Mercurial > repos > bgruening > nanopolish_eventalign

annotate nanopolish_eventalign.xml @ 3:ec4ac1a63682 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 4478b7f7e16d56ff6c1ffa24ded1fc106f2379c6
author bgruening
date Fri, 14 Jun 2019 08:36:58 -0400
parents 16803ac0f871
children 67049a071226
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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 &&
3
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9
0
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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 &&
3
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ec4ac1a63682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 4478b7f7e16d56ff6c1ffa24ded1fc106f2379c6
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13 #else if $input_reads_raw.extension == 'fast5.tar':
ec4ac1a63682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 4478b7f7e16d56ff6c1ffa24ded1fc106f2379c6
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14 ln -s '$input_reads_raw' fast5_files.tar &&
ec4ac1a63682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 4478b7f7e16d56ff6c1ffa24ded1fc106f2379c6
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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
ec4ac1a63682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 4478b7f7e16d56ff6c1ffa24ded1fc106f2379c6
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21 #else:
0
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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 &&
3
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24
0
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25 #end if
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3
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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
ec4ac1a63682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 4478b7f7e16d56ff6c1ffa24ded1fc106f2379c6
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32 reads.fasta &&
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33
0
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34 ln -s '$b' reads.bam &&
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35 ln -s '${b.metadata.bam_index}' reads.bam.bai &&
1
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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 &&
16803ac0f871 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
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38 #else:
16803ac0f871 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
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39 ln -f -s '$reference_source.ref_file.fields.path' genome.fa &&
16803ac0f871 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
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40 #end if
0
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41
b47693f10b20 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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42 nanopolish eventalign
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43 -r reads.fasta
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44 -b reads.bam
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45 -g genome.fa
1
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46 #if str($min_mapping_quality):
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47 -q $min_mapping_quality
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48 #end if
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49 --threads "\${GALAXY_SLOTS:-4}"
0
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50 $samples
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51 $scale_events
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52 $sam
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53 $print_read_names
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54 #if $w and str($w).strip():
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55 -w "${w}"
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56 #end if
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57 #if $input_models_fofn:
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58 --models-fofn '$input_models_fofn'
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59 #end if
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60 #if $summary:
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61 --summary eventalign-summary.txt
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62 #end if
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63 > eventalign.out
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64
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65
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66 ]]></command>
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67 <inputs>
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68 <!-- index inputs -->
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69 <param type="data" name="input_merged" format="fasta,fastq" label="Basecalled merged reads.fa"/>
3
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70 <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"/>
0
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71
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72 <!-- variants consensus inputs -->
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73 <param type="data" argument="-b" format="bam" label="Reads aligned to the reference genome" />
1
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74 <conditional name="reference_source">
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75 <param name="reference_source_selector" type="select" label="Load reference genome from">
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76 <option value="cached">Local cache</option>
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77 <option value="history">History</option>
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78 </param>
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79 <when value="cached">
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80 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
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81 <options from_data_table="all_fasta">
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82 </options>
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83 <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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84 </param>
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85 </when>
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86 <when value="history">
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87 <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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88 </when>
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89 </conditional>
0
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90
3
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91 <section name="adv" title="Optional data inputs">
ec4ac1a63682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 4478b7f7e16d56ff6c1ffa24ded1fc106f2379c6
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92 <!-- optional inputs -->
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93 <param type="data" name="input_seq_summary" format="txt" optional="true" label="Sequencing summary file from albacore" help="(-s)"/>
ec4ac1a63682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 4478b7f7e16d56ff6c1ffa24ded1fc106f2379c6
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94 </section>
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95
0
b47693f10b20 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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96 <!-- optional inputs -->
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97 <param type="data" name="input_models_fofn" argument="--models-fofn" format="txt" optional="true"
b47693f10b20 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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98 label="Read alternative k-mer models (optional)" />
b47693f10b20 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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99
b47693f10b20 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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diff changeset
100 <!-- optional params -->
b47693f10b20 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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101 <param argument="-w" type="text" optional="true"
b47693f10b20 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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102 label="find variants in window of region chromsome:start-end" />
1
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103 <param name="min_mapping_quality" type="integer" optional="true" value=""
16803ac0f871 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
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104 label="Only use reads with mapping quality of at least this value" help="(-q)"/>
0
b47693f10b20 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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diff changeset
105
b47693f10b20 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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106 <!-- optional flags -->
b47693f10b20 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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107 <param argument="--summary" type="boolean" truevalue="--summary" falsevalue="" checked="true"
b47693f10b20 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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108 label="Summarize the alignment of each read/strand" />
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109 <param argument="--samples" type="boolean" truevalue="--samples" falsevalue="" checked="false"
b47693f10b20 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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110 label="Write the raw samples for the event to the tsv output" />
b47693f10b20 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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111 <param name="scale_events" argument="--scale-events" type="boolean" truevalue="--scale-events" falsevalue="" checked="false"
