Mercurial > repos > jdv > porechop

annotate porechop.xml @ 7:18d17a5bfe11 draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit da020fbee6e2bd91bc4a8d0850dc601db34ac82b
author jdv
date Sun, 15 Oct 2017 17:32:40 -0400
parents 15e64c5938e6
children 852b3fe95c20
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1 <tool id="porechop" name="Porechop" version="0.2.2">
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3 <description>Demux and adapter removal</description>
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5 <!-- ***************************************************************** -->
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7 <!-- not yet working with Bioconda
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8 <requirements>
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9 <requirement type="package" version="0.2.1">porechop</requirement>
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10 </requirements>
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11 -->
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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13 <!-- ***************************************************************** -->
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15 <version_command>porechop --version</version_command>
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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17 <!-- ***************************************************************** -->
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19 <command detect_errors="aggressive">
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20 <![CDATA[
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22 #set filename = str($input.name)
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24 mkdir out &&
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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26 porechop
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28 --input ${input}
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30 --format ${out_format}
f84a33bc5c3e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 19e515145381f7a8b16662e33678df7087019f19
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31
0
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32 #if str($demux_section.demux_options.demux) == "yes":
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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33 --barcode_dir out
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34 #else:
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35 --output "out/$filename"
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36 #end if
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38 --threads \${GALAXY_SLOTS:-1}
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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40 ##--Demultiplex Options--------------------------
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42 #if str($demux_section.demux_options.demux) == "yes":
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44 --barcode_threshold $demux_section.demux_options.barcode_threshold
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45 --barcode_diff $demux_section.demux_options.barcode_diff
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46 $demux_section.demux_options.require_two_barcodes
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47 $demux_section.demux_options.discard_unassigned
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49 #end if
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51 ##--Adapter Trim Options--------------------------
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53 #if str($trim_section.trim_options.trim) == "yes":
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55 --adapter_threshold $trim_section.trim_options.adapter_threshold
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56 --check_reads $trim_section.trim_options.check_reads
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57 --scoring_scheme $trim_section.trim_options.scoring_scheme
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59 --end_size $trim_section.trim_options.end_size
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60 --end_threshold $trim_section.trim_options.end_threshold
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61 --min_trim_size $trim_section.trim_options.min_trim_size
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62 --extra_end_trim $trim_section.trim_options.extra_end_trim
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64 $trim_section.trim_options.discard_middle
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65 --middle_threshold $trim_section.trim_options.middle_threshold
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66 --extra_middle_trim_good_side $trim_section.trim_options.extra_middle_trim_good_side
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67 --extra_middle_trim_bad_side $trim_section.trim_options.extra_middle_trim_bad_side
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68 --min_split_read_size $trim_section.trim_options.min_split_read_size
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71 #else:
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72 --untrimmed
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74 #end if
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75
3
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76 | perl $__tool_directory__/porechop_summarize.pl
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77 > $result_table
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78
0
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79 ]]>
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80 </command>
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82 <!-- ***************************************************************** -->
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84 <inputs>
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86 <param argument="--input" type="data" format="fastq,fasta" label="Input reads" />
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87
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88 <param name="out_format" type="select" label="Output format">
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89 <option value="fastq" selected="true">fastq</option>
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90 <option value="fasta">fasta</option>
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91 </param>
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92
0
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93 <section name="demux_section" title="Demultiplexing Options" expanded="True">
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94 <conditional name="demux_options">
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95 <param name="demux" type="select" label="Perform demultiplexing" help="">
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96 <option value="no" selected="true">no</option>
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97 <option value="yes">yes</option>
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98 </param>
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99 <when value="no" />
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100 <when value="yes">
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101 <param argument="--barcode_threshold" size="5" type="float" value="75.0" min="0" max="100" label="Barcode threshold identity" />
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102 <param argument="--barcode_diff" size="5" type="float" value="5.0" min="0" max="100" label="Barcode threshold difference" />
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103 <param argument="--require_two_barcodes" type="boolean" truevalue="--require_two_barcodes" falsevalue="" checked="false" label="Require two barcodes" />
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104 <param argument="--discard_unassigned" type="boolean" truevalue="--discard_unassigned" falsevalue="" checked="false" label="Discard unassigned reads" />
0
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105 </when>
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106 </conditional>
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107 </section>
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108
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109 <section name="trim_section" title="Trimming Options" expanded="True">
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110 <conditional name="trim_options">
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111 <param name="trim" type="select" label="Perform adapter trimming" help="">
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112 <option value="no" selected="true">no</option>
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113 <option value="yes">yes</option>
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114 </param>
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115 <when value="no" />
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116 <when value="yes">
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117 <param argument="--adapter_threshold" size="4" type="float" value="90.0" min="0" max="100" label="Adapter set threshold identity" />
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118 <param argument="--check_reads" size="7" type="integer" value="10000" label="Number of reads to check to determine adapter sets" />
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119 <param argument="--barcode_diff" size="4" type="float" value="5.0" min="0" max="100" label="Barcode threshold difference" />
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120 <param argument="--scoring_scheme" type="text" value="3,-6,-5,-2" label="Scoring scheme" />
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121 <param argument="--end_size" size="4" type="integer" value="150" label="Number of terminal bases to search" />
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122 <param argument="--min_trim_size" size="4" type="integer" value="4" label="Minimum adapter match length" />
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123 <param argument="--extra_end_trim" size="4" type="integer" value="2" label="Adjacent bases to trim " />
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124 <param argument="--end_threshold" size="4" type="float" value="75.0" min="0" max="100" label="End adapter trim threshold identity" />
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125
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126 <param argument="--discard_middle" type="boolean" truevalue="--discard_middle" falsevalue="" checked="false" label="Discard reads with middle adapters" />
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127 <param argument="--middle_threshold" size="4" type="float" value="85.0" min="0" max="100" label="Middle adapter trim threshold identity" />
