Mercurial > repos > bgruening > nanopolish_polya

annotate nanopolish_polya.xml @ 5:4857d5bcce52 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
author bgruening
date Thu, 30 Nov 2023 17:59:18 +0000
parents be717b65851f
children
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1 <tool id="nanopolish_polya" name="Nanopolish polyA" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>- Estimate the length of the poly-A tail on direct RNA reads.</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 <command detect_errors="exit_code"><![CDATA[
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8 @PREPROCESS_INPUTS@
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9
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10 nanopolish polya
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11 -r reads.fasta
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12 -b reads.bam
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13 -g genome.fa
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14 --threads "\${GALAXY_SLOTS:-4}"
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15 #if $w and str($w).strip():
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16 -w "${w}"
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17 #end if
0
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18 > polya_results.tsv
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19 ]]></command>
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20 <inputs>
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21 <!-- index inputs -->
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22 <param type="data" name="input_merged" format="fasta,fastq" label="Basecalled merged reads.fa"/>
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23 <param type="data" name="input_reads_raw" format="fast5.tar.gz,fast5.tar.bz2,fast5.tar" label="Flat archive file of raw fast5 files"/>
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25 <param type="data" argument="-b" format="bam" label="Reads aligned to the reference genome" />
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26 <conditional name="reference_source">
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27 <param name="reference_source_selector" type="select" label="Load reference genome from">
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28 <option value="cached">Local cache</option>
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29 <option value="history">History</option>
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30 </param>
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31 <when value="cached">
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32 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
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33 <options from_data_table="all_fasta">
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34 </options>
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35 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
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36 </param>
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37 </when>
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38 <when value="history">
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39 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" />
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40 </when>
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41 </conditional>
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42
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43 <section name="adv" title="Optional data inputs">
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44 <!-- optional inputs -->
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45 <param type="data" name="input_seq_summary" format="txt" optional="true" label="Sequencing summary file from albacore" help="(-s)"/>
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46 </section>
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47
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48 <param argument="-w" type="text" optional="true"
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49 label="only compute the poly-A lengths for reads in window STR (format: ctg:start_id-end_id)" />
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50
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51 </inputs>
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52
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53 <outputs>
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54 <data name="polya_results" format="tabular" from_work_dir="polya_results.tsv" label="called methylation sites" />
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55 </outputs>
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56 <tests>
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57 <test>
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58 <param name="input_merged" ftype="fastq" value="30xpolyA-small-subset.fastq" />
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59 <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files_30xpolyA-small-subset.tar.gz" />
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60 <param name="b" value="30xpolyA-small-subset.sorted.bam" />
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61 <param name="reference_source_selector" value="history" />
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62 <param name="ref_file" value="enolase_reference.fas" />
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63 <!-- <param name="w" value="tig00000001:200000-202000" /> -->
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64 <output name="polya_results" file="30xpolyA-small-subset-results.tsv" compare="sim_size">
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65 <assert_contents>
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66 <has_n_lines n="14"/>
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67 <has_n_columns n="10"/>
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68 <has_line_matching expression="readname\scontig\sposition\sleader_start\sadapter_start\spolya_start\stranscript_start\sread_rate\spolya_length\sqc_tag"/>
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69 <has_text text="453f3f3e-d22f-4d9c-81a6-8576e23390ed"/>
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70 <has_text text="YHR174W"/>
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71 <has_text text="READ_FAILED_LOAD"/>
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72 </assert_contents>
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73 </output>
0
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74 </test>
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75 <test>
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76 <param name="input_merged" ftype="fastq" value="30xpolyA-small-subset.fastq" />
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77 <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files_30xpolyA-small-subset.tar.gz" />
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78 <param name="b" value="30xpolyA-small-subset.sorted.bam" />
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79 <param name="reference_source_selector" value="history" />
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80 <param name="ref_file" value="enolase_reference.fas" />
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81 <param name="w" value="YHR174W:600-900" />
5
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82 <output name="polya_results" file="30xpolyA-small-subset-win-results.tsv" compare="sim_size">
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83 <assert_contents>
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84 <has_n_lines n="12"/>
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85 <has_n_columns n="10"/>
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86 <has_line_matching expression="readname\scontig\sposition\sleader_start\sadapter_start\spolya_start\stranscript_start\sread_rate\spolya_length\sqc_tag"/>
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87 <has_text text="453f3f3e-d22f-4d9c-81a6-8576e23390ed"/>
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88 <has_text text="YHR174W"/>
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89 <has_text text="READ_FAILED_LOAD"/>
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90 </assert_contents>
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91 </output>
0
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92 </test>
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93 <test>
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94 <param name="input_merged" ftype="fastq" value="30xpolyA-small-subset.fastq" />
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95 <param name="input_reads_raw" ftype="fast5.tar" value="fast5_files_30xpolyA-small-subset.tar" />
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96 <param name="b" value="30xpolyA-small-subset.sorted.bam" />
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97 <param name="reference_source_selector" value="history" />
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98 <param name="ref_file" value="enolase_reference.fas" />
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99 <param name="w" value="YHR174W:600-900" />
5
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100 <output name="polya_results" file="30xpolyA-small-subset-win-results-t3.tsv" compare="sim_size">
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101 <assert_contents>
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102 <has_n_lines n="12"/>
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103 <has_n_columns n="10"/>
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104 <has_line_matching expression="readname\scontig\sposition\sleader_start\sadapter_start\spolya_start\stranscript_start\sread_rate\spolya_length\sqc_tag"/>
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105 <has_text text="453f3f3e-d22f-4d9c-81a6-8576e23390ed"/>
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106 <has_text text="YHR174W"/>
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107 <has_text text="READ_FAILED_LOAD"/>
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108 </assert_contents>
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109 </output>
0
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110 </test>
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111 </tests>
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112 <help><![CDATA[
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113 Usage: nanopolish polya [OPTIONS] --reads reads.fa --bam alignments.bam --genome genome.fa
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114 Estimate the length of the poly-A tail on direct RNA reads
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115
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116 Quickstart tutorial and manual available at:
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117 http://nanopolish.readthedocs.io/en/latest/quickstart_polya.html
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118
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119 ]]></help>
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120 <expand macro="citations" />
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121 </tool>