Mercurial > repos > iuc > nanoplot

annotate nanoplot.xml @ 7:7b379e98b9a9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 15a00502ecd67b4908f392660c12988f972b6eab
author iuc
date Thu, 07 Mar 2024 08:46:06 +0000
parents 0f1c34698076
children a02b8b3f5a0c
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7b379e98b9a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 15a00502ecd67b4908f392660c12988f972b6eab
iuc
parents: 6
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1 <tool id="nanoplot" name="NanoPlot" version="@TOOL_VERSION@+galaxy0" profile="22.05">
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2 <description>Plotting suite for Oxford Nanopore sequencing data and alignments</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">1.42.0</token>
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5 </macros>
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7b379e98b9a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 15a00502ecd67b4908f392660c12988f972b6eab
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6 <xrefs>
7b379e98b9a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 15a00502ecd67b4908f392660c12988f972b6eab
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7 <xref type="bio.tools">nanoplot</xref>
7b379e98b9a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 15a00502ecd67b4908f392660c12988f972b6eab
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8 </xrefs>
0
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9 <requirements>
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10 <requirement type="package" version="@TOOL_VERSION@">nanoplot</requirement>
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11 </requirements>
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7b379e98b9a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 15a00502ecd67b4908f392660c12988f972b6eab
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12 <!--stdio>
7b379e98b9a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 15a00502ecd67b4908f392660c12988f972b6eab
iuc
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13 Not needed anymore, because we do not generate the static PNGs anymore.
7b379e98b9a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 15a00502ecd67b4908f392660c12988f972b6eab
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14 I will leave this in, in the case we activate the PNGs at some point again.
7b379e98b9a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 15a00502ecd67b4908f392660c12988f972b6eab
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15 <regex match="kaleido problem" source="stderr" level="fatal" description="No static plots are saved due to some kaleido problem"/>
7b379e98b9a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 15a00502ecd67b4908f392660c12988f972b6eab
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16 </stdio-->
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17 <version_command>NanoPlot --version</version_command>
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18 <command detect_errors="exit_code"><![CDATA[
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19 ## set TMPDIR if not already set by admin
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
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20 ## otherwise kalleido fails with `Less than 64MB of free space in temporary directory for shared memory files: 0`
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
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21 ## export TMPDIR=\${TMPDIR:-\$_GALAXY_JOB_TMP_DIR};
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
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22
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23 #set $myfiles = $mode.reads.files
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24 #set reads_temp = []
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
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25 #if $mode.choice == 'combined':
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26 #for $i, $f in enumerate($myfiles)
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27 #if $f.ext.startswith("fastq"):
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28 #set $extension = 'fastq'
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9
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29 #else
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30 #set $extension = $f.ext
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31 #end if
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32 #if $f.ext.endswith(".gz"):
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
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33 #set $f = $extension + ".gz"
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
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34 #else if $f.ext.endswith(".bz"):
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
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35 #set $extension = $extension + "bz2"
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
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36 #end if
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37 ln -s '$f' './read_${i}.$extension' &&
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38 #if "bam" in $extension
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
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39 ln -s '$f.metadata.bam_index' './read_${i}.${extension}.bai' &&
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
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40 #end if
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41 $reads_temp.append("read_" + str($i) + "." + str($extension))
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42 #end for
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43 #else
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44 #if $myfiles.ext.startswith("fastq"):
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45 #set $extension = 'fastq'
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46 #else
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47 #set $extension = $myfiles.ext
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48 #end if
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49 #if $myfiles.ext.endswith(".gz"):
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50 #set $extension = $extension + ".gz"
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51 #else if $myfiles.ext.endswith(".bz"):
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52 #set $extension = $extension + "bz2"
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53 #end if
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
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54 ln -s '$myfiles' './read.$extension' &&
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
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55 #if "bam" in $extension
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
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56 ln -s '$myfiles.metadata.bam_index' './read.${extension}.bai' &&
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57 #end if
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58 $reads_temp.append("read." + str($extension))
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59 #end if
0
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60
3
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61 NanoPlot
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62 --threads \${GALAXY_SLOTS:-4}
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63 --tsv_stats
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64 --no_static
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65 --$mode.reads.type ${' '.join($reads_temp)}
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66 #if $filter.maxlength
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67 --maxlength $filter.maxlength
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68 #end if
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69 #if $filter.minlength
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70 --minlength $filter.minlength
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71 #end if
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72 #if $filter.downsample
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73 --downsample $filter.downsample
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74 #end if
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75 #if $filter.minqual
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76 --minqual $filter.minqual
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77 #end if
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78 #if $filter.runtime_until
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79 -- $filter.runtime_until
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80 #end if
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81 #if $filter.readtype
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82 --readtype $filter.readtype
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83 #end if
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84 #if $customization.color
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85 --color $customization.color
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86 #end if
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87 #if $customization.plots
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88 --plots ${str($customization.plots).replace(',', ' ')}
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89 #end if
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90 $filter.drop_outliers
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91 $filter.loglength
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92 $filter.percentqual
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93 $filter.alength
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94 $filter.barcoded
5
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95 $filter.no_supplementary
3
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96 $customization.N50
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97 -o '.'