b47693f10b20 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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112 label="Scale events to the model, rather than vice-versa" />
b47693f10b20 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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113 <param argument="--sam" type="boolean" truevalue="--sam" falsevalue="" checked="false"
b47693f10b20 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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114 label="write output in SAM format" />
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115 <param name="print_read_names" argument="--print-read-names" type="boolean" truevalue="--print-read-names" falsevalue="" checked="false"
b47693f10b20 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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116 label="Print read names instead of indexes" />
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117
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118 </inputs>
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119
b47693f10b20 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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120 <outputs>
b47693f10b20 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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121 <!-- variants consensus outputs -->
b47693f10b20 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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122 <data name="output_summary" format="txt" from_work_dir="eventalign-summary.txt" label="eventalign summary of reads/strands" />
1
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123 <data name="output_eventalign" format="txt" from_work_dir="eventalign.out" label="Aligned squiggles"/>
0
b47693f10b20 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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124 </outputs>
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125 <tests>
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126 <test>
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127 <param name="input_merged" ftype="fasta" value="reads.fasta" />
b47693f10b20 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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128 <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" />
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129 <param name="b" value="reads.sorted.bam" />
1
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130 <param name="reference_source_selector" value="history" />
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131 <param name="ref_file" value="draft.fa" />
0
b47693f10b20 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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132 <param name="w" value="tig00000001:200000-200010" />
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133 <param name="sam" value="true" />
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134 <output name="output_summary" file="eventalign-summary.txt" />
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135 <output name="output_eventalign" file="reads-draft.eventalign.sam"/>
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136 </test>
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137 <test>
b47693f10b20 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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138 <param name="input_merged" ftype="fasta" value="reads.fasta" />
b47693f10b20 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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139 <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" />
b47693f10b20 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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140 <param name="b" value="reads.sorted.bam" />
1
16803ac0f871 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
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141 <param name="reference_source_selector" value="history" />
16803ac0f871 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
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142 <param name="ref_file" value="draft.fa" />
0
b47693f10b20 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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143 <param name="w" value="tig00000001:200000-200010" />
b47693f10b20 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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144 <param name="sam" value="false" />
b47693f10b20 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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145 <param name="summary" value="false" />
b47693f10b20 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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146 <param name="scale_events" value="true" />
b47693f10b20 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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147 <param name="print_read_names" value="true" />
1
16803ac0f871 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
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148 <param name="min_mapping_quality" value="0" />
16803ac0f871 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
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149 <output name="output_summary" file="t2-eventalign-summary.txt" />
16803ac0f871 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
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150 <output name="output_eventalign">
16803ac0f871 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
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151 <assert_contents>
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152 <has_text text="contig" />
16803ac0f871 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
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153 <has_text text="position" />
16803ac0f871 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
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154 <has_text text="event_index" />
16803ac0f871 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
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155 <has_text text="tig00000001" />
16803ac0f871 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
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156 </assert_contents>
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157 </output>
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158 </test>
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159 <test>
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160 <!-- test data table reference -->
16803ac0f871 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
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161 <param name="input_merged" ftype="fasta" value="reads.fasta" />
16803ac0f871 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
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162 <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" />
16803ac0f871 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
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163 <param name="b" value="reads.sorted.bam" />
16803ac0f871 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
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164 <param name="reference_source_selector" value="cached" />
16803ac0f871 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
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165 <param name="ref_file" value="draft"/>
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166 <param name="w" value="tig00000001:200000-200010" />
16803ac0f871 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
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167 <param name="sam" value="false" />
16803ac0f871 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
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168 <param name="summary" value="false" />
16803ac0f871 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
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169 <param name="scale_events" value="true" />
16803ac0f871 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
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170 <param name="print_read_names" value="true" />
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171 <param name="min_mapping_quality" value="0" />
0
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172 <output name="output_summary" file="t2-eventalign-summary.txt" />
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173 <output name="output_eventalign">
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174 <assert_contents>
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175 <has_text text="contig" />
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176 <has_text text="position" />
b47693f10b20 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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177 <has_text text="event_index" />
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178 <has_text text="tig00000001" />
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179 </assert_contents>
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180 </output>
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181 </test>
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182 </tests>
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183 <help><![CDATA[
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184 Usage: nanopolish eventalign [OPTIONS] --reads reads.fa --bam alignments.bam --genome genome.fa
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185 Align nanopore events to reference k-mers
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186
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187 Tutorial and manual available at:
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188 http://nanopolish.readthedocs.io/en/latest/quickstart_eventalign.html
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189
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190 ]]></help>
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191 <expand macro="citations" />
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192 </tool>