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annotate nanocomp.xml @ 0:719f83a2b91c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
author iuc
date Wed, 21 May 2025 21:08:19 +0000
parents
children ce9c8a64ea7c
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0
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
iuc
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1 <tool id="nanocomp" name="NanoComp" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.2">
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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2 <description>Compare multiple runs of long read sequencing data and alignments.</description>
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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3 <macros>
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
iuc
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4 <token name="@TOOL_VERSION@">1.25.2</token>
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
iuc
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5 <token name="@VERSION_SUFFIX@">0</token>
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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6 </macros>
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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7 <xrefs>
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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8 <xref type="bio.tools">nanocomp</xref>
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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9 </xrefs>
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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10 <requirements>
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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11 <requirement type="package" version="@TOOL_VERSION@">nanocomp</requirement>
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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12 </requirements>
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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13 <version_command>NanoComp -v</version_command>
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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14 <command detect_errors="exit_code"><![CDATA[
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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15 #import re
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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16 ##link input file with names
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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17 #for $file in $inputs.input_type.input_data
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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18 #if '.' in str($file.name)
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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19 #set $in_name = re.sub('[\-\:\s]', '_', str($file.name))
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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20 #else
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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21 #set $in_name = re.sub('[\-\:\s]', '_', str($file.name)) + "." + $file.ext
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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22 #end if
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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23 ln -sf $file $in_name &&
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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24 #end for
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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25
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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26 ##run nanocomp
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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27 NanoComp
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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28
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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29 ##no need for the static images (becomes deprecated)
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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30 --make_no_static
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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31
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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32 ## Compute options
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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33 --threads \${GALAXY_SLOTS:-4}
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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34
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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35 ##add input files
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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36 #if $inputs.input_type.input_type_selector == "fastq"
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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37 --fastq
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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38 #else if $inputs.input_type.input_type_selector == "fastq_r"
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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39 --fastq_rich
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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40 #else if $inputs.input_type.input_type_selector == "fasta"
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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41 --fasta
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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42 #else if $inputs.input_type.input_type_selector == "bam"
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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43 --bam
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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44 #else if $inputs.input_type.input_type_selector == "ubam"
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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45 --ubam
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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46 #else if $inputs.input_type.input_type_selector == "cram"
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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47 --cram
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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48 #else if $inputs.input_type.input_type_selector == "pickle"
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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49 --pickle
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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50 #else if $inputs.input_type.input_type_selector == "arrow"
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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51 --arrow
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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52 #end if
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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53
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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54 #for $file in $inputs.input_type.input_data
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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55 #if '.' in str($file.name)
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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56 #set $in_name = re.sub('[\-\:\s]', '_', str($file.name))
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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57 #else
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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58 #set $in_name = re.sub('[\-\:\s]', '_', str($file.name)) + "." + $file.ext
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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59 #end if
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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60 $in_name
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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61 #end for
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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62
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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63 ##Filter options
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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64 #if $filters.maxlength
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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65 --maxlength $filters.maxlength
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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66 #end if
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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67 #if $filters.minlength
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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68 --minlength $filters.minlength
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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69 #end if
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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70
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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71 ##Plot options
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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72 #if $plot_options.plot
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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73 --plot $plot_options.plot
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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74 #end if
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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75
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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76 #if $plot_options.title
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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77 --title "$plot_options.title"
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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78 #end if
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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79
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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80 #if $plot_options.names
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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81 --names $plot_options.names
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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82 #end if
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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83
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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84 #if $plot_options.colors
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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85 --colors $plot_options.colors
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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86 #end if
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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87
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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88 ##Output options
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89 #if $output_options.tsv_stats
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90 $output_options.tsv_stats
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91 #end if
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92
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93 --verbose
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94 >& $out_log
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95
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96 ]]></command>
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97 <inputs>
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98 <section name="inputs" title="Input data" expanded="True">
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99 <conditional name="input_type">
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100 <param name="input_type_selector" type="select" label="Choose Input Format and Files">
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101 <option value="fastq" selected="true">FASTQ files</option>
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102 <option value="fastq_r">FASTQ-rich files</option>
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103 <option value="fasta">FASTA files</option>
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104 <option value="bam">BAM files</option>
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105 <option value="ubam">uBAM files</option>
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106 <option value="cram">CRAM files</option>
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107 <option value="pickle">PICKLE files</option>
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108 <option value="arrow">ARROW files</option>
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109 </param>
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110 <when value="fastq">
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111 <param name="input_data" type="data" format="fastq,fastq.gz" multiple="true" label="FASTQ input files" help="Data is in (compressed) fastq format" />
