annotate nanoplot.xml @ 0:db1eeffba23e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
author iuc
date Fri, 28 Sep 2018 19:30:29 -0400
parents
children 4c172a4a4c9e
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db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
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1 <tool id="nanoplot" name="NanoPlot" version="1.13.0">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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2 <description>Plotting suite for Oxford Nanopore sequencing data and alignments</description>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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3 <requirements>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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4 <requirement type="package" version="1.18.2">nanoplot</requirement>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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5 </requirements>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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6 <command detect_errors="exit_code">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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7 <![CDATA[
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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8
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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9 #set reads_temp = []
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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10 #for $i, $f in enumerate($reads.files)
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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11 #set $extension = $f.ext
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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12 #if $extension == 'fastqsanger'
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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13 #set $extension = 'fastq'
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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14 #end if
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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15 ln -s '$f' './read_${i}.$extension' &&
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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16 $reads_temp.append("read_" + str($i) + "." + str($extension))
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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17 #end for
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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18
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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19 NanoPlot
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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20 --$reads.type ${' '.join($reads_temp)}
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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21
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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22 #if $filter.maxlength
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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23 --maxlength $filter.maxlength
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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24 #end if
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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25 #if $filter.minlength
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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26 --minlength $filter.minlength
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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27 #end if
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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28 #if $filter.downsample
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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29 --downsample $filter.downsample
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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30 #end if
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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31 #if $filter.minqual
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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32 --minqual $filter.minqual
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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33 #end if
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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34 #if $filter.readtype
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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35 --readtype $filter.readtype
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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36 #end if
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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37 #if $customization.color
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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38 --color $customization.color
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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39 #end if
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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40 #if $customization.format
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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41 --format $customization.format
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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42 #end if
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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43 #if $customization.plots
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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44 --plots ${str($customization.plots).replace(',', ' ')}
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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45 #end if
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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46 $filter.drop_outliers
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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47 $filter.loglength
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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48 $filter.percentqual
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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49 $filter.alength
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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50 $filter.barcoded
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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51 $customization.noN50
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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52 $customization.N50
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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53 -o '.'
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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54 ]]>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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55 </command>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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56 <inputs>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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57 <conditional name="reads">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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58 <param name="type" type="select" label="Type of the file(s) to work on">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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59 <option value="fastq" selected="true">fastq</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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60 <option value="fasta">fasta</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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61 <option value="fastq_rich">fastq_rich</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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62 <option value="fastq_minimal">fastq_minimal</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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63 <option value="summary">summary</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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64 <option value="bam">bam</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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65 <option value="cram">cram</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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66 </param>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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67 <when value="fastq">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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68 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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69 type="data"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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70 argument="--fastq"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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71 name="files"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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72 format="fastq,fastq.gz,fastq.bz2,vcf_bgzip"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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73 multiple="true"/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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74 </when>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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75 <when value="fasta">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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76 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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77 type="data"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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78 argument="--fasta"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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79 name="files"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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80 format="fasta,fasta.gz,vcf_bgzip"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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81 multiple="true"/>
