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annotate nanocomp.xml @ 3:9b1836ad6c2e draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp commit 69a2f2135f021f6e7bc35bce7b4954d2779efc07
author iuc
date Fri, 12 Dec 2025 08:20:12 +0000
parents 0a8f9bce9dd6
children
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53440b7599a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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1 <tool id="nanocomp" name="NanoComp" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.2">
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2 <description>Compare multiple runs of long read sequencing data and alignments</description>
9b1836ad6c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp commit 69a2f2135f021f6e7bc35bce7b4954d2779efc07
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3 <macros>
9b1836ad6c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp commit 69a2f2135f021f6e7bc35bce7b4954d2779efc07
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4 <token name="@TOOL_VERSION@">1.25.6</token>
9b1836ad6c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp commit 69a2f2135f021f6e7bc35bce7b4954d2779efc07
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5 <token name="@VERSION_SUFFIX@">1</token>
9b1836ad6c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp commit 69a2f2135f021f6e7bc35bce7b4954d2779efc07
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6 </macros>
9b1836ad6c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp commit 69a2f2135f021f6e7bc35bce7b4954d2779efc07
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7 <xrefs>
9b1836ad6c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp commit 69a2f2135f021f6e7bc35bce7b4954d2779efc07
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8 <xref type="bio.tools">nanocomp</xref>
9b1836ad6c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp commit 69a2f2135f021f6e7bc35bce7b4954d2779efc07
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9 </xrefs>
9b1836ad6c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp commit 69a2f2135f021f6e7bc35bce7b4954d2779efc07
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10 <requirements>
9b1836ad6c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp commit 69a2f2135f021f6e7bc35bce7b4954d2779efc07
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11 <requirement type="package" version="@TOOL_VERSION@">nanocomp</requirement>
9b1836ad6c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp commit 69a2f2135f021f6e7bc35bce7b4954d2779efc07
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12 </requirements>
9b1836ad6c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp commit 69a2f2135f021f6e7bc35bce7b4954d2779efc07
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13 <version_command>NanoComp -v</version_command>
9b1836ad6c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp commit 69a2f2135f021f6e7bc35bce7b4954d2779efc07
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14 <command detect_errors="exit_code"><![CDATA[
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15 #import re
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17 ##link input files with proper names (Nanocomp checks file-extensions)
9b1836ad6c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp commit 69a2f2135f021f6e7bc35bce7b4954d2779efc07
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18 #set $linked_files = []
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53440b7599a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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19 #for $file in $inputs.input_type.input_data
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20 #if '.' in str($file.name)
9b1836ad6c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp commit 69a2f2135f021f6e7bc35bce7b4954d2779efc07
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21 #set $in_name = re.sub('[\-\:\s]', '_', str($file.name))
9b1836ad6c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp commit 69a2f2135f021f6e7bc35bce7b4954d2779efc07
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22 #else
9b1836ad6c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp commit 69a2f2135f021f6e7bc35bce7b4954d2779efc07
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23 #set $in_name = re.sub('[\-\:\s]', '_', str($file.name)) + "." + $file.ext
9b1836ad6c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp commit 69a2f2135f021f6e7bc35bce7b4954d2779efc07
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24 #end if
9b1836ad6c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp commit 69a2f2135f021f6e7bc35bce7b4954d2779efc07
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25 ln -sf '$file' '$in_name' &&
9b1836ad6c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp commit 69a2f2135f021f6e7bc35bce7b4954d2779efc07
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26 #silent $linked_files.append($in_name)
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53440b7599a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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27 #end for
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53440b7599a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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29 ##run nanocomp
53440b7599a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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30 NanoComp
53440b7599a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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31
53440b7599a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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32 ##no need for the static images (becomes deprecated)
53440b7599a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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33 --make_no_static
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34
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35 ##Compute options
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36 --threads \${GALAXY_SLOTS:-4}
53440b7599a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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53440b7599a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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38 ##add input files
53440b7599a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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39 #if $inputs.input_type.input_type_selector == "fastq"
53440b7599a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
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40 --fastq
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41 #else if $inputs.input_type.input_type_selector == "fastq_r"
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42 --fastq_rich
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43 #else if $inputs.input_type.input_type_selector == "fasta"
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44 --fasta
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45 #else if $inputs.input_type.input_type_selector == "bam"
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46 --bam
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47 #else if $inputs.input_type.input_type_selector == "ubam"
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48 --ubam
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49 #else if $inputs.input_type.input_type_selector == "cram"
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50 --cram
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51 #else if $inputs.input_type.input_type_selector == "pickle"
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52 --pickle
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53 #else if $inputs.input_type.input_type_selector == "arrow"
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54 --arrow
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55 #end if
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56
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57 ## add the input files
9b1836ad6c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp commit 69a2f2135f021f6e7bc35bce7b4954d2779efc07
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58 #for $file in $linked_files
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59 '$file'
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60 #end for
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61
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62 ##Filter options
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63 #if $filters.maxlength
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64 --maxlength $filters.maxlength
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65 #end if
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66 #if $filters.minlength
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67 --minlength $filters.minlength
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68 #end if
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69
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70 ##Plot options
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71 #if $plot_options.plot
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72 --plot $plot_options.plot
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73 #end if
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74
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75 #if $plot_options.title
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76 --title "$plot_options.title"
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77 #end if
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78
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79 #if $plot_options.names
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80 --names $plot_options.names
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81 #end if
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82
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83 #if $plot_options.colors
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84 --colors $plot_options.colors
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85 #end if
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86
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87 ##Output options
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88 #if $output_options.tsv_stats
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89 $output_options.tsv_stats
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90 #end if
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91
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92 --verbose
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93 >& $out_log
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94
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95 ]]></command>
3
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96 <inputs>
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97 <section name="inputs" title="Input data" expanded="True">
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98 <conditional name="input_type">
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99 <param name="input_type_selector" type="select" label="Choose Input Format and Files">
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100 <option value="fastq" selected="true">FASTQ files</option>
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101 <option value="fastq_r">FASTQ-rich files</option>
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102 <option value="fasta">FASTA files</option>
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103 <option value="bam">BAM files</option>
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104 <option value="ubam">uBAM files</option>
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105 <option value="cram">CRAM files</option>
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106 <option value="pickle">PICKLE files</option>
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107 <option value="arrow">ARROW files</option>
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108 </param>
