nanoplot: nanoplot.xml annotate

annotate nanoplot.xml @ 5:a3c4fe6f49ab draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38

author	iuc
date	Thu, 16 Jun 2022 20:08:15 +0000
parents	edbb6c5028f5
children	0f1c34698076

rev	line source
5 a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	1 <tool id="nanoplot" name="NanoPlot" version="@TOOL_VERSION@+galaxy1" profile="20.05">
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>
2 acd337269171 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit fae386db359dd61fd5e4e2e808413ae478b279ee iuc parents: 1 diff changeset	3 <macros>
5 a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	4 <token name="@TOOL_VERSION@">1.36.2</token>
2 acd337269171 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit fae386db359dd61fd5e4e2e808413ae478b279ee iuc parents: 1 diff changeset	5 </macros>
0 db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	6 <requirements>
2 acd337269171 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit fae386db359dd61fd5e4e2e808413ae478b279ee iuc parents: 1 diff changeset	7 <requirement type="package" version="@TOOL_VERSION@">nanoplot</requirement>
0 db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	8 </requirements>
5 a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	9 <stdio>
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	10 <regex match="kaleido problem" source="stderr" level="fatal" description="No static plots are saved due to some kaleido problem" />
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	11 </stdio>
2 acd337269171 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit fae386db359dd61fd5e4e2e808413ae478b279ee iuc parents: 1 diff changeset	12 <version_command>NanoPlot --version</version_command>
3 645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	13 <command detect_errors="exit_code"><![CDATA[
5 a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	14 ## set TMPDIR if not already set by admin
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	15 ## otherwise kalleido fails with `Less than 64MB of free space in temporary directory for shared memory files: 0`
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	16 ## export TMPDIR=\${TMPDIR:-\$_GALAXY_JOB_TMP_DIR};
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	17
3 645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	18 #set $myfiles = $mode.reads.files
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	19 #set reads_temp = []
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	20 #if $mode.choice == 'combined':
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	21 #for $i, $f in enumerate($myfiles)
5 a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	22 #if $f.ext.startswith("fastq"):
3 645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	23 #set $extension = 'fastq'
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	24 #else
0 db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	25 #set $extension = $f.ext
3 645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	26 #end if
5 a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	27 #if $f.ext.endswith(".gz"):
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	28 #set $f = $extension + ".gz"
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	29 #else if $f.ext.endswith(".bz"):
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	30 #set $extension = $extension + "bz2"
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	31 #end if
3 645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	32 ln -s '$f' './read_${i}.$extension' &&
5 a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	33 #if "bam" in $extension
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	34 ln -s '$f.metadata.bam_index' './read_${i}.${extension}.bai' &&
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	35 #end if
3 645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	36 $reads_temp.append("read_" + str($i) + "." + str($extension))
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	37 #end for
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	38 #else
5 a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	39 #if $myfiles.ext.startswith("fastq"):
3 645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	40 #set $extension = 'fastq'
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	41 #else
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	42 #set $extension = $myfiles.ext
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	43 #end if
5 a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	44 #if $myfiles.ext.endswith(".gz"):
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	45 #set $extension = $extension + ".gz"
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	46 #else if $myfiles.ext.endswith(".bz"):
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	47 #set $extension = $extension + "bz2"
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	48 #end if
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	49 ln -s '$myfiles' './read.$extension' &&
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	50 #if "bam" in $extension
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	51 ln -s '$myfiles.metadata.bam_index' './read.${extension}.bai' &&
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	52 #end if
3 645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	53 $reads_temp.append("read." + str($extension))
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	54 #end if
0 db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	55
3 645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	56 NanoPlot
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	57 --threads \${GALAXY_SLOTS:-4}
5 a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	58 --tsv_stats
3 645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	59 --$mode.reads.type ${' '.join($reads_temp)}
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	60 #if $filter.maxlength
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	61 --maxlength $filter.maxlength
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	62 #end if
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	63 #if $filter.minlength
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	64 --minlength $filter.minlength
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	65 #end if
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	66 #if $filter.downsample
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	67 --downsample $filter.downsample
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	68 #end if
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	69 #if $filter.minqual
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	70 --minqual $filter.minqual
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	71 #end if
5 a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	72 #if $filter.runtime_until
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	73 -- $filter.runtime_until
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	74 #end if
3 645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	75 #if $filter.readtype
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	76 --readtype $filter.readtype
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	77 #end if
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	78 #if $customization.color
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	79 --color $customization.color
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	80 #end if
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	81 #if $customization.plots
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	82 --plots ${str($customization.plots).replace(',', ' ')}
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	83 #end if
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	84 $filter.drop_outliers
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	85 $filter.loglength
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	86 $filter.percentqual
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	87 $filter.alength
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	88 $filter.barcoded
5 a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	89 $filter.no_supplementary
3 645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	90 $customization.N50
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	91 -o '.'