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82 </when>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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83 <when value="fastq_rich">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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84 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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85 type="data"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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86 argument="--fastq_rich"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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87 name="files"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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88 format="fastq,fastq.gz,fastq.bz2,vcf_bgzip"
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89 multiple="true"/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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90 </when>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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91 <when value="fastq_minimal">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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92 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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93 type="data"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
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diff changeset
94 argument="--fastq_minimal"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
95 name="files"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
96 format="fastq,fastq.gz,fastq.bz2,vcf_bgzip"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
97 multiple="true"/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
98 </when>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
99 <when value="summary">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
100 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
101 type="data"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
102 argument="--summary"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
103 name="files"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
104 format="txt,zip"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
105 multiple="true"/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
106 </when>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
107 <when value="bam">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
108 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
109 type="data"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
110 argument="--bam"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
111 name="files"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
112 format="bam"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
113 multiple="true"/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
114 </when>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
115 <when value="cram">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
116 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
117 type="data"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
118 argument="--cram"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
119 name="files"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
120 format="cram"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
121 multiple="true"/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
122 </when>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
123 </conditional>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
124 <section
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
125 name="filter"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
126 title="Options for filtering or transforming input prior to plotting"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
127 expanded="false">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
128 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
129 type="integer"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
130 argument="--maxlength"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
131 optional="true"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
132 label="Drop reads longer than length specified."/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
133 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
134 type="integer"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
135 argument="--minlength"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
136 optional="true"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
137 label="Drop reads shorter than length specified."/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
138 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
139 type="boolean"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
140 argument="--drop_outliers"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
141 truevalue="--drop_outliers"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
142 falsevalue=""
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
143 label="Drop outlier reads with extreme long length."/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
144 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
145 type="integer"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
146 argument="--downsample"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
147 optional="true"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
148 label="Reduce dataset to N reads by random sampling."/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
149 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
150 type="boolean"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
151 argument="--loglength"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
152 truevalue="--loglength"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
153 falsevalue=""
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
154 label="Logarithmic scaling of lengths in plots."/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
155 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
156 type="boolean"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
157 argument="--percentqual"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
158 truevalue="--percentqual"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
159 falsevalue=""
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
160 label="Use qualities as theoretical percent identities."/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
161 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
162 type="boolean"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
163 argument="--alength"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
164 truevalue="--alength"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
165 falsevalue=""
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
166 label="Use aligned read lengths rather than sequenced length (bam mode)."/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
167 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
168 type="integer"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
169 argument="--minqual"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
170 optional="true"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
171 label="Drop reads with an average quality lower than specified."/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
172 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
173 type="select"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
174 argument="--readtype"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
175 optional="true"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
176 label="Which read type to extract information about from summary.">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
177 <option value="1D">1D</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
178 <option value="2D">2D</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
179 <option value="1D2">1D2</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
180 </param>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
181 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
182 type="boolean"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
183 argument="--barcoded"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
184 truevalue="--barcoded"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
185 falsevalue=""
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
186 label="Use if you want to split the summary file by barcode."/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
187 </section>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
188 <section
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
189 name="customization"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
190 title="Options for customizing the plots created"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
191 expanded="false">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
192 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
193 type="select"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
194 argument="--color"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
195 optional="true"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
196 label="Specify a color for the plots.">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
197 <option value="aliceblue">aliceblue</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
198 <option value="antiquewhite">antiquewhite</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
199 <option value="aqua">aqua</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
200 <option value="aquamarine">aquamarine</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
201 <option value="azure">azure</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
202 <option value="beige">beige</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
203 <option value="bisque">bisque</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
204 <option value="black">black</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
205 <option value="blanchedalmond">blanchedalmond</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
206 <option value="blue">blue</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
207 <option value="blueviolet">blueviolet</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
208 <option value="brown">brown</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
209 <option value="burlywood">burlywood</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
210 <option value="cadetblue">cadetblue</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
211 <option value="chartreuse">chartreuse</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
212 <option value="chocolate">chocolate</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
213 <option value="coral">coral</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
