence
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151 - dwell_time: Cumulative dwell time in seconds for the entire resquiggled sequence
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152 - kmers: Overall number of resquiggled kmers
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153 - NNNNN_kmers: Number of resquiggled kmers containing at least 1 event for which the model sequence was "NNNNN"
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154 - mismatching_kmers: Number of resquiggled kmers containing at least 1 event for which the model sequence diverged from the reference sequence
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155 - missing_kmers: Number of skipped/missing reference positions in nanopolish output
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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.
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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.
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158
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159 .. class:: infomark
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160
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161 **References**
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162
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163 @REFERENCES@
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164 ]]></help>
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165 <expand macro="citations"/>
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166 </tool>