5 a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	92 && >&2 cat *log
3 645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	93 ]]></command>
0 db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	94 <inputs>
3 645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	95 <conditional name="mode">
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	96 <param name="choice" type="select" label="Select multifile mode" help="When supplying multiple files, batch mode will run NanoPlot on each file separately, while combined mode will run NanoPlot once on all the reads together. When only supplying a single input file, this setting does not matter.">
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	97 <option value="batch" selected="true">batch</option>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	98 <option value="combined">combined</option>
0 db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	99 </param>
3 645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	100 <when value="batch">
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	101 <conditional name="reads">
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	102 <param name="type" type="select" label="Type of the file(s) to work on">
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	103 <option value="fastq" selected="true">fastq</option>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	104 <option value="fasta">fasta</option>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	105 <option value="fastq_rich">fastq_rich</option>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	106 <option value="fastq_minimal">fastq_minimal</option>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	107 <option value="summary">summary</option>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	108 <option value="bam">bam</option>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	109 <option value="cram">cram</option>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	110 </param>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	111 <when value="fastq">
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	112 <param type="data" argument="--fastq" name="files" format="fastq,fastq.gz,fastq.bz2,vcf_bgzip"/>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	113 </when>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	114 <when value="fasta">
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	115 <param type="data" argument="--fasta" name="files" format="fasta,fasta.gz,vcf_bgzip"/>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	116 </when>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	117 <when value="fastq_rich">
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	118 <param type="data" argument="--fastq_rich" name="files" format="fastq,fastq.gz,fastq.bz2,vcf_bgzip"/>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	119 </when>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	120 <when value="fastq_minimal">
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	121 <param type="data" argument="--fastq_minimal" name="files" format="fastq,fastq.gz,fastq.bz2,vcf_bgzip"/>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	122 </when>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	123 <when value="summary">
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	124 <param type="data" argument="--summary" name="files" format="txt,zip"/>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	125 </when>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	126 <when value="bam">
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	127 <param type="data" argument="--bam" name="files" format="bam"/>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	128 </when>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	129 <when value="cram">
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	130 <param type="data" argument="--cram" name="files" format="cram"/>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	131 </when>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	132 </conditional>
0 db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	133 </when>
3 645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	134 <when value="combined">
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	135 <conditional name="reads">
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	136 <param name="type" type="select" label="Type of the file(s) to work on">
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	137 <option value="fastq" selected="true">fastq</option>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	138 <option value="fasta">fasta</option>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	139 <option value="fastq_rich">fastq_rich</option>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	140 <option value="fastq_minimal">fastq_minimal</option>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	141 <option value="summary">summary</option>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	142 <option value="bam">bam</option>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	143 <option value="cram">cram</option>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	144 </param>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	145 <when value="fastq">
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	146 <param type="data" argument="--fastq" name="files" format="fastq,fastq.gz,fastq.bz2,vcf_bgzip" multiple="true"/>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	147 </when>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	148 <when value="fasta">
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	149 <param type="data" argument="--fasta" name="files" format="fasta,fasta.gz,vcf_bgzip" multiple="true"/>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	150 </when>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	151 <when value="fastq_rich">
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	152 <param type="data" argument="--fastq_rich" name="files" format="fastq,fastq.gz,fastq.bz2,vcf_bgzip" multiple="true"/>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	153 </when>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	154 <when value="fastq_minimal">
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	155 <param type="data" argument="--fastq_minimal" name="files" format="fastq,fastq.gz,fastq.bz2,vcf_bgzip" multiple="true"/>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	156 </when>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	157 <when value="summary">
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	158 <param type="data" argument="--summary" name="files" format="txt,zip" multiple="true"/>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	159 </when>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	160 <when value="bam">
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	161 <param type="data" argument="--bam" name="files" format="bam" multiple="true"/>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	162 </when>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	163 <when value="cram">
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	164 <param type="data" argument="--cram" name="files" format="cram" multiple="true"/>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	165 </when>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	166 </conditional>
0 db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	167 </when>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	168 </conditional>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	169 <section
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	170 name="filter"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	171 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	172 expanded="false">
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="integer"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	175 argument="--maxlength"
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="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	178 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	179 type="integer"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	180 argument="--minlength"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	181 optional="true"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	182 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	183 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	184 type="boolean"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	185 argument="--drop_outliers"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	186 truevalue="--drop_outliers"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	187 falsevalue=""