5
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98 && >&2 cat *log
3
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99 ]]></command>
0
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100 <inputs>
3
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101 <conditional name="mode">
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102 <param name="choice" type="select" label="Select multifile mode" help="When supplying multiple files, batch mode will run NanoPlot on each file separately, while combined mode will run NanoPlot once on all the reads together. When only supplying a single input file, this setting does not matter.">
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103 <option value="batch" selected="true">batch</option>
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104 <option value="combined">combined</option>
0
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105 </param>
3
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106 <when value="batch">
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107 <conditional name="reads">
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108 <param name="type" type="select" label="Type of the file(s) to work on">
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109 <option value="fastq" selected="true">fastq</option>
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110 <option value="fasta">fasta</option>
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111 <option value="fastq_rich">fastq_rich</option>
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112 <option value="fastq_minimal">fastq_minimal</option>
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113 <option value="summary">summary</option>
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114 <option value="bam">bam</option>
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115 <option value="cram">cram</option>
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116 </param>
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117 <when value="fastq">
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118 <param type="data" argument="--fastq" name="files" format="fastq,fastq.gz,fastq.bz2,vcf_bgzip"/>
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119 </when>
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120 <when value="fasta">
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121 <param type="data" argument="--fasta" name="files" format="fasta,fasta.gz,vcf_bgzip"/>
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122 </when>
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123 <when value="fastq_rich">
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124 <param type="data" argument="--fastq_rich" name="files" format="fastq,fastq.gz,fastq.bz2,vcf_bgzip"/>
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125 </when>
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126 <when value="fastq_minimal">
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127 <param type="data" argument="--fastq_minimal" name="files" format="fastq,fastq.gz,fastq.bz2,vcf_bgzip"/>
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128 </when>
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129 <when value="summary">
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130 <param type="data" argument="--summary" name="files" format="txt,zip"/>
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131 </when>
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132 <when value="bam">
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133 <param type="data" argument="--bam" name="files" format="bam"/>
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134 </when>
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135 <when value="cram">
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136 <param type="data" argument="--cram" name="files" format="cram"/>
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137 </when>
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138 </conditional>
0
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139 </when>
3
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140 <when value="combined">
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141 <conditional name="reads">
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142 <param name="type" type="select" label="Type of the file(s) to work on">
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143 <option value="fastq" selected="true">fastq</option>
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144 <option value="fasta">fasta</option>
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145 <option value="fastq_rich">fastq_rich</option>
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146 <option value="fastq_minimal">fastq_minimal</option>
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147 <option value="summary">summary</option>
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148 <option value="bam">bam</option>
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149 <option value="cram">cram</option>
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150 </param>
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151 <when value="fastq">
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152 <param type="data" argument="--fastq" name="files" format="fastq,fastq.gz,fastq.bz2,vcf_bgzip" multiple="true"/>
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153 </when>
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154 <when value="fasta">
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155 <param type="data" argument="--fasta" name="files" format="fasta,fasta.gz,vcf_bgzip" multiple="true"/>
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156 </when>
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157 <when value="fastq_rich">
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158 <param type="data" argument="--fastq_rich" name="files" format="fastq,fastq.gz,fastq.bz2,vcf_bgzip" multiple="true"/>
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159 </when>
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160 <when value="fastq_minimal">
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161 <param type="data" argument="--fastq_minimal" name="files" format="fastq,fastq.gz,fastq.bz2,vcf_bgzip" multiple="true"/>
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162 </when>
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163 <when value="summary">
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164 <param type="data" argument="--summary" name="files" format="txt,zip" multiple="true"/>
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165 </when>
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166 <when value="bam">
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167 <param type="data" argument="--bam" name="files" format="bam" multiple="true"/>
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168 </when>
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169 <when value="cram">
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170 <param type="data" argument="--cram" name="files" format="cram" multiple="true"/>
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171 </when>
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172 </conditional>
0
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173 </when>
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174 </conditional>
7
7b379e98b9a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 15a00502ecd67b4908f392660c12988f972b6eab
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175 <section name="filter" title="Options for filtering or transforming input prior to plotting" expanded="false">
7b379e98b9a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 15a00502ecd67b4908f392660c12988f972b6eab
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176 <param argument="--maxlength" type="integer" optional="true" label="Drop reads longer than length specified."/>
7b379e98b9a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 15a00502ecd67b4908f392660c12988f972b6eab
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177 <param argument="--minlength" type="integer" optional="true" label="Drop reads shorter than length specified."/>
7b379e98b9a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 15a00502ecd67b4908f392660c12988f972b6eab
