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annotate filtlong.xml @ 3:41b2ad601cf0 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit adf0341da7282c80c25336ae03130b2dc44c65bb"
author iuc
date Thu, 24 Feb 2022 21:22:16 +0000
parents a72af9de6bf5
children 1f296803dfa3
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41b2ad601cf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit adf0341da7282c80c25336ae03130b2dc44c65bb"
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1 <tool id="filtlong" name="filtlong" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>Filtering long reads by quality</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <version_command>filtlong --version</version_command>
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8 <command detect_errors="exit_code"><![CDATA[
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9 filtlong
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10 #if $output_thresholds.target_bases:
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11 --target_bases '$output_thresholds.target_bases'
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12 #end if
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13 #if $output_thresholds.keep_percent:
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14 --keep_percent '$output_thresholds.keep_percent'
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15 #end if
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16 #if $output_thresholds.min_length:
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17 --min_length '$output_thresholds.min_length'
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18 #end if
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19 #if $output_thresholds.min_mean_q:
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20 --min_mean_q '$output_thresholds.min_mean_q'
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21 #end if
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22 #if $output_thresholds.min_window_q:
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23 --min_window_q '$output_thresholds.min_window_q'
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24 #end if
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25 #if $output_thresholds.max_length:
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26 --max_length '$output_thresholds.max_length'
41b2ad601cf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit adf0341da7282c80c25336ae03130b2dc44c65bb"
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27 #end if
0
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28 #if $external_references.assembly:
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29 --assembly '$external_references.assembly'
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30 #end if
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31 #if $external_references.illumina_1:
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32 --illumina_1 '$external_references.illumina_1'
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33 #end if
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34 #if $external_references.illumina_2:
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35 --illumina_2 '$external_references.illumina_2'
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36 #end if
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37 --length_weight '$score_weights.length_weight'
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38 --mean_q_weight '$score_weights.mean_q_weight'
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39 --window_q_weight '$score_weights.window_q_weight'
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40 $read_manipulation.trim
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41 #if $read_manipulation.split:
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42 --split '$read_manipulation.split'
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43 #end if
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44 #if $other.window_size:
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45 --window_size '$other.window_size'
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46 #end if
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47 '$input_file' > output.fastq
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48 ]]></command>
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49 <inputs>
2
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50 <param name="input_file" type="data" format="fastqsanger,fastqsanger.gz" label="Input FASTQ" help="FASTQ of input reads"/>
0
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51 <section name="output_thresholds" title="Output thresholds">
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52 <param argument="--target_bases" type="integer" min="0" optional="True" label="Total bases" help="Keep only the best reads up to this many total bases"/>
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53 <param argument="--keep_percent" type="float" min="0" max="100" optional="True" label="Keep percentage" help="Keep only this percentage of the best reads (measured by bases)"/>
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54 <param argument="--max_length" type="integer" min="0" optional="True" label="Max. length" help="Maximum length threshold"/>
0
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55 <param argument="--min_length" type="integer" min="0" optional="True" label="Min. length" help="Minimum length threshold"/>
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56 <param argument="--min_mean_q" type="float" min="0" optional="True" label="Min. mean quality" help="Minimum mean quality threshold"/>
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57 <param argument="--min_window_q" type="float" min="0" optional="True" label="Min. window quality" help="Minimum window quality threshold"/>
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58 </section>
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59 <section name="external_references" title="External references">
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60 <param argument="--assembly" type="data" format="fasta,fasta.gz" optional="True" label="Reference assembly" help="Reference assembly in FASTA format"/>
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61 <param argument="--illumina_1" type="data" format="fastqsanger,fastqsanger.gz" optional="True" label="Reference Illumina read" help="Reference Illumina reads in FASTQ format"/>
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62 <param argument="--illumina_2" type="data" format="fastqsanger,fastqsanger.gz" optional="True" label="Reference Illumina read" help="Reference Illumina reads in FASTQ format"/>
0
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63 </section>
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64 <section name="score_weights" title="Score weights">
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65 <param argument="--length_weight" type="float" min="0" value="1" optional="True" label="Weight length score" help="Weight given to the length score (default: 1)"/>
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66 <param argument="--mean_q_weight" type="float" min="0" value="1" optional="True" label="Weight mean quality" help="Weight given to the mean quality score (default: 1)"/>
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67 <param argument="--window_q_weight" type="float" min="0" value="1" optional="True" label="Weight window quality" help="Weight given to the window quality score (default: 1)"/>
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68 </section>
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69 <section name="read_manipulation" title="Read manipulation">
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70 <param argument="--trim" type="boolean" checked="false" truevalue="--trim" falsevalue="" label="Trim non-k-mer-matching" help="Trim non-k-mer-matching bases from start/end of reads"/>
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71 <param argument="--split" type="integer" min="0" optional="True" label="Split at nr. of bases" help="split reads at this many (or more) consecutive non-k-mer-matching bases"/>
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72 </section>
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73 <section name="other" title="Other">
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74 <param argument="--window_size" type="integer" min="0" value="250" optional="True" label="Sliding window size" help="size of sliding window used when measuring window quality (default: 250)"/>
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75 </section>
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76 </inputs>
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77 <outputs>
1
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78 <data name="outfile" format="fastqsanger" from_work_dir="output.fastq" label="${tool.name} on ${on_string}: Filtered FASTQ"/>
0
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79 </outputs>
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80 <tests>
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81 <test>
2
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82 <param name="input_file" ftype="fastqsanger" value="test.fastq.gz"/>
0
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83 <param name="min_length" value="1000"/>
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84 <param name="keep_percent" value="50"/>
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85 <param name="target_bases" value="500000000"/>
1
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86 <output name="outfile" ftype="fastqsanger" file="output.fastq"/>
0
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87 </test>
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88 <test>
2
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89 <param name="input_file" ftype="fastqsanger" value="test.fastq.gz"/>
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90 <param name="assembly" ftype="fasta.gz" value="test_reference.fasta.gz"/>
1
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91 <param name="illumina_1" ftype="fastqsanger.gz" value="test_reference_1.fastq.gz"/>
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92 <param name="illumina_2" ftype="fastqsanger.gz" value="test_reference_2.fastq.gz"/>
0
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93 <param name="min_length" value="1000"/>
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94 <param name="keep_percent" value="90"/>
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95 <param name="target_bases" value="500000000"/>
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96 <param name="trim" value="True"/>
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97 <param name="split" value="500"/>
1
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98 <output name="outfile" ftype="fastqsanger" file="output_reference.fastq"/>
0
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99 </test>
3
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100 <test>
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101 <param name="input_file" ftype="fastqsanger" value="test.fastq.gz"/>
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102 <param name="max_length" value="5000"/>
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103 <output name="outfile" ftype="fastqsanger" file="output_max_length.fastq"/>
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104 </test>
0
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105 </tests>
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106 <help><![CDATA[
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107 Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.
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108 ]]></help>
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109 <citations>
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110 <citation type="bibtex">
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111 @misc{rrwick2017,
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112 author = {Wick, Ryan},
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113 year = {2017},
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114 title = {Filtlong},
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115 publisher = {GitHub},
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116 journal = {GitHub repository},
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117 url = {https://github.com/rrwick/Filtlong},
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118 }
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119 </citation>
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120 </citations>
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121 </tool>