214 <option value="cornflowerblue">cornflowerblue</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
215 <option value="cornsilk">cornsilk</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
216 <option value="crimson">crimson</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
217 <option value="cyan">cyan</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
218 <option value="darkblue">darkblue</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
219 <option value="darkcyan">darkcyan</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
220 <option value="darkgoldenrod">darkgoldenrod</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
221 <option value="darkgray">darkgray</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
222 <option value="darkgreen">darkgreen</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
223 <option value="darkgrey">darkgrey</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
224 <option value="darkkhaki">darkkhaki</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
225 <option value="darkmagenta">darkmagenta</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
226 <option value="darkolivegreen">darkolivegreen</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
227 <option value="darkorange">darkorange</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
228 <option value="darkorchid">darkorchid</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
229 <option value="darkred">darkred</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
230 <option value="darksalmon">darksalmon</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
231 <option value="darkseagreen">darkseagreen</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
232 <option value="darkslateblue">darkslateblue</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
233 <option value="darkslategray">darkslategray</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
234 <option value="darkslategrey">darkslategrey</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
235 <option value="darkturquoise">darkturquoise</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
236 <option value="darkviolet">darkviolet</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
237 <option value="deeppink">deeppink</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="deepskyblue">deepskyblue</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
239 <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
240 <option value="dimgrey">dimgrey</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
241 <option value="dodgerblue">dodgerblue</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
242 <option value="firebrick">firebrick</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
243 <option value="floralwhite">floralwhite</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
244 <option value="forestgreen">forestgreen</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
245 <option value="fuchsia">fuchsia</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
246 <option value="gainsboro">gainsboro</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
247 <option value="ghostwhite">ghostwhite</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="goldenrod">goldenrod</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
249 <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
250 <option value="gray">gray</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="green">green</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
252 <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
253 <option value="grey">grey</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
254 <option value="honeydew">honeydew</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
255 <option value="hotpink">hotpink</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
256 <option value="indianred">indianred</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
257 <option value="indigo">indigo</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
258 <option value="ivory">ivory</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="khaki">khaki</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="lavenderblush">lavenderblush</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="lavender">lavender</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="lawngreen">lawngreen</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="lemonchiffon">lemonchiffon</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="lightblue">lightblue</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="lightcoral">lightcoral</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="lightcyan">lightcyan</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="lightgoldenrodyellow">lightgoldenrodyellow</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="lightgray">lightgray</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="lightgreen">lightgreen</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="lightgrey">lightgrey</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="lightpink">lightpink</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="lightsalmon">lightsalmon</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="lightseagreen">lightseagreen</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="lightskyblue">lightskyblue</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="lightslategray">lightslategray</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="lightslategrey">lightslategrey</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="lightsteelblue">lightsteelblue</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="lightyellow">lightyellow</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="limegreen">limegreen</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="lime">lime</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="linen">linen</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="magenta">magenta</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="maroon">maroon</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="mediumaquamarine">mediumaquamarine</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="mediumblue">mediumblue</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="mediumorchid">mediumorchid</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="mediumpurple">mediumpurple</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="mediumseagreen">mediumseagreen</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="mediumslateblue">mediumslateblue</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="mediumspringgreen">mediumspringgreen</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="mediumturquoise">mediumturquoise</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="mediumvioletred">mediumvioletred</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="midnightblue">midnightblue</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="mintcream">mintcream</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="mistyrose">mistyrose</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="moccasin">moccasin</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="navajowhite">navajowhite</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="navy">navy</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="oldlace">oldlace</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="olivedrab">olivedrab</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="olive">olive</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="orange">orange</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="orangered">orangered</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="orchid">orchid</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="palegoldenrod">palegoldenrod</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="palegreen">palegreen</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="paleturquoise">paleturquoise</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="palevioletred">palevioletred</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="papayawhip">papayawhip</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="peachpuff">peachpuff</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="peru">peru</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="pink">pink</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="plum">plum</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="powderblue">powderblue</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="purple">purple</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="rebeccapurple">rebeccapurple</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="red">red</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="rosybrown">rosybrown</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="royalblue">royalblue</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="saddlebrown">saddlebrown</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="salmon">salmon</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="sandybrown">sandybrown</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="seagreen">seagreen</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="seashell">seashell</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="sienna">sienna</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="silver">silver</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="skyblue">skyblue</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="slateblue">slateblue</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="slategray">slategray</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="slategrey">slategrey</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="snow">snow</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="springgreen">springgreen</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="steelblue">steelblue</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="tan">tan</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="teal">teal</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="thistle">thistle</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="tomato">tomato</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="turquoise">turquoise</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="violet">violet</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="wheat">wheat</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="whitesmoke">whitesmoke</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="white">white</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
343 <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
344 <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
345 </param>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
346 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
347 type="select"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
