Mercurial > repos > bgruening > nanopolish_eventalign

annotate nanopolish_eventalign.xml @ 1:16803ac0f871 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
author bgruening
date Tue, 05 Jun 2018 07:51:55 -0400
parents b47693f10b20
children ec4ac1a63682
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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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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 '$input_reads_raw' fast5_files.tar.gz &&
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14 mkdir fast5_files && tar -xzf fast5_files.tar.gz -C fast5_files &&
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15 #end if
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17 nanopolish index -d fast5_files/ reads.fasta &&
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18 ln -s '$b' reads.bam &&
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19 ln -s '${b.metadata.bam_index}' reads.bam.bai &&
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20 #if $reference_source.reference_source_selector == 'history':
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21 ln -f -s '$reference_source.ref_file' genome.fa &&
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22 #else:
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23 ln -f -s '$reference_source.ref_file.fields.path' genome.fa &&
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24 #end if
0
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25
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26 nanopolish eventalign
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27 -r reads.fasta
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28 -b reads.bam
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29 -g genome.fa
1
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30 #if str($min_mapping_quality):
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31 -q $min_mapping_quality
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32 #end if
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33 --threads "\${GALAXY_SLOTS:-4}"
0
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34 $samples
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35 $scale_events
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36 $sam
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37 $print_read_names
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38 #if $w and str($w).strip():
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39 -w "${w}"
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40 #end if
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41 #if $input_models_fofn:
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42 --models-fofn '$input_models_fofn'
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43 #end if
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44 #if $summary:
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45 --summary eventalign-summary.txt
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46 #end if
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47 > eventalign.out
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48
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49
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50 ]]></command>
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51 <inputs>
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52 <!-- index inputs -->
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53 <param type="data" name="input_merged" format="fasta,fastq" label="Basecalled merged reads.fa"/>
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54 <param type="data" name="input_reads_raw" format="h5,fast5.tar.gz" label="Flat archive file of raw fast5 files"/>
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55
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56 <!-- variants consensus inputs -->
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57 <param type="data" argument="-b" format="bam" label="Reads aligned to the reference genome" />
1
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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>
0
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74
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75 <!-- optional inputs -->
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76 <param type="data" name="input_models_fofn" argument="--models-fofn" format="txt" optional="true"
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77 label="Read alternative k-mer models (optional)" />
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78
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79 <!-- optional params -->
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80 <param argument="-w" type="text" optional="true"
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81 label="find variants in window of region chromsome:start-end" />
1
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82 <param name="min_mapping_quality" type="integer" optional="true" value=""
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83 label="Only use reads with mapping quality of at least this value" help="(-q)"/>
0
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84
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85 <!-- optional flags -->
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86 <param argument="--summary" type="boolean" truevalue="--summary" falsevalue="" checked="true"
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87 label="Summarize the alignment of each read/strand" />
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88 <param argument="--samples" type="boolean" truevalue="--samples" falsevalue="" checked="false"
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89 label="Write the raw samples for the event to the tsv output" />
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90 <param name="scale_events" argument="--scale-events" type="boolean" truevalue="--scale-events" falsevalue="" checked="false"
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91 label="Scale events to the model, rather than vice-versa" />
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92 <param argument="--sam" type="boolean" truevalue="--sam" falsevalue="" checked="false"
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93 label="write output in SAM format" />
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94 <param name="print_read_names" argument="--print-read-names" type="boolean" truevalue="--print-read-names" falsevalue="" checked="false"
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95 label="Print read names instead of indexes" />
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96
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97 </inputs>
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98
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99 <outputs>
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100 <!-- variants consensus outputs -->
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101 <data name="output_summary" format="txt" from_work_dir="eventalign-summary.txt" label="eventalign summary of reads/strands" />
1
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102 <data name="output_eventalign" format="txt" from_work_dir="eventalign.out" label="Aligned squiggles"/>
0
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103 </outputs>
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104 <tests>
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105 <test>
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106 <param name="input_merged" ftype="fasta" value="reads.fasta" />
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107 <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" />
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108 <param name="b" value="reads.sorted.bam" />
1
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109 <param name="reference_source_selector" value="history" />
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110 <param name="ref_file" value="draft.fa" />
0
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111 <param name="w" value="tig00000001:200000-200010" />
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112 <param name="sam" value="true" />
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113 <output name="output_summary" file="eventalign-summary.txt" />
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114 <output name="output_eventalign" file="reads-draft.eventalign.sam"/>
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115 </test>
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116 <test>
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117 <param name="input_merged" ftype="fasta" value="reads.fasta" />
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118 <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" />
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119 <param name="b" value="reads.sorted.bam" />
1
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120 <param name="reference_source_selector" value="history" />
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121 <param name="ref_file" value="draft.fa" />
0
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122 <param name="w" value="tig00000001:200000-200010" />
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123 <param name="sam" value="false" />
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124 <param name="summary" value="false" />
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125 <param name="scale_events" value="true" />
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126 <param name="print_read_names" value="true" />
1
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127 <param name="min_mapping_quality" value="0" />
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128 <output name="output_summary" file="t2-eventalign-summary.txt" />
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129 <output name="output_eventalign">
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130 <assert_contents>
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131 <has_text text="contig" />
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132 <has_text text="position" />
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133 <has_text text="event_index" />
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134 <has_text text="tig00000001" />
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135 </assert_contents>
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136 </output>
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137 </test>
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138 <test>
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139 <!-- test data table reference -->
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140 <param name="input_merged" ftype="fasta" value="reads.fasta" />
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141 <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" />
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142 <param name="b" value="reads.sorted.bam" />
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143 <param name="reference_source_selector" value="cached" />
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144 <param name="ref_file" value="draft"/>
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145 <param name="w" value="tig00000001:200000-200010" />
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146 <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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147 <param name="summary" value="false" />
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148 <param name="scale_events" value="true" />
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149 <param name="print_read_names" value="true" />
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150 <param name="min_mapping_quality" value="0" />
0
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151 <output name="output_summary" file="t2-eventalign-summary.txt" />
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152 <output name="output_eventalign">
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153 <assert_contents>
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154 <has_text text="contig" />
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155 <has_text text="position" />
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156 <has_text text="event_index" />
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157 <has_text text="tig00000001" />
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158 </assert_contents>
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159 </output>
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160 </test>
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161 </tests>
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162 <help><![CDATA[
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163 Usage: nanopolish eventalign [OPTIONS] --reads reads.fa --bam alignments.bam --genome genome.fa
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164 Align nanopore events to reference k-mers
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165
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166 Tutorial and manual available at:
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167 http://nanopolish.readthedocs.io/en/latest/quickstart_eventalign.html
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168
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169 ]]></help>
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170 <expand macro="citations" />
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171 </tool>