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	188 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	189 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	190 type="integer"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	191 argument="--downsample"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	192 optional="true"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	193 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	194 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	195 type="boolean"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	196 argument="--loglength"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	197 truevalue="--loglength"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	198 falsevalue=""
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	199 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	200 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	201 type="boolean"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	202 argument="--percentqual"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	203 truevalue="--percentqual"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	204 falsevalue=""
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	205 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	206 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	207 type="boolean"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	208 argument="--alength"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	209 truevalue="--alength"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	210 falsevalue=""
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	211 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	212 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	213 type="integer"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	214 argument="--minqual"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	215 optional="true"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	216 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	217 <param
5 a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	218 type="integer"
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	219 argument="--runtime_until"
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	220 optional="true"
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	221 label="Only take the N first hours of a run"/>
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	222 <param
0 db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	223 type="select"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	224 argument="--readtype"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	225 optional="true"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	226 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	227 <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	228 <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	229 <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	230 </param>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	231 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	232 type="boolean"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	233 argument="--barcoded"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	234 truevalue="--barcoded"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	235 falsevalue=""
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	236 label="Use if you want to split the summary file by barcode."/>
5 a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	237 <param
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	238 type="boolean"
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	239 argument="--no_supplementary"
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	240 truevalue="--no_supplementary"
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	241 falsevalue=""
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	242 label="Use if you want to remove supplementary alignments"/>
0 db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	243 </section>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	244 <section
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	245 name="customization"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	246 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	247 expanded="false">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	248 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	249 type="select"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	250 argument="--color"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	251 optional="true"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	252 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	253 <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	254 <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	255 <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	256 <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	257 <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	258 <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	259 <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	260 <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	261 <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	262 <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	263 <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	264 <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	265 <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	266 <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	267 <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	268 <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	269 <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	270 <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	271 <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	272 <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	273 <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	274 <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	275 <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	276 <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	277 <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	278 <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	279 <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	280 <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	281 <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	282 <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	283 <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	284 <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	285 <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	286 <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	287 <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	288 <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	289 <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	290 <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	291 <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	292 <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	293 <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	294 <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	295 <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	296 <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	297 <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	298 <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	299 <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	300 <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	301 <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	302 <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	303 <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	304 <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	305 <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	306 <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	307 <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	308 <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	309 <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	310 <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	311 <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	312 <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	313 <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	314 <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	315 <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	316 <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	317 <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	318 <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	319 <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	320 <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	321 <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	322 <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	323 <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	324 <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	325 <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	326 <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	327 <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	328 <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	329 <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	330 <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	331 <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	332 <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	333 <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	334 <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	335 <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	336 <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	337 <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	338 <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	339 <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	340 <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	341 <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	342 <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	343 <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	344 <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	345 <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	346 <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	347 <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	348 <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	349 <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	350 <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	351 <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	352 <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	353 <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	354 <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	355 <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	356 <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	357 <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	358 <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	359 <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	360 <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	361 <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	362 <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	363 <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	364 <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	365 <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	366 <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	367 <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	368 <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	369 <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	370 <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	371 <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	372 <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	373 <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	374 <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	375 <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	376 <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	377 <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	378 <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	379 <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	380 <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	381 <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	382 <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	383 <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	384 <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	385 <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	386 <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	387 <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	388 <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	389 <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	390 <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	391 <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	392 <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	393 <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	394 <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	395 <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	396 <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	397 <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	398 <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	399 <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	400 <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	401 </param>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	402 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	403 type="select"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	404 argument="--plots"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	405 optional="true"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	406 multiple="true"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	407 display="checkboxes"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	408 label="Specify the bivariate format of the plots.">
5 a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	409 <option value="kde">kernel density estimation (kde)</option>
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	410 <option value="dot">dots (dot)</option>
0 db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	411 </param>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	412 <param
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	413 type="boolean"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	414 argument="--N50"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	415 truevalue="--N50"
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	416 falsevalue=""
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	417 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	418 </section>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	419 </inputs>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	420 <outputs>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	421 <data name="output_html" format="html" from_work_dir="NanoPlot-report.html" label="${tool.name} on ${on_string}: HTML report"/>
5 a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	422 <data name="nanostats" format="tabular" from_work_dir="NanoStats.txt" label="${tool.name} on ${on_string}: NanoStats"/>
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	423 <data name="nanostats_post_filtering" format="tabular" from_work_dir="NanoStats_post_filtering.txt" label="${tool.name} on ${on_string}: NanoStats post filtering" />
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	424 <data name="read_length" format="png" from_work_dir="Non_weightedHistogramReadlength.png" label="${tool.name} on ${on_string}: Histogram Read Length"/>
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	425 <data name="log_read_length" format="png" from_work_dir="Non_weightedLogTransformed_HistogramReadlength.png" label="${tool.name} on ${on_string}: Log Transformed Histogram Read Length"/>
0 db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	426 </outputs>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	427 <tests>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	428 <test>
3 645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	429 <conditional name="mode">
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	430 <param name="choice" value="batch"/>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	431 <conditional name="reads">
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	432 <param name="type" value="fastq_rich"/>
5 a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	433 <param name="files" value="reads.fastq.gz" ftype="fastqsanger.gz"/>
3 645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	434 </conditional>
0 db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	435 </conditional>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	436 <section name="filter">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	437 <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	438 </section>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	439 <section name="customization">
5 a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	440 <param name="plots" value="kde"/>