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109 <when value="fastq">
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110 <param name="input_data" type="data" format="fastqsanger,fastqsanger.gz" multiple="true" label="FASTQ input files" help="Data is in (compressed) fastq format" />
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111 </when>
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112 <when value="fastq_r">
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113 <param name="input_data" type="data" format="fastqsanger,fastqsanger.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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114 </when>
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115 <when value="fasta">
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116 <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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117 </when>
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118 <when value="bam">
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119 <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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120 </when>
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121 <when value="ubam">
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122 <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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123 </when>
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124 <when value="cram">
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125 <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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126 </when>
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127 <when value="pickle">
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128 <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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129 </when>
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130 <when value="arrow">
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131 <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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132 </when>
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133 </conditional>
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134 </section>
0
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135
3
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136 <section name="filters" title="Filtering Input Prior To Plotting" expanded="false">
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137 <param argument="--maxlength" type="integer" optional="true" label="Max read length filtering" help="Drop reads longer than length specified." />
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138 <param argument="--minlength" type="integer" optional="true" label="Min read length filtering" help="Drop reads shorter than length specified." />
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139 </section>
0
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140
3
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141 <section name="plot_options" title="Plot Customization Options" expanded="false">
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142 <param argument="--plot" type="select" label="Plot Type" help="Specify the type of plot to be used.">
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143 <option value="box">Box plot</option>
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144 <option value="violin" selected="true">Violin plot</option>
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145 <option value="ridge">Ridge (joyplot) plot</option>
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146 <option value="not">No plot</option>
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147 </param>
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148 <param argument="--title" type="text" label="Custom plot titles" help="Add a title to all plots." />
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149 <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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150 <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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151 </section>
0
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152
3
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153 <section name="output_options" title="Output Options" expanded="false">
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154 <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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155 </section>
0
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156
3
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157 </inputs>
0
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158
3
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159 <outputs>
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160 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log file"/>
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161 <data name="stats_file" format="txt" from_work_dir="NanoStats.txt" label="${tool.name} on ${on_string}: Statistics file"/>
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162 <data name="html_report" format="html" from_work_dir="NanoComp-report.html" label="${tool.name} on ${on_string}: Html Report"/>
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163 </outputs>
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164 <tests>
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165 <!-- 1) fastq.gz input -->
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166 <test expect_num_outputs="3">
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167 <section name="inputs">
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168 <conditional name="input_type">
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169 <param name="input_type_selector" value="fastq" />
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170 <param name="input_data" ftype="fastqsanger.gz" value="in1.fastq.gz,in2.fastq.gz,in3.fastq.gz" />
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171 </conditional>
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172 </section>
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173 <output name="stats_file" ftype="txt">
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174 <assert_contents>
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175 <has_text text="General summary" />
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176 </assert_contents>
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177 </output>
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178 <output name="html_report" ftype="html">
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179 <assert_contents>
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180 <has_text text="html"/>
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181 <has_text text="Summary statistics"/>
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182 </assert_contents>
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183 </output>
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184 </test>
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185 <!-- 2) bam input -->
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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" ftype="bam" 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" ftype="html">
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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 <!-- 3) fastq.gz input, tsv output -->
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205 <test expect_num_outputs="3">
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206 <section name="inputs">
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207 <conditional name="input_type">
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208 <param name="input_type_selector" value="fastq" />
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209 <param name="input_data" ftype="fastqsanger.gz" value="in1.fastq.gz,in3.fastq.gz" />
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210 </conditional>
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211 </section>
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212 <section name="output_options">
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213 <param name="tsv_stats" value="true"/>
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214 </section>
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215 <output name="stats_file" ftype="txt">
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216 <assert_contents>
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217 <has_text text="Metrics" />
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218 </assert_contents>
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219 </output>
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220 </test>
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221 <!-- 4) bam input, box plot output -->
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222 <test expect_num_outputs="3">
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223 <section name="inputs">
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224 <conditional name="input_type">
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225 <param name="input_type_selector" value="bam" />
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226 <param name="input_data" ftype="bam" value="in4.bam,in5.bam" />
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227 </conditional>
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228 </section>
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229 <section name="plot_options" >
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230 <param name="plot" value="box"/>
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231 </section>
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232 <output name="html_report" ftype="html">
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233 <assert_contents>
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234 <has_text text="html"/>
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235 <has_text text="Plots"/>
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236 </assert_contents>
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237 </output>
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238 </test>
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239 </tests>
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240 <help><![CDATA[
0
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241 **NanoComp**
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242
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243 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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244
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245 **Usage Instructions**
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246
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247 Multiple input files (of the same type) are allowed
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248
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249 **Output Files**
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250
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251 HTML file with the stats report and associated plots
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252
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253 **More Information**
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254
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255 - **Official Repository**: [GitHub - wdecoster/nanocomp](https://github.com/wdecoster/nanocomp)
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256 ]]></help>
3
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257 <citations>
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258 <citation type="doi">10.1093/bioinformatics/btad311</citation>
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259 </citations>
0
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260 </tool>