nanoplot: nanoplot.xml annotate

annotate nanoplot.xml @ 1:4c172a4a4c9e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 16878097949f0af33d825e62b20b789a7f8ad319

author	iuc
date	Tue, 23 Oct 2018 08:30:58 -0400
parents	db1eeffba23e
children	acd337269171

rev	line source
0 db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	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 iuc parents: diff changeset	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 iuc parents: diff changeset	3 <requirements>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	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 iuc parents: diff changeset	5 </requirements>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	6 <command detect_errors="exit_code">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	7 <![CDATA[
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	8
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	9 #set reads_temp = []
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	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 iuc parents: diff changeset	11 #set $extension = $f.ext
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	12 #if $extension == 'fastqsanger'
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	13 #set $extension = 'fastq'
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	14 #end if
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	15 ln -s '$f' './read_${i}.$extension' &&
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	16 $reads_temp.append("read_" + str($i) + "." + str($extension))
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	17 #end for
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	18
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	19 NanoPlot
1 4c172a4a4c9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 16878097949f0af33d825e62b20b789a7f8ad319 iuc parents: 0 diff changeset	20 --threads \${GALAXY_SLOTS:-4}
0 db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	21 --$reads.type ${' '.join($reads_temp)}
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	22
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	23 #if $filter.maxlength
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	24 --maxlength $filter.maxlength
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	25 #end if
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	26 #if $filter.minlength
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	27 --minlength $filter.minlength
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	28 #end if
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	29 #if $filter.downsample
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	30 --downsample $filter.downsample
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	31 #end if
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	32 #if $filter.minqual
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	33 --minqual $filter.minqual
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	34 #end if
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	35 #if $filter.readtype
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	36 --readtype $filter.readtype
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	37 #end if
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	38 #if $customization.color
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	39 --color $customization.color
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	40 #end if
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	41 #if $customization.format
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	42 --format $customization.format
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	43 #end if
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	44 #if $customization.plots
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	45 --plots ${str($customization.plots).replace(',', ' ')}
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	46 #end if
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	47 $filter.drop_outliers
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	48 $filter.loglength
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	49 $filter.percentqual
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	50 $filter.alength
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	51 $filter.barcoded
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	52 $customization.noN50
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	53 $customization.N50
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	54 -o '.'
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	55 ]]>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	56 </command>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	57 <inputs>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	58 <conditional name="reads">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	59 <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 iuc parents: diff changeset	60 <option value="fastq" selected="true">fastq</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	61 <option value="fasta">fasta</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	62 <option value="fastq_rich">fastq_rich</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	63 <option value="fastq_minimal">fastq_minimal</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	64 <option value="summary">summary</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	65 <option value="bam">bam</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	66 <option value="cram">cram</option>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	67 </param>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	68 <when value="fastq">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	69 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	70 type="data"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	71 argument="--fastq"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	72 name="files"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	73 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	74 multiple="true"/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	75 </when>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	76 <when value="fasta">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	77 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	78 type="data"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	79 argument="--fasta"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	80 name="files"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	81 format="fasta,fasta.gz,vcf_bgzip"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	82 multiple="true"/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	83 </when>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	84 <when value="fastq_rich">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	85 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	86 type="data"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	87 argument="--fastq_rich"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	88 name="files"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	89 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	90 multiple="true"/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	91 </when>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	92 <when value="fastq_minimal">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	93 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	94 type="data"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	95 argument="--fastq_minimal"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	96 name="files"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	97 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	98 multiple="true"/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	99 </when>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	100 <when value="summary">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	101 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	102 type="data"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	103 argument="--summary"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	104 name="files"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	105 format="txt,zip"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	106 multiple="true"/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	107 </when>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	108 <when value="bam">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	109 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	110 type="data"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	111 argument="--bam"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	112 name="files"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	113 format="bam"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	114 multiple="true"/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	115 </when>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	116 <when value="cram">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	117 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	118 type="data"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	119 argument="--cram"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	120 name="files"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	121 format="cram"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	122 multiple="true"/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	123 </when>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	124 </conditional>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	125 <section
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	126 name="filter"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	127 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	128 expanded="false">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	129 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	130 type="integer"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	131 argument="--maxlength"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	132 optional="true"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	133 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	134 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	135 type="integer"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	136 argument="--minlength"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	137 optional="true"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	138 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	139 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	140 type="boolean"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	141 argument="--drop_outliers"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	142 truevalue="--drop_outliers"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	143 falsevalue=""
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	144 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	145 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	146 type="integer"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	147 argument="--downsample"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	148 optional="true"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	149 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	150 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	151 type="boolean"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	152 argument="--loglength"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	153 truevalue="--loglength"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	154 falsevalue=""
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	155 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	156 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	157 type="boolean"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	158 argument="--percentqual"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	159 truevalue="--percentqual"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	160 falsevalue=""
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	161 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	162 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	163 type="boolean"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	164 argument="--alength"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	165 truevalue="--alength"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	166 falsevalue=""
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	167 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	168 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	169 type="integer"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	170 argument="--minqual"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	171 optional="true"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	172 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	173 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	174 type="select"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	175 argument="--readtype"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	176 optional="true"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	177 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	178 <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	179 <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	180 <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	181 </param>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	182 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	183 type="boolean"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	184 argument="--barcoded"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	185 truevalue="--barcoded"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	186 falsevalue=""
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	187 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	188 </section>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	189 <section
