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annotate chopper.xml @ 0:b248113ccb9d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopper/ commit 56d3f713ca5685bb56f65386c224fdf54d443ea6
author iuc
date Wed, 24 Sep 2025 11:53:42 +0000
parents
children 885c104a6667
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b248113ccb9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopper/ commit 56d3f713ca5685bb56f65386c224fdf54d443ea6
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1 <tool id="chopper" name="Chopper" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.2">
b248113ccb9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopper/ commit 56d3f713ca5685bb56f65386c224fdf54d443ea6
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2 <description>Filtering and trimming of long reads.</description>
b248113ccb9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopper/ commit 56d3f713ca5685bb56f65386c224fdf54d443ea6
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3 <macros>
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4 <token name="@TOOL_VERSION@">0.11.0</token>
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5 <token name="@VERSION_SUFFIX@">0</token>
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">chopper</requirement>
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9 </requirements>
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10 <version_command>chopper --version</version_command>
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11 <command detect_errors="exit_code"><![CDATA[
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12 chopper
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b248113ccb9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopper/ commit 56d3f713ca5685bb56f65386c224fdf54d443ea6
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14 --input $input
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16 #if $contam
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17 --contam $contam
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18 #end if
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20 #if $option_params.quality
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21 --quality $option_params.quality.value
b248113ccb9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopper/ commit 56d3f713ca5685bb56f65386c224fdf54d443ea6
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22 #end if
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24 #if $option_params.maxqual
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25 --maxqual $option_params.maxqual.value
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26 #end if
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28 #if $option_params.minlength
b248113ccb9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopper/ commit 56d3f713ca5685bb56f65386c224fdf54d443ea6
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29 --minlength $option_params.minlength.value
b248113ccb9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopper/ commit 56d3f713ca5685bb56f65386c224fdf54d443ea6
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30 #end if
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31
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32 #if $option_params.maxlength
b248113ccb9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopper/ commit 56d3f713ca5685bb56f65386c224fdf54d443ea6
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33 --maxlength $option_params.maxlength.value
b248113ccb9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopper/ commit 56d3f713ca5685bb56f65386c224fdf54d443ea6
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34 #end if
b248113ccb9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopper/ commit 56d3f713ca5685bb56f65386c224fdf54d443ea6
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35
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36 #if $option_params.headcrop
b248113ccb9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopper/ commit 56d3f713ca5685bb56f65386c224fdf54d443ea6
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37 --headcrop $option_params.headcrop.value
b248113ccb9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopper/ commit 56d3f713ca5685bb56f65386c224fdf54d443ea6
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38 #end if
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39
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40 #if $option_params.tailcrop
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41 --tailcrop $option_params.tailcrop.value
b248113ccb9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopper/ commit 56d3f713ca5685bb56f65386c224fdf54d443ea6
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42 #end if
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43
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44 #if $option_params.mingc
b248113ccb9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopper/ commit 56d3f713ca5685bb56f65386c224fdf54d443ea6
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45 --mingc $option_params.mingc.value
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46 #end if
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47
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48 #if $option_params.maxgc
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49 --maxgc $option_params.maxgc.value
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50 #end if
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51
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52 ##output capture
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53 #if $output_params.inverse == "yes"
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54 $output_params.inverse
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55 #end if
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56
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57 #if $output_params.gzip == "no"
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58 > $fq_filt
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59 #else
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60 | gzip > $fq_filt_gz
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61 #end if
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62
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63 ]]></command>
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64 <inputs>
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65 <param argument="--input" type="data" label="FASTQ file to check" format="fastq,fastq.gz,fastqsanger.gz,fastqsanger" />
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66 <param argument="--contam" type="data" format="fasta" optional="True" label="Reference FASTA" help="FASTA file with reference to check potential contaminants against."/>
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67
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68 <section name="option_params" title="Optional Parameters" expanded="True">
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69 <param argument="--quality" type="integer" label="Minimal quality score" value="0" min="0" max="60" help="Sets a minimum Phred average quality score."/>
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70 <param argument="--maxqual" type="integer" label="Maximal quality score" value="60" min="0" max="60" help="Sets a maximum Phred average quality score."/>
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71 <param argument="--minlength" type="integer" label="Sets a minimum read length" value="1" min="1" help="Minimal length of read to keep." optional="True"/>
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72 <param argument="--maxlength" type="integer" label="Sets a maximum read length" help="Maximal length of read to keep" optional="True"/>
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73 <param argument="--headcrop" type="integer" optional="True" label="Headcrop" value="0" min="0" help="Trim N nucleotides from the start of a read."/>
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74 <param argument="--tailcrop" type="integer" optional="True" label="Tailcrop" value="0" min="0" help="Trim N nucleotides from the end of a read."/>
