annotate eventaligncollapse.xml @ 1:ad011fc670d6 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
author iuc
date Tue, 12 May 2020 17:08:45 -0400
parents 6847a625db4d
children 74d7b06c2b92
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1 <?xml version="1.0"?>
1
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2 <tool id="nanopolishcomp_eventaligncollapse" name="NanopolishComp: EventalignCollapse" 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"/>
1
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8 <expand macro="version_command"/>
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9 <command detect_errors="exit_code"><![CDATA[
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10 ## initialize
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11 ## requires a minimum of 3 threads
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12 threads=\$((3 > \${GALAXY_SLOTS:-3} ? 3 : \${GALAXY_SLOTS:-3})) &&
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13
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14 ## run
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15 NanopolishComp
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16 Eventalign_collapse
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17 -i '$i'
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18 -s
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19 -r $r
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20 -f
0
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21 #for $current in $f
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22 $current
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23 #end for
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24 -o 'results'
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25 -p 'out'
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26 -t \$threads
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27 -v
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28 ]]></command>
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29 <inputs>
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30 <param argument="-i" type="data" format="tabular" label="Select nanopolish eventalign file"/>
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31 <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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32 <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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33 <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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34 <option value="mean" selected="true">Mean</option>
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35 <option value="std">Std</option>
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36 <option value="median" selected="true">Median</option>
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37 <option value="mad">Mad</option>
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38 <option value="num_signals" selected="true">Number of signals</option>
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39 </param>
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40 <param name="out" type="select" multiple="true" label="Select output file(s)">
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41 <option value="eventalign_collapse" selected="true">Eventalign Collapse</option>
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42 <option value="index" selected="true">Index</option>
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43 <option value="log">Log</option>
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44 </param>
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45 </inputs>
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46 <outputs>
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47 <data name="out_eventalign_collapse" format="tabular" from_work_dir="results/out_eventalign_collapse.tsv" label="${tool.name} on ${on_string}: Eventalign Collapse">
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48 <filter>'eventalign_collapse' in out</filter>
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49 </data>
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50 <data name="out_index" format="tabular" from_work_dir="results/out_eventalign_collapse.tsv.idx" label="${tool.name} on ${on_string}: Index">
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51 <filter>'index' in out</filter>
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52 </data>
1
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53 <data name="out_log" format="txt" from_work_dir="results/out_eventalign_collapse.log" label="${tool.name} on ${on_string}: Log">
0
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54 <filter>'log' in out</filter>
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55 </data>
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56 </outputs>
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57 <tests>
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58 <!-- #1 default -->
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59 <test expect_num_outputs="3">
1
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60 <param name="i" value="sample_event.tsv"/>
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61 <param name="out" value="eventalign_collapse,index,log"/>
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62 <output name="out_eventalign_collapse">
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63 <assert_contents>
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64 <has_n_lines n="236"/>
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65 <has_text_matching expression="ref_pos&#009;ref_kmer"/>
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66 <has_text_matching expression="22102&#009;GGAAA"/>
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67 </assert_contents>
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68 </output>
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69 <output name="out_index">
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70 <assert_contents>
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71 <has_n_lines n="60"/>
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72 <has_text_matching expression="ref_id&#009;ref_start"/>
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73 <has_text_matching expression="chr&#009;22102"/>
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74 </assert_contents>
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75 </output>
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76 <output name="out_log">
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77 <assert_contents>
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78 <has_n_lines n="13"/>
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79 <has_line line="General options:"/>
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80 </assert_contents>
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81 </output>
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82 </test>
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83 <!-- #2 -->
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84 <test expect_num_outputs="2">
1
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85 <param name="i" value="sample_event.tsv"/>
0
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86 <param name="s" value="true"/>
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87 <param name="r" value="10"/>
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88 <param name="f" value="mean,std,median,mad,num_signals"/>
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89 <param name="out" value="eventalign_collapse,index"/>
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90 <output name="out_eventalign_collapse">
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91 <assert_contents>
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92 <has_n_lines n="236"/>
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93 <has_text_matching expression="ref_pos&#009;ref_kmer"/>
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94 <has_text_matching expression="22102&#009;GGAAA"/>
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95 </assert_contents>
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96 </output>
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97 <output name="out_index">
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98 <assert_contents>
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99 <has_n_lines n="60"/>
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100 <has_text_matching expression="ref_id&#009;ref_start"/>
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101 <has_text_matching expression="chr&#009;22102"/>
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102 </assert_contents>
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103 </output>
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104 </test>
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105 </tests>
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106 <help><![CDATA[
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107 .. class:: infomark
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108
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109 **What it does**
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110
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111 @WID@
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112
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113 Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event.
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114
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115 **Input**
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116
1
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117 A nanopolish eventalign tabular output file.
0
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118
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119 **Output**
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120
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121 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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122
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123 ::
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124
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125 Example : #7ef1d7b9-5824-4382-b23b-78d82c07ebbd YHR055C.
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126
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127 The main data file contains the following fields:
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128
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129 - ref_pos: Reference sequence ID (contig).
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130 - ref_kmer: Sequence of the reference kmers.
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131 - -num_events: Number of events for this kmer before collapsing.
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132 - dwell_time: dwell time for this kmer in seconds
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133 - NNNNN_dwell_time: dwell time of events for this kmers with a model sequence "NNNNN" (events ignored by nanopolish HMM).
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134 - mismatch_dwell_time: dwell time of events for this kmers with a model sequence different from the reference kmer
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135 - start_idx: Only if nanopolish eventalign called with --signal_idx. Start coordinate on original raw signal in fast5 file
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136 - end_idx: Only if nanopolish eventalign called with --signal_idx. End coordinate on original raw signal in fast5 file
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137 - mean: Only if nanopolish eventalign called with --samples. Mean of the normalised signal values provided by Nanopolish eventalign
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138 - median: Only if nanopolish eventalign called with --samples. Median of the normalised signal values provided by Nanopolish eventalign
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139 - std: Only if nanopolish eventalign called with --samples. Standard deviation of the normalised signal values provided by Nanopolish eventalign
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140 - mad: Only if nanopolish eventalign called with --samples. Median absolute deviation of the normalised signal values provided by Nanopolish eventalign
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141 - num_signals: Only if nanopolish eventalign called with --samples. Number of raw signal points.
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142 - 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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143
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144 In addition Eventalign_collapse also generates an useful index file containing reads level information. It contains the following fields:
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145
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146 - read_id: Name or index of the read
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147 - ref_id: Name of the reference sequence the read was aligned on (contig)
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148 - ref_start: Start coordinate of the alignment on the reference sequence
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149 - ref_end: End coordinate of the alignment on the reference sequence
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150 - dwell_time: Cumulative dwell time in seconds for the entire resquiggled sequence
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151 - kmers: Overall number of resquiggled kmers
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152 - NNNNN_kmers: Number of resquiggled kmers containing at least 1 event for which the model sequence was "NNNNN"
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153 - 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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154 - missing_kmers: Number of skipped/missing reference positions in nanopolish output
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155 - 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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156 - 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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157
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158 .. class:: infomark
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159
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160 **References**
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161
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162 @REFERENCES@
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163 ]]></help>
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164 <expand macro="citations"/>
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165 </tool>