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	190 name="customization"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	191 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	192 expanded="false">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	193 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	194 type="select"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	195 argument="--color"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	196 optional="true"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	197 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	198 <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	199 <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	200 <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	201 <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	202 <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	203 <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	204 <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	205 <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	206 <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	207 <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	208 <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	209 <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	210 <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	211 <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	212 <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	213 <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	214 <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	215 <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	216 <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	217 <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	218 <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	219 <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	220 <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	221 <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	222 <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	223 <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	224 <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	225 <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	226 <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	227 <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	228 <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	229 <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	230 <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	231 <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	232 <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	233 <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	234 <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	235 <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	236 <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	237 <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	238 <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	239 <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	240 <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	241 <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	242 <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	243 <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	244 <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	245 <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	246 <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	247 <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	248 <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	249 <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	250 <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	251 <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	252 <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	253 <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	254 <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	255 <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	256 <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	257 <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	258 <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	259 <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	260 <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	261 <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	262 <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	263 <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	264 <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	265 <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	266 <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	267 <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	268 <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	269 <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	270 <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	271 <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	272 <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	273 <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	274 <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	275 <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	276 <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	277 <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	278 <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	279 <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	280 <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	281 <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	282 <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	283 <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	284 <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	285 <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	286 <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	287 <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	288 <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	289 <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	290 <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	291 <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	292 <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	293 <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	294 <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	295 <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	296 <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	297 <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	298 <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	299 <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	300 <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	301 <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	302 <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	303 <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	304 <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	305 <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	306 <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	307 <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	308 <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	309 <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	310 <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	311 <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	312 <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	313 <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	314 <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	315 <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	316 <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	317 <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	318 <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	319 <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	320 <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	321 <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	322 <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	323 <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	324 <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	325 <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	326 <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	327 <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	328 <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	329 <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	330 <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	331 <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	332 <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	333 <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	334 <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	335 <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	336 <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	337 <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	338 <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	339 <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	340 <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	341 <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	342 <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	343 <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	344 <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	345 <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	346 </param>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	347 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	348 type="select"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	349 argument="--format"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	350 optional="true"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	351 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	352 <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	353 <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	354 <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	355 </param>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	356 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	357 type="select"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	358 argument="--plots"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	359 optional="true"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	360 multiple="true"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	361 display="checkboxes"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	362 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	363 <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	364 <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	365 <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	366 <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	367 </param>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	368 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	369 type="boolean"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	370 name="noN50"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	371 truevalue="--no-N50"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	372 falsevalue=""
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	373 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	374 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	375 type="boolean"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	376 argument="--N50"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	377 truevalue="--N50"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	378 falsevalue=""
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	379 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	380 </section>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	381 </inputs>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	382 <outputs>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	383 <data name="output_html" format="html" from_work_dir="NanoPlot-report.html" label="${tool.name} on ${on_string}: HTML report"/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	384 <data name="nanostats" format="txt" from_work_dir="NanoStats.txt" label="${tool.name} on ${on_string}: NanoStats"/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	385 <data name="nanostats_post_filtering" format="txt" from_work_dir="NanoStats_post_filtering.txt" label="${tool.name} on ${on_string}: NanoStats post filtering"/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	386 <data name="read_length" format="png" from_work_dir="HistogramReadlength.*" label="${tool.name} on ${on_string}: Histogram Read Length ">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	387 <change_format>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	388 <when input="customization.format" value="jpg" format="jpg"/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	389 <when input="customization.format" value="svg" format="svg"/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	390 </change_format>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	391 </data>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	392 <data name="log_read_length" format="png" from_work_dir="LogTransformed_HistogramReadlength.*" label="${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	393 <change_format>
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="jpg" format="jpg"/>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	395 <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	396 </change_format>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	397 </data>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	398 </outputs>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	399 <tests>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	400 <test>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	401 <conditional name="reads">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	402 <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	403 <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	404 </conditional>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	405 <section name="filter">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	406 <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	407 </section>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	408 <section name="customization">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	409 <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	410 <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	411 <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	412 </section>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	413 <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	414 <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	415 <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	416 <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	417 </test>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	418 <test>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	419 <conditional name="reads">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	420 <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	421 <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	422 </conditional>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	423 <section name="filter">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	424 <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	425 <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	426 </section>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	427 <section name="customization">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	428 <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	429 <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	430 <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	431 </section>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	432 <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	433 <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	434 </test>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	435
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	436 </tests>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	437 <help>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	438 <![CDATA[
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	439
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	440 What it does
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	441
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	442 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	443
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	444 .. _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	445 .. _`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	446
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	447 Input
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	448
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	449 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	450 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	451 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	452
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	453 Output
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	454
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	455 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	456 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	457 is generated.
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	458
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	459 .. _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	460 ]]>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	461 </help>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	462 <citations>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	463 <citation type="bibtex">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	464 @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: diff changeset	465 {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: diff changeset	466 {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: diff changeset	467 <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 iuc parents: diff changeset	468 </citations>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	469 </tool>

Mercurial > repos > iuc > nanoplot

annotate nanoplot.xml @ 1:4c172a4a4c9e draft