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178 <param argument="--drop_outliers" type="boolean" truevalue="--drop_outliers" falsevalue="" label="Drop outlier reads with extreme long length."/>
7b379e98b9a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 15a00502ecd67b4908f392660c12988f972b6eab
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179 <param argument="--downsample" type="integer" optional="true" label="Reduce dataset to N reads by random sampling."/>
7b379e98b9a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 15a00502ecd67b4908f392660c12988f972b6eab
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180 <param argument="--loglength" type="boolean" truevalue="--loglength" falsevalue="" label="Logarithmic scaling of lengths in plots."/>
7b379e98b9a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 15a00502ecd67b4908f392660c12988f972b6eab
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181 <param argument="--percentqual" type="boolean" truevalue="--percentqual" falsevalue="" label="Use qualities as theoretical percent identities."/>
7b379e98b9a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 15a00502ecd67b4908f392660c12988f972b6eab
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182 <param argument="--alength" type="boolean" truevalue="--alength" falsevalue="" label="Use aligned read lengths rather than sequenced length (bam mode)."/>
7b379e98b9a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 15a00502ecd67b4908f392660c12988f972b6eab
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183 <param argument="--minqual" type="integer" optional="true" label="Drop reads with an average quality lower than specified."/>
7b379e98b9a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 15a00502ecd67b4908f392660c12988f972b6eab
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184 <param argument="--runtime_until" type="integer" optional="true" label="Only take the N first hours of a run"/>
7b379e98b9a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 15a00502ecd67b4908f392660c12988f972b6eab
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185 <param argument="--readtype" type="select" optional="true" label="Which read type to extract information about from summary.">
0
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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186 <option value="1D">1D</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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187 <option value="2D">2D</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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188 <option value="1D2">1D2</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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189 </param>
7
7b379e98b9a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 15a00502ecd67b4908f392660c12988f972b6eab
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190 <param argument="--barcoded" type="boolean" truevalue="--barcoded" falsevalue="" label="Use if you want to split the summary file by barcode."/>
7b379e98b9a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 15a00502ecd67b4908f392660c12988f972b6eab
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191 <param argument="--no_supplementary" type="boolean" truevalue="--no_supplementary" falsevalue="" label="Use if you want to remove supplementary alignments"/>
0
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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192 </section>
7
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193 <section name="customization" title="Options for customizing the plots created" expanded="false">
7b379e98b9a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 15a00502ecd67b4908f392660c12988f972b6eab
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194 <param type="select" argument="--color" optional="true" label="Specify a color for the plots.">
0
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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195 <option value="aliceblue">aliceblue</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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196 <option value="antiquewhite">antiquewhite</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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197 <option value="aqua">aqua</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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198 <option value="aquamarine">aquamarine</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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199 <option value="azure">azure</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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200 <option value="beige">beige</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
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201 <option value="bisque">bisque</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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202 <option value="black">black</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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203 <option value="blanchedalmond">blanchedalmond</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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204 <option value="blue">blue</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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205 <option value="blueviolet">blueviolet</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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parents:
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206 <option value="brown">brown</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
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207 <option value="burlywood">burlywood</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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208 <option value="cadetblue">cadetblue</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
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209 <option value="chartreuse">chartreuse</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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210 <option value="chocolate">chocolate</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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211 <option value="coral">coral</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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212 <option value="cornflowerblue">cornflowerblue</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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213 <option value="cornsilk">cornsilk</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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214 <option value="crimson">crimson</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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215 <option value="cyan">cyan</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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216 <option value="darkblue">darkblue</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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217 <option value="darkcyan">darkcyan</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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218 <option value="darkgoldenrod">darkgoldenrod</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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parents:
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219 <option value="darkgray">darkgray</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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220 <option value="darkgreen">darkgreen</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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221 <option value="darkgrey">darkgrey</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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222 <option value="darkkhaki">darkkhaki</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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223 <option value="darkmagenta">darkmagenta</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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parents:
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224 <option value="darkolivegreen">darkolivegreen</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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225 <option value="darkorange">darkorange</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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226 <option value="darkorchid">darkorchid</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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227 <option value="darkred">darkred</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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228 <option value="darksalmon">darksalmon</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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229 <option value="darkseagreen">darkseagreen</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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230 <option value="darkslateblue">darkslateblue</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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231 <option value="darkslategray">darkslategray</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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232 <option value="darkslategrey">darkslategrey</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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233 <option value="darkturquoise">darkturquoise</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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234 <option value="darkviolet">darkviolet</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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235 <option value="deeppink">deeppink</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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236 <option value="deepskyblue">deepskyblue</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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237 <option value="dimgray">dimgray</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
238 <option value="dimgrey">dimgrey</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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239 <option value="dodgerblue">dodgerblue</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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240 <option value="firebrick">firebrick</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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241 <option value="floralwhite">floralwhite</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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242 <option value="forestgreen">forestgreen</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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243 <option value="fuchsia">fuchsia</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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244 <option value="gainsboro">gainsboro</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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245 <option value="ghostwhite">ghostwhite</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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246 <option value="goldenrod">goldenrod</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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247 <option value="gold">gold</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
248 <option value="gray">gray</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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249 <option value="green">green</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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250 <option value="greenyellow">greenyellow</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
251 <option value="grey">grey</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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252 <option value="honeydew">honeydew</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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253 <option value="hotpink">hotpink</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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254 <option value="indianred">indianred</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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255 <option value="indigo">indigo</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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256 <option value="ivory">ivory</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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257 <option value="khaki">khaki</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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258 <option value="lavenderblush">lavenderblush</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
259 <option value="lavender">lavender</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
260 <option value="lawngreen">lawngreen</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
261 <option value="lemonchiffon">lemonchiffon</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
262 <option value="lightblue">lightblue</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
263 <option value="lightcoral">lightcoral</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
264 <option value="lightcyan">lightcyan</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
265 <option value="lightgoldenrodyellow">lightgoldenrodyellow</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
266 <option value="lightgray">lightgray</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
267 <option value="lightgreen">lightgreen</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
268 <option value="lightgrey">lightgrey</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
269 <option value="lightpink">lightpink</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
270 <option value="lightsalmon">lightsalmon</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
271 <option value="lightseagreen">lightseagreen</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
272 <option value="lightskyblue">lightskyblue</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
273 <option value="lightslategray">lightslategray</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
274 <option value="lightslategrey">lightslategrey</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
275 <option value="lightsteelblue">lightsteelblue</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
276 <option value="lightyellow">lightyellow</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
277 <option value="limegreen">limegreen</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
278 <option value="lime">lime</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
279 <option value="linen">linen</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
280 <option value="magenta">magenta</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
281 <option value="maroon">maroon</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
282 <option value="mediumaquamarine">mediumaquamarine</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
283 <option value="mediumblue">mediumblue</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
284 <option value="mediumorchid">mediumorchid</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
285 <option value="mediumpurple">mediumpurple</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
286 <option value="mediumseagreen">mediumseagreen</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
287 <option value="mediumslateblue">mediumslateblue</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
288 <option value="mediumspringgreen">mediumspringgreen</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
289 <option value="mediumturquoise">mediumturquoise</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
290 <option value="mediumvioletred">mediumvioletred</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
291 <option value="midnightblue">midnightblue</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
292 <option value="mintcream">mintcream</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
