Mercurial > repos > bgruening > nanopolish_polya

annotate nanopolish_polya.xml @ 0:7739a9b0dd83 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
author bgruening
date Wed, 19 Jun 2019 07:00:20 -0400
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children 449e9aeded2d
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1 <tool id="nanopolish_polya" name="Nanopolish polyA" version="0.1.0">
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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 ln -s '$input_merged' reads.fasta &&
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9
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10 #if $input_reads_raw.extension == 'fast5':
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11 mkdir fast5_files && ln -s '$input_reads_raw' fast5_files/read1.fast5 &&
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12
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13 #else if $input_reads_raw.extension == 'fast5.tar':
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14 ln -s '$input_reads_raw' fast5_files.tar &&
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15 mkdir fast5_files && tar -xf fast5_files.tar -C fast5_files &&
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17 #else if $input_reads_raw.extension == 'fast5.tar.bz2':
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18 ln -s '$input_reads_raw' fast5_files.tar.bz2 &&
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19 mkdir fast5_files && tar -xjf fast5_files.tar.bz2 -C fast5_files &&
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20
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21 #else:
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22 ln -s '$input_reads_raw' fast5_files.tar.gz &&
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23 mkdir fast5_files && tar -xzf fast5_files.tar.gz -C fast5_files &&
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24
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25 #end if
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26
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27 nanopolish index
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28 -d fast5_files/
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29 #if $adv.input_seq_summary:
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30 -s '$adv.input_seq_summary'
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31 #end if
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32 reads.fasta &&
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33
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34 ln -s '$b' reads.bam &&
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35 ln -s '${b.metadata.bam_index}' reads.bam.bai &&
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36 #if $reference_source.reference_source_selector == 'history':
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37 ln -f -s '$reference_source.ref_file' genome.fa &&
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38 #else:
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39 ln -f -s '$reference_source.ref_file.fields.path' genome.fa &&
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40 #end if
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41
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42 nanopolish polya
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43 -r reads.fasta
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44 -b reads.bam
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45 -g genome.fa
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46 --threads "\${GALAXY_SLOTS:-4}"
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47 #if $w and str($w).strip():
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48 -w "${w}"
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49 #end if
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50 > polya_results.tsv
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51 ]]></command>
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52 <inputs>
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53 <!-- index inputs -->
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54 <param type="data" name="input_merged" format="fasta,fastq" label="Basecalled merged reads.fa"/>
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55 <param type="data" name="input_reads_raw" format="h5,fast5.tar.gz,fast5.tar.bz2,fast5.tar" label="Flat archive file of raw fast5 files"/>
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56
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57 <param type="data" argument="-b" format="bam" label="Reads aligned to the reference genome" />
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58 <conditional name="reference_source">
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59 <param name="reference_source_selector" type="select" label="Load reference genome from">
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60 <option value="cached">Local cache</option>
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61 <option value="history">History</option>
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62 </param>
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63 <when value="cached">
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64 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
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65 <options from_data_table="all_fasta">
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66 </options>
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67 <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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68 </param>
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69 </when>
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70 <when value="history">
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71 <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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72 </when>
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73 </conditional>
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74
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75 <section name="adv" title="Optional data inputs">
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76 <!-- optional inputs -->
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77 <param type="data" name="input_seq_summary" format="txt" optional="true" label="Sequencing summary file from albacore" help="(-s)"/>
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78 </section>
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79
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80 <param argument="-w" type="text" optional="true"
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81 label="only compute the poly-A lengths for reads in window STR (format: ctg:start_id-end_id)" />
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82
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83 </inputs>
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84
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85 <outputs>
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86 <data name="polya_results" format="tabular" from_work_dir="polya_results.tsv" label="called methylation sites" />
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87 </outputs>
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88 <tests>
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89 <test>
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90 <param name="input_merged" ftype="fastq" value="30xpolyA-small-subset.fastq" />
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91 <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files_30xpolyA-small-subset.tar.gz" />
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92 <param name="b" value="30xpolyA-small-subset.sorted.bam" />
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93 <param name="reference_source_selector" value="history" />
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94 <param name="ref_file" value="enolase_reference.fas" />
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95 <!-- <param name="w" value="tig00000001:200000-202000" /> -->
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96 <output name="polya_results" file="30xpolyA-small-subset-results.tsv" />
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97 </test>
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98 <test>
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99 <param name="input_merged" ftype="fastq" value="30xpolyA-small-subset.fastq" />
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100 <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files_30xpolyA-small-subset.tar.gz" />
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101 <param name="b" value="30xpolyA-small-subset.sorted.bam" />
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102 <param name="reference_source_selector" value="history" />
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103 <param name="ref_file" value="enolase_reference.fas" />
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104 <param name="w" value="YHR174W:600-900" />
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105 <output name="polya_results" file="30xpolyA-small-subset-win-results.tsv" />
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106 </test>
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107 <test>
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108 <param name="input_merged" ftype="fastq" value="30xpolyA-small-subset.fastq" />
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109 <param name="input_reads_raw" ftype="fast5.tar" value="fast5_files_30xpolyA-small-subset.tar" />
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110 <param name="b" value="30xpolyA-small-subset.sorted.bam" />
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111 <param name="reference_source_selector" value="history" />
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112 <param name="ref_file" value="enolase_reference.fas" />
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113 <param name="w" value="YHR174W:600-900" />
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114 <output name="polya_results" file="30xpolyA-small-subset-win-results-t3.tsv" />
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115 </test>
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116 </tests>
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117 <help><![CDATA[
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118 Usage: nanopolish polya [OPTIONS] --reads reads.fa --bam alignments.bam --genome genome.fa
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119 Estimate the length of the poly-A tail on direct RNA reads
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120
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121 Quickstart tutorial and manual available at:
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122 http://nanopolish.readthedocs.io/en/latest/quickstart_polya.html
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123
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124 ]]></help>
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125 <expand macro="citations" />
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126 </tool>