0 db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	441 </section>
5 a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	442 <output name="output_html" ftype="html">
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	443 <assert_contents>
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	444 <has_text text="html"/>
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	445 <has_text text="mean_qual"/>
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	446 </assert_contents>
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	447 </output>
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	448 <output name="nanostats" file="NanoStats.txt" ftype="tabular"/>
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	449 <output name="nanostats_post_filtering" file="NanoStats_post_filtering.txt" ftype="tabular"/>
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	450 <output name="read_length" ftype="png" file="HistogramReadlength.png" compare="sim_size">
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	451 </output>
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	452 <output name="log_read_length" ftype="png">
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	453 <assert_contents>
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	454 <has_text text="PNG"/>
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	455 </assert_contents>
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	456 </output>
0 db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	457 </test>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	458 <test>
3 645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	459 <conditional name="mode">
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	460 <param name="choice" value="combined"/>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	461 <conditional name="reads">
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	462 <param name="type" value="bam"/>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	463 <param name="files" value="alignment.bam" ftype="bam"/>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	464 </conditional>
0 db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	465 </conditional>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	466 <section name="filter">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	467 <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	468 <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	469 </section>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	470 <section name="customization">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	471 <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	472 </section>
5 a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	473 <output name="output_html" ftype="html">
2 acd337269171 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit fae386db359dd61fd5e4e2e808413ae478b279ee iuc parents: 1 diff changeset	474 <assert_contents>
acd337269171 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit fae386db359dd61fd5e4e2e808413ae478b279ee iuc parents: 1 diff changeset	475 <has_text text="html"/>
acd337269171 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit fae386db359dd61fd5e4e2e808413ae478b279ee iuc parents: 1 diff changeset	476 <has_text text="Aligned read length vs Percent identity plot using dots"/> <!-- bam report specific -->
acd337269171 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit fae386db359dd61fd5e4e2e808413ae478b279ee iuc parents: 1 diff changeset	477 </assert_contents>
acd337269171 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit fae386db359dd61fd5e4e2e808413ae478b279ee iuc parents: 1 diff changeset	478 </output>
5 a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	479 <output name="read_length" ftype="png">
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	480 <assert_contents>
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	481 <has_text text="PNG"/>
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	482 </assert_contents>
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	483 </output>
0 db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	484 </test>
2 acd337269171 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit fae386db359dd61fd5e4e2e808413ae478b279ee iuc parents: 1 diff changeset	485 <test><!-- test with multiple input files -->
3 645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	486 <conditional name="mode">
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	487 <param name="choice" value="combined"/>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	488 <conditional name="reads">
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	489 <param name="type" value="fasta"/>
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	490 <param name="files" ftype="fasta" value="reads1.fasta,reads2.fasta" />
645159bcee2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 iuc parents: 2 diff changeset	491 </conditional>
2 acd337269171 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit fae386db359dd61fd5e4e2e808413ae478b279ee iuc parents: 1 diff changeset	492 </conditional>
acd337269171 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit fae386db359dd61fd5e4e2e808413ae478b279ee iuc parents: 1 diff changeset	493 <output name="output_html" ftype="html">
acd337269171 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit fae386db359dd61fd5e4e2e808413ae478b279ee iuc parents: 1 diff changeset	494 <assert_contents>
acd337269171 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit fae386db359dd61fd5e4e2e808413ae478b279ee iuc parents: 1 diff changeset	495 <has_text text="html"/>
5 a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	496 <not_has_text text="Aligned read length vs Percent identity plot using dots"/>
a3c4fe6f49ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 iuc parents: 4 diff changeset	497 <has_text text="<td>9</td>"/> <!--check both files were used 4+5 reads -->
2 acd337269171 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit fae386db359dd61fd5e4e2e808413ae478b279ee iuc parents: 1 diff changeset	498 </assert_contents>
acd337269171 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit fae386db359dd61fd5e4e2e808413ae478b279ee iuc parents: 1 diff changeset	499 </output>
acd337269171 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit fae386db359dd61fd5e4e2e808413ae478b279ee iuc parents: 1 diff changeset	500 </test>
0 db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	501 </tests>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	502 <help>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	503 <![CDATA[
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	504 What it does
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	505
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	506 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	507
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	508 .. _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	509 .. _`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	510
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	511 Input
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	512
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	513 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	514 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	515 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	516
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	517 Output
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	518
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	519 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	520 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	521 is generated.
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	522
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	523 .. _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	524 ]]>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	525 </help>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	526 <citations>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	527 <citation type="bibtex">
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	528 @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	529 {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	530 {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	531 <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	532 </citations>
db1eeffba23e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 iuc parents: diff changeset	533 </tool>

Mercurial > repos > iuc > nanoplot

annotate nanoplot.xml @ 5:a3c4fe6f49ab draft