348 argument="--format"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
349 optional="true"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
350 label="Specify the output format of the plots.">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
351 <option selected="True" value="png">png</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
352 <option value="jpg">jpg</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
353 <option value="svg">svg</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
354 </param>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
355 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
356 type="select"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
357 argument="--plots"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
358 optional="true"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
359 multiple="true"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
360 display="checkboxes"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
361 label="Specify the bivariate format of the plots.">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
362 <option value="kde">kde</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
363 <option value="hex">hex</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
364 <option value="dot">dot</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
365 <option value="pauvre">pauvre</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
366 </param>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
367 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
368 type="boolean"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
369 name="noN50"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
370 truevalue="--no-N50"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
371 falsevalue=""
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
372 label="Hide the N50 mark in the read length histogram."/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
373 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
374 type="boolean"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
375 argument="--N50"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
376 truevalue="--N50"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
377 falsevalue=""
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
378 label="Show the N50 mark in the read length histogram."/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
379 </section>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
380 </inputs>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
381 <outputs>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
382 <data name="output_html" format="html" from_work_dir="NanoPlot-report.html" label="${tool.name} on ${on_string}: HTML report"/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
383 <data name="nanostats" format="txt" from_work_dir="NanoStats.txt" label="${tool.name} on ${on_string}: NanoStats"/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
384 <data name="nanostats_post_filtering" format="txt" from_work_dir="NanoStats_post_filtering.txt" label="${tool.name} on ${on_string}: NanoStats post filtering"/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
385 <data name="read_length" format="png" from_work_dir="HistogramReadlength.*" label="${tool.name} on ${on_string}: Histogram Read Length ">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
386 <change_format>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
387 <when input="customization.format" value="jpg" format="jpg"/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
388 <when input="customization.format" value="svg" format="svg"/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
389 </change_format>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
390 </data>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
391 <data name="log_read_length" format="png" from_work_dir="LogTransformed_HistogramReadlength.*" label="${tool.name} on ${on_string}: Log Transformed Histogram Read Length ">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
392 <change_format>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
393 <when input="customization.format" value="jpg" format="jpg"/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
394 <when input="customization.format" value="svg" format="svg"/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
395 </change_format>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
396 </data>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
397 </outputs>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
398 <tests>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
399 <test>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
400 <conditional name="reads">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
401 <param name="type" value="fastq_rich"/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
402 <param name="files" value="reads.fastq.gz" ftype="fastq.gz"/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
403 </conditional>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
404 <section name="filter">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
405 <param name="downsample" value="800"/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
406 </section>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
407 <section name="customization">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
408 <param name="plots" value="hex,kde"/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
409 <param name="title" value="My Plot"/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
410 <param name="format" value="jpg"/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
411 </section>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
412 <output name="output_html" file="NanoPlot-report.html" ftype="html"/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
413 <output name="nanostats" file="NanoStats.txt" ftype="txt"/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
414 <output name="nanostats_post_filtering" file="NanoStats_post_filtering.txt" ftype="txt"/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
415 <output name="read_length" file="HistogramReadlength.jpg" ftype="jpg" compare="sim_size" delta="30000"/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
416 </test>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
417 <test>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
418 <conditional name="reads">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
419 <param name="type" value="bam"/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
420 <param name="files" value="alignment.bam" ftype="bam"/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
421 </conditional>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
422 <section name="filter">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
423 <param name="maxlength" value="2000"/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
424 <param name="minlenght" value="1000"/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
425 </section>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
426 <section name="customization">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
427 <param name="color" value="yellow"/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
428 <param name="format" value="svg"/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
429 <param name="noN50" value="True"/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
430 </section>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
431 <output name="output_html" file="bam-report.html" ftype="html" compare="sim_size" delta="50000"/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
432 <output name="read_length" file="bam-LogTransformed_HistogramReadlength.svg" ftype="svg" compare="sim_size"/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
433 </test>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
434
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
435 </tests>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
436 <help>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
437 <![CDATA[
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
438
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
439 **What it does**
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
440
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
441 NanoPlot_ is a plotting tool for long read sequencing data and alignments written by `Wouter De Coster`_
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
442
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
443 .. _NanoPlot: https://github.com/wdecoster/NanoPlot
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
444 .. _`Wouter De Coster`: https://github.com/wdecoster
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
445
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
446 **Input**
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
447
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
448 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
iuc
parents:
diff changeset
449 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
iuc
parents:
diff changeset
450 sorted cram or sequencing summary.
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
451
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
452 **Output**
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
453
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
454 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
iuc
parents:
diff changeset
455 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
iuc
parents:
diff changeset
456 is generated.
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
457
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
458 .. _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
iuc
parents:
diff changeset
459 ]]>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
460 </help>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
461 <citations>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
462 <citation type="bibtex">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
diff changeset
463 @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
iuc
parents:
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464 {NanoPlot}, publisher = {GitHub}, journal = {GitHub repository}, url =
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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465 {https://github.com/wdecoster/NanoPlot}, }</citation>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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466 <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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parents:
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467 </citations>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
iuc
parents:
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468 </tool>