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112 </when>
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113 <when value="fastq_r">
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114 <param name="input_data" type="data" format="fastq,fastq.gz" multiple="true" label="FASTQ input files" help="Data is in one or more fastq file(s) generated by MinKNOW or guppy with additional information concerning channel and time" />
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115 </when>
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116 <when value="fasta">
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117 <param name="input_data" type="data" format="fasta,fasta.gz" multiple="true" label="FASTA input files" help="Data is in (compressed) fasta format" />
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118 </when>
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119 <when value="bam">
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120 <param name="input_data" type="data" format="bam" multiple="true" label="BAM input files" help="Data is in sorted bam files." />
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121 </when>
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122 <when value="ubam">
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123 <param name="input_data" type="data" format="bam" multiple="true" label="Unmapped BAM input files" help="Data is in one or more unmapped bam files." />
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124 </when>
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125 <when value="cram">
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126 <param name="input_data" type="data" format="cram" multiple="true" label="CRAM input files" help="Data is in sorted cram files." />
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127 </when>
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128 <when value="pickle">
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129 <param name="input_data" type="data" format="binary" multiple="true" label="PICKLE input files" help="Data is in one or more pickle file(s) from using NanoComp/NanoPlot." />
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130 </when>
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131 <when value="arrow">
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132 <param name="input_data" type="data" format="binary" multiple="true" label="ARROW input files" help="Data is in one or more feather/arrow file(s)." />
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133 </when>
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134 </conditional>
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135 </section>
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136
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137 <section name="filters" title="Filtering Input Prior To Plotting" expanded="false">
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138 <param argument="--maxlength" type="integer" optional="true" label="Max read length filtering" help="Drop reads longer than length specified." />
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139 <param argument="--minlength" type="integer" optional="true" label="Min read length filtering" help="Drop reads shorter than length specified." />
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140 </section>
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141
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142 <section name="plot_options" title="Plot Customization Options" expanded="false">
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143 <param argument="--plot" type="select" label="Plot Type" help="Specify the type of plot to be used.">
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144 <option value="box">Box plot</option>
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145 <option value="violin" selected="true">Violin plot</option>
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146 <option value="ridge">Ridge (joyplot) plot</option>
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147 <option value="not">No plot</option>
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148 </param>
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149 <param argument="--title" type="text" label="Custom plot titles" help="Add a title to all plots." />
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150 <param argument="--names" type="text" label="Custom names" help="Specify the names (space seperated, respective to input) to be used for the datasets." />
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151 <param argument="--colors" type="text" label="Custom colors" help="Specify the colors (space seperated, respective to input) to be used for each the datasets. Can be any valid Matplotlib color: Named, HEX-string, RGB, ... " />
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152 </section>
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153
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154 <section name="output_options" title="Output Options" expanded="false">
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155 <param argument="--tsv_stats" type="boolean" truevalue="--tsv_stats" falsevalue="" optional="true" checked="false" label="TSV Output Format" help="Output the statistics file as properly formatted TSV."/>
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156 </section>
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157
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158 </inputs>
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159
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160
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161 <outputs>
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162 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log file"/>
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163 <data name="stats_file" format="txt" from_work_dir="NanoStats.txt" label="${tool.name} on ${on_string}: Statistics file"/>
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164 <data name="html_report" format="html" from_work_dir="NanoComp-report.html" label="${tool.name} on ${on_string}: Html Report"/>
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165 </outputs>
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166 <tests>
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167 <test expect_num_outputs="3">
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168 <section name="inputs">
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169 <conditional name="input_type">
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170 <param name="input_type_selector" value="fastq" />
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171 <param name="input_data" value="in1.fastq.gz,in2.fastq.gz,in3.fastq.gz" />
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172 </conditional>
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173 </section>
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174 <output name="stats_file" >
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175 <assert_contents>
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176 <has_text text="General summary" />
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177 </assert_contents>
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178 </output>
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179 <output name="html_report">
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180 <assert_contents>
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181 <has_text text="html"/>
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182 <has_text text="Summary statistics"/>
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183 </assert_contents>
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184 </output>
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185 </test>
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186 <test expect_num_outputs="3">
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187 <section name="inputs">
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188 <conditional name="input_type">
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189 <param name="input_type_selector" value="bam" />
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190 <param name="input_data" value="in4.bam,in5.bam" />
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191 </conditional>
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192 </section>
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193 <section name="filters" >
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194 <param name="maxlength" value="15000"/>
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195 <param name="minlength" value="500"/>
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196 </section>
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197 <output name="html_report">
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198 <assert_contents>
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199 <has_text text="html"/>
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200 <has_text text="Summary statistics"/>
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201 </assert_contents>
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202 </output>
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203 </test>
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204 <test expect_num_outputs="3">
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205 <section name="inputs">
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206 <conditional name="input_type">
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207 <param name="input_type_selector" value="fastq" />
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208 <param name="input_data" value="in1.fastq.gz,in3.fastq.gz" />
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209 </conditional>
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210 </section>
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211 <section name="output_options">
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212 <param name="tsv_stats" value="true"/>
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213 </section>
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214 <output name="stats_file" >
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215 <assert_contents>
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216 <has_text text="Metrics" />
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217 </assert_contents>
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218 </output>
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219 </test>
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220 <test expect_num_outputs="3">
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221 <section name="inputs">
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222 <conditional name="input_type">
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223 <param name="input_type_selector" value="bam" />
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224 <param name="input_data" value="in4.bam,in5.bam" />
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225 </conditional>
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226 </section>
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227 <section name="plot_options" >
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228 <param name="plot" value="box"/>
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229 </section>
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230 <output name="html_report">
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231 <assert_contents>
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232 <has_text text="html"/>
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233 <has_text text="Plots"/>
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234 </assert_contents>
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235 </output>
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236 </test>
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237 </tests>
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238 <help><![CDATA[
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239 **NanoComp**
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240
719f83a2b91c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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241 Compare multiple runs of long read sequencing data and alignments. Creates violin plots or box plots of length, quality and percent identity and creates dynamic, overlaying read length histograms and a cumulative yield plot.
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242
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243 **Usage Instructions**
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244
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245 Multiple input files (of the same type) are allowed
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246
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247 **Output Files**
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248
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249 HTML file with the stats report and associated plots
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250
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251 **More Information**
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252
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253 - **Official Repository**: [GitHub - wdecoster/nanocomp](https://github.com/wdecoster/nanocomp)
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254 ]]></help>
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255 <citations>
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256 <citation type="doi">10.1093/bioinformatics/btad311</citation>
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257 </citations>
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258 </tool>