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75 <param argument="--mingc" type="float" optional="True" label="Minimum GC content" value="0.0" min="0.0" max="1.0" help="Sets a minimum GC content for reads to keep."/>
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76 <param argument="--maxgc" type="float" optional="True" label="Maximum GC content" value="1.0" min="0.0" max="1.0" help="Sets a maximum GC content for reads to keep."/>
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77 <param argument="--trim" type="integer" label="Q-score cutoff to trim read ends" value="0" min="0" max="60" help="Takes a quality score and will trim the ends of the reads if they are below the specified cut-off (window-size = 1)."/>
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78 </section>
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79
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80 <section name="output_params" title="Output Parameters" expanded="False">
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81 <param argument="--inverse" type="boolean" checked="false" truevalue="--inverse" falsevalue="" label="Output the opposite of the normal results" help="Reverse the output results (aka, the 'failed reads')"/>
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82 <param name="gzip" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Gzip output data" help="Set to 'no' to NOT gzip the output file [default gzip output]."/>
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83 </section>
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84 </inputs>
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85
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86 <outputs>
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87 <data name="fq_filt_gz" format="fastq.gz" label="${tool.name} on ${input.name} ($on_string), gzipped" >
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88 <filter> output_params['gzip'] is True </filter>
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89 </data>
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90 <data name="fq_filt" format="fastq" label="${tool.name} on ${input.name} ($on_string)" >
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91 <filter> output_params['gzip'] is False </filter>
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92 </data>
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93 </outputs>
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94
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95 <tests>
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96 <test expect_num_outputs="1">
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97 <param name="input" value="other-test.fastq"/>
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98 <section name="output_params">
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99 <param name="gzip" value="false"/>
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100 </section>
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101 <output name="fq_filt">
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102 <assert_contents>
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103 <has_text text="@35febf09-dcbc-424c-987e-9f3f80fe73a5"/>
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104 <has_text text="@3fda06e9-62ef-4448-9993-b90124a793d5"/>
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105 <has_text text="@19d9337f-4fb6-46e5-b484-14d05f562506"/>
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106 </assert_contents>
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107 </output>
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108 </test>
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109 <test expect_num_outputs="1">
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110 <param name="input" value="other-test.fastq"/>
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111 <param name="contam" value="random_contam.fa"/>
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112 <output name="fq_filt" ftype="fastq.gz" decompress="true"> <!-- file="out2.fq.gz"/> -->
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113 <assert_contents>
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114 <has_text text="@35febf09-dcbc-424c-987e-9f3f80fe73a5"/>
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115 <has_text text="@3fda06e9-62ef-4448-9993-b90124a793d5"/>
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116 <has_text text="@19d9337f-4fb6-46e5-b484-14d05f562506"/>
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117 </assert_contents>
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118 </output>
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119 </test>
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120 <test expect_num_outputs="1">
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121 <param name="input" value="testGC.fastq"/>
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122 <section name="option_params">
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123 <param name="mingc" value="0.3"/>
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124 <param name="maxgc" value="0.8"/>
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125 </section>
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126 <section name="output_params">
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127 <param name="gzip" value="false"/>
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128 </section>
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129 <output name="fq_filt" >
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130 <assert_contents>
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131 <not_has_text text='@GC20'/>
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132 <not_has_text text='@GC0'/>
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133 <not_has_text text='@GC100'/>
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134 <has_text text='@GC50'/>
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135 <has_text text='@GC80'/>
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136 </assert_contents>
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137 </output>
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138 </test>
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139 </tests>
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140 <help><![CDATA[
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141 **Chopper**
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142
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143 Rust implementation of NanoFilt+NanoLyse, both originally written in Python. This tool, intended for long read sequencing such as PacBio or ONT, filters and trims a fastq file.
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144 Filtering is done on average read quality and minimal or maximal read length, and applying a headcrop (start of read) and tailcrop (end of read) while printing the reads passing the filter.
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145
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146 Compared to the Python implementation the scope is to deliver the same results, almost the same functionality, at much faster execution times. At the moment this tool does not support filtering using a sequencing_summary file.
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147
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148 **More Information**
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149
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150 - **Official Repository**: `Chopper on GitHub`_
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151
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152 .. _Chopper on GitHub: https://github.com/wdecoster/chopper
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153
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154 ]]></help>
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155 <citations>
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156 <citation type="doi">10.1093/bioinformatics/btad311</citation>
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157 </citations>
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158 </tool>