Mercurial > repos > bgruening > nanopolish_eventalign

annotate nanopolish_eventalign.xml @ 0:b47693f10b20 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
author bgruening
date Wed, 30 May 2018 11:53:41 -0400
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children 16803ac0f871
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b47693f10b20 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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1 <tool id="nanopolish_eventalign" name="Nanopolish eventalign" version="0.1.0">
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2 <description>- Align nanopore events to reference k-mers</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 #else
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13 ln -s '$input_reads_raw' fast5_files.tar.gz &&
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14 mkdir fast5_files && tar -xzf fast5_files.tar.gz -C fast5_files &&
b47693f10b20 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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15 #end if
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17 nanopolish index -d fast5_files/ reads.fasta &&
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18 ln -s '$b' reads.bam &&
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19 ln -s '${b.metadata.bam_index}' reads.bam.bai &&
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20 ln -s '$g' genome.fa &&
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21
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22 nanopolish eventalign
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23 -r reads.fasta
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24 -b reads.bam
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25 -g genome.fa
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26 $samples
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27 $scale_events
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28 $sam
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29 $print_read_names
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30 #if $w and str($w).strip():
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31 -w "${w}"
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32 #end if
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33 #if $input_models_fofn:
b47693f10b20 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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34 --models-fofn '$input_models_fofn'
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35 #end if
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36 #if $summary:
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37 --summary eventalign-summary.txt
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38 #end if
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39 > eventalign.out
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40
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41
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42 ]]></command>
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43 <inputs>
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44 <!-- index inputs -->
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45 <param type="data" name="input_merged" format="fasta,fastq" label="Basecalled merged reads.fa"/>
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46 <param type="data" name="input_reads_raw" format="h5,fast5.tar.gz" label="Flat archive file of raw fast5 files"/>
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47
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48 <!-- variants consensus inputs -->
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49 <param type="data" argument="-b" format="bam" label="Reads aligned to the reference genome" />
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50 <param type="data" argument="-g" format="fasta" label="The reference genome"/>
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51
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52 <!-- optional inputs -->
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53 <param type="data" name="input_models_fofn" argument="--models-fofn" format="txt" optional="true"
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54 label="Read alternative k-mer models (optional)" />
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55
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56 <!-- optional params -->
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57 <param argument="-w" type="text" optional="true"
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58 label="find variants in window of region chromsome:start-end" />
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59
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60 <!-- optional flags -->
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61 <param argument="--summary" type="boolean" truevalue="--summary" falsevalue="" checked="true"
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62 label="Summarize the alignment of each read/strand" />
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63 <param argument="--samples" type="boolean" truevalue="--samples" falsevalue="" checked="false"
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64 label="Write the raw samples for the event to the tsv output" />
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65 <param name="scale_events" argument="--scale-events" type="boolean" truevalue="--scale-events" falsevalue="" checked="false"
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66 label="Scale events to the model, rather than vice-versa" />
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67 <param argument="--sam" type="boolean" truevalue="--sam" falsevalue="" checked="false"
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68 label="write output in SAM format" />
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69 <param name="print_read_names" argument="--print-read-names" type="boolean" truevalue="--print-read-names" falsevalue="" checked="false"
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70 label="Print read names instead of indexes" />
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71
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72 </inputs>
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73
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74 <outputs>
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75 <!-- variants consensus outputs -->
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76 <data name="output_summary" format="txt" from_work_dir="eventalign-summary.txt" label="eventalign summary of reads/strands" />
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77 <data name="output_eventalign" format="txt" from_work_dir="eventalign.out" label="Computed variants"/>
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78 </outputs>
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79 <tests>
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80 <test>
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81 <!-- index test -->
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82 <param name="input_merged" ftype="fasta" value="reads.fasta" />
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83 <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" />
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84
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85 <!-- variants consensus test -->
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86 <param name="b" value="reads.sorted.bam" />
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87 <param name="g" value="draft.fa" />
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88 <param name="w" value="tig00000001:200000-200010" />
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89 <param name="sam" value="true" />
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90
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91 <output name="output_summary" file="eventalign-summary.txt" />
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92 <output name="output_eventalign" file="reads-draft.eventalign.sam"/>
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93 </test>
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94 <test>
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95 <!-- index test -->
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96 <param name="input_merged" ftype="fasta" value="reads.fasta" />
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97 <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" />
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98
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99 <!-- variants consensus test -->
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100 <param name="b" value="reads.sorted.bam" />
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101 <param name="g" value="draft.fa" />
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102 <param name="w" value="tig00000001:200000-200010" />
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103 <param name="sam" value="false" />
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104 <param name="summary" value="false" />
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105 <param name="scale_events" value="true" />
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106 <param name="print_read_names" value="true" />
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107
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108 <output name="output_summary" file="t2-eventalign-summary.txt" />
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109 <output name="output_eventalign">
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110 <assert_contents>
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111 <has_text text="contig" />
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112 <has_text text="position" />
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113 <has_text text="event_index" />
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114 <has_text text="tig00000001" />
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115 </assert_contents>
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116 </output>
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117 </test>
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118 </tests>
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119 <help><![CDATA[
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120 Usage: nanopolish eventalign [OPTIONS] --reads reads.fa --bam alignments.bam --genome genome.fa
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121 Align nanopore events to reference k-mers
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122
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123 Tutorial and manual available at:
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124 http://nanopolish.readthedocs.io/en/latest/quickstart_eventalign.html
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125
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126 ]]></help>
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127 <expand macro="citations" />
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128 </tool>