293 <option value="mistyrose">mistyrose</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
294 <option value="moccasin">moccasin</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
295 <option value="navajowhite">navajowhite</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
296 <option value="navy">navy</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
297 <option value="oldlace">oldlace</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
298 <option value="olivedrab">olivedrab</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
299 <option value="olive">olive</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
300 <option value="orange">orange</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
301 <option value="orangered">orangered</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
302 <option value="orchid">orchid</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
303 <option value="palegoldenrod">palegoldenrod</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
304 <option value="palegreen">palegreen</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
305 <option value="paleturquoise">paleturquoise</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
306 <option value="palevioletred">palevioletred</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
307 <option value="papayawhip">papayawhip</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
308 <option value="peachpuff">peachpuff</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
309 <option value="peru">peru</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
310 <option value="pink">pink</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
311 <option value="plum">plum</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
312 <option value="powderblue">powderblue</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
313 <option value="purple">purple</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
314 <option value="rebeccapurple">rebeccapurple</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
315 <option value="red">red</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
316 <option value="rosybrown">rosybrown</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
317 <option value="royalblue">royalblue</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
318 <option value="saddlebrown">saddlebrown</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
319 <option value="salmon">salmon</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
320 <option value="sandybrown">sandybrown</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
321 <option value="seagreen">seagreen</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
322 <option value="seashell">seashell</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
323 <option value="sienna">sienna</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
324 <option value="silver">silver</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
325 <option value="skyblue">skyblue</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
326 <option value="slateblue">slateblue</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
327 <option value="slategray">slategray</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
328 <option value="slategrey">slategrey</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
329 <option value="snow">snow</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
330 <option value="springgreen">springgreen</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
331 <option value="steelblue">steelblue</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
332 <option value="tan">tan</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
333 <option value="teal">teal</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
334 <option value="thistle">thistle</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
335 <option value="tomato">tomato</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
336 <option value="turquoise">turquoise</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
337 <option value="violet">violet</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
338 <option value="wheat">wheat</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
339 <option value="whitesmoke">whitesmoke</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
340 <option value="white">white</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
341 <option value="yellowgreen">yellowgreen</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
342 <option value="yellow">yellow</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
343 </param>
7
7b379e98b9a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 15a00502ecd67b4908f392660c12988f972b6eab
iuc
parents: 6
diff changeset
344 <param type="select" argument="--plots" optional="true" multiple="true" display="checkboxes" label="Specify the bivariate format of the plots.">
5
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents: 4
diff changeset
345 <option value="kde">kernel density estimation (kde)</option>
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38
iuc
parents: 4
diff changeset
346 <option value="dot">dots (dot)</option>
0
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
347 </param>
7
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348 <param type="boolean" argument="--N50" truevalue="--N50" falsevalue="" label="Show the N50 mark in the read length histogram."/>
0
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349 </section>
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350 </inputs>
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351 <outputs>
7
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352 <data name="output_html" format="html" from_work_dir="NanoPlot-report.html" label="${tool.name} on ${on_string}: HTML report"/>
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353 <data name="nanostats" format="tabular" from_work_dir="NanoStats.txt" label="${tool.name} on ${on_string}: NanoStats"/>
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354 <data name="nanostats_post_filtering" format="tabular" from_work_dir="NanoStats_post_filtering.txt" label="${tool.name} on ${on_string}: NanoStats post filtering"/>
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355 <!-- https://github.com/wdecoster/NanoPlot/issues/352 generating PNGs can take much much longer to process. Not sure if this output is relevant at all -->
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356 <!--data name="read_length" format="png" from_work_dir="Non_weightedHistogramReadlength.png" label="${tool.name} on ${on_string}: Histogram Read Length"/>
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357 <data name="log_read_length" format="png" from_work_dir="Non_weightedLogTransformed_HistogramReadlength.png" label="${tool.name} on ${on_string}: Log Transformed Histogram Read Length"/-->
0
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358 </outputs>
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359 <tests>
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360 <test>
3
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361 <conditional name="mode">
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362 <param name="choice" value="batch"/>
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363 <conditional name="reads">
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364 <param name="type" value="fastq_rich"/>
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365 <param name="files" value="reads.fastq.gz" ftype="fastqsanger.gz"/>
3
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366 </conditional>
0
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367 </conditional>
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368 <section name="filter">
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369 <param name="downsample" value="800"/>
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370 </section>
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371 <section name="customization">
5
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372 <param name="plots" value="kde"/>
0
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373 </section>
5
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374 <output name="output_html" ftype="html">
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375 <assert_contents>
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376 <has_text text="html"/>
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377 <has_text text="mean_qual"/>
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378 </assert_contents>
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379 </output>
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380 <output name="nanostats" file="NanoStats.txt" ftype="tabular"/>
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381 <output name="nanostats_post_filtering" file="NanoStats_post_filtering.txt" ftype="tabular"/>
0
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382 </test>
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383 <test>
3
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384 <conditional name="mode">
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385 <param name="choice" value="combined"/>
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386 <conditional name="reads">
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387 <param name="type" value="bam"/>
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388 <param name="files" value="alignment.bam" ftype="bam"/>
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389 </conditional>
0
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390 </conditional>
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391 <section name="filter">
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392 <param name="maxlength" value="2000"/>
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393 <param name="minlenght" value="1000"/>
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394 </section>
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395 <section name="customization">
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396 <param name="color" value="yellow"/>
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397 </section>
5
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398 <output name="output_html" ftype="html">
2
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399 <assert_contents>
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400 <has_text text="html"/>
7
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401 <has_text text="Aligned read length vs Percent identity plot using dots"/>
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402 <!-- bam report specific -->
5
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403 </assert_contents>
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404 </output>
0
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405 </test>
7
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406 <test>
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407 <!-- test with multiple input files -->
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408 <conditional name="mode">
3
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409 <param name="choice" value="combined"/>
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410 <conditional name="reads">
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411 <param name="type" value="fasta"/>
7
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412 <param name="files" ftype="fasta" value="reads1.fasta,reads2.fasta"/>
3
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413 </conditional>
2
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414 </conditional>
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415 <output name="output_html" ftype="html">
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416 <assert_contents>
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417 <has_text text="html"/>
5
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418 <not_has_text text="Aligned read length vs Percent identity plot using dots"/>
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419 <has_text text="&lt;td&gt;9&lt;/td&gt;"/>
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420 <!--check both files were used 4+5 reads -->
2
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421 </assert_contents>
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422 </output>
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423 </test>
0
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424 </tests>
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425 <help>
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426 <![CDATA[
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427 **What it does**
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428
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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429 NanoPlot_ is a plotting tool for long read sequencing data and alignments written by `Wouter De Coster`_
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430
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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431 .. _NanoPlot: https://github.com/wdecoster/NanoPlot
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432 .. _`Wouter De Coster`: https://github.com/wdecoster
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433
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434 **Input**
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435
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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436 NanoPlot requires 1 or more files as input. They can either be fastq (can be generated
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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437 by albacore, guppy or MinKNOW containing additional information), fasta, sorted bam,
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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438 sorted cram or sequencing summary.
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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439
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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440 **Output**
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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441
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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442 NanoPlot produces different number of plots depending on the data and customizations.
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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443 A detailed view can be seen on here_. Additionally a file showing the statistics
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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444 is generated.
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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445
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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446 .. _here: https://github.com/wdecoster/NanoPlot#plots-generated
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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447 ]]>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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448 </help>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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449 <citations>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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450 <citation type="bibtex">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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451 @misc{githubnanoplot, author = {De Coster, Wouter}, year = {2018}, title =
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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452 {NanoPlot}, publisher = {GitHub}, journal = {GitHub repository}, url =
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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453 {https://github.com/wdecoster/NanoPlot}, }</citation>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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454 <citation type="doi">10.1093/bioinformatics/bty149</citation>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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455 </citations>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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456 </tool>