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128 <param argument="--extra_middle_trim_good_side" size="4" type="integer" value="10" label="Adjacent bases to trim on good side" />
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129 <param argument="--extra_middle_trim_bad_side" size="4" type="integer" value="100" label="Adjacent bases to trim on bad side" />
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130 <param argument="--min_split_read_size" size="4" type="integer" value="1000" label="Minimum length of split reads to keep" />
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131 </when>
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132 </conditional>
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133 </section>
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134
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135 </inputs>
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136
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137 <!-- ***************************************************************** -->
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138
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139 <outputs>
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140
2
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141 <collection type="list" name="output_collection_fastq" label="${tool.name} on ${on_string}">
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142 <filter>out_format == 'fastq'</filter>
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143 <discover_datasets pattern="__designation_and_ext__" directory="out" format="fastqsanger" />
2
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144 </collection>
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145 <collection type="list" name="output_collection_fasta" label="${tool.name} on ${on_string}">
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146 <filter>out_format == 'fasta'</filter>
7
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147 <discover_datasets pattern="__designation_and_ext__" directory="out" format="fasta" />
2
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148 </collection>
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149
7
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150 <data format="tabular" name="result_table" label="${tool.name} on ${on_string} (summary)" />
0
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151 </outputs>
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152
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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153 <!-- ***************************************************************** -->
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154
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155 <tests>
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156 <test>
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157 <param name="input" value="test_barcodes.fastq" ftype="fastq" />
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158 <param name="demux" value="yes" />
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159 <output_collection name="output_collection_fastq" type="list" count="4">
0
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160 <element name="BC01.fastq" file="bar1/BC01.fastq" compare="diff" decompress="true"/>
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161 <element name="BC02.fastq" file="bar1/BC02.fastq" compare="diff" decompress="true"/>
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162 <element name="BC03.fastq" file="bar1/BC03.fastq" compare="diff" decompress="true"/>
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163 <element name="none.fastq" file="bar1/none.fastq" compare="diff" decompress="true"/>
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164 </output_collection>
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165 </test>
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166 <test>
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167 <param name="input" value="test_barcodes.fastq" ftype="fastq" />
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168 <param name="demux" value="yes" />
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169 <param name="require_two_barcodes" value="True" />
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170 <output_collection name="output_collection_fastq" type="list" count="4">
0
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171 <element name="BC01.fastq" file="bar2/BC01.fastq" compare="diff" decompress="true"/>
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172 <element name="BC02.fastq" file="bar2/BC02.fastq" compare="diff" decompress="true"/>
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173 <element name="BC03.fastq" file="bar2/BC03.fastq" compare="diff" decompress="true"/>
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174 <element name="none.fastq" file="bar2/none.fastq" compare="diff" decompress="true"/>
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175 </output_collection>
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176 </test>
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177 <test>
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178 <param name="input" value="test_barcodes.fastq" ftype="fastq" />
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179 <param name="demux" value="yes" />
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180 <param name="trim" value="yes" />
6
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181 <param name="discard_unassigned" value="yes" />
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182 <output_collection name="output_collection_fastq" type="list" count="3">
0
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183 <element name="BC01.fastq" file="bar1_trim/BC01.fastq" compare="diff" decompress="true"/>
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184 <element name="BC02.fastq" file="bar1_trim/BC02.fastq" compare="diff" decompress="true"/>
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185 <element name="BC03.fastq" file="bar1_trim/BC03.fastq" compare="diff" decompress="true"/>
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186 </output_collection>
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187 </test>
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188 </tests>
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189
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190 <!-- ***************************************************************** -->
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191
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192 <help>
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193 <![CDATA[
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194
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195 **Description**
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196
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197 Porechop is a tool for finding and removing adapters from Oxford Nanopore
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198 reads. Adapters on the ends of reads are trimmed off, and when a read has an
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199 adapter in its middle, it is treated as chimeric and chopped into separate
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200 reads. Porechop performs thorough alignments to effectively find adapters,
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201 even at low sequence identity.
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202
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203 Porechop also supports demultiplexing of Nanopore reads that were barcoded
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204 with the Native Barcoding Kit, PCR Barcoding Kit or Rapid Barcoding Kit.
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205
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206 **Options**
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207 ::
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208
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209 *** Barcode binning settings ***
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210
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211 -b BARCODE_DIR, --barcode_dir BARCODE_DIR
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212 Reads will be binned based on their barcode and saved to separate
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213 files in this directory (incompatible with --output)
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214 --barcode_threshold BARCODE_THRESHOLD
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215 A read must have at least this percent identity to a barcode to be
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216 binned (default: 75.0)
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217 --barcode_diff BARCODE_DIFF If the difference between a read's best barcode identity and its
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218 second-best barcode identity is less than this value, it will not be
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219 put in a barcode bin (to exclude cases which are too close to call)
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220 (default: 5.0)
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221 --require_two_barcodes Reads will only be put in barcode bins if they have a strong match for
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222 the barcode on both their start and end (default: a read can be binned
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223 with a match at its start or end)
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224 --untrimmed Bin reads but do not trim the ends (appropriate if reads are to be
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225 used with Nanopolish) (default: False)
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226
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227 *** Adapter search settings ***
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228
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229 --adapter_threshold ADAPTER_THRESHOLD
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230 An adapter set has to have at least this percent identity to be
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231 labelled as present and trimmed off (0 to 100) (default: 90.0)
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232 --check_reads CHECK_READS This many reads will be aligned to all possible adapters to determine
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233 which adapter sets are present (default: 10000)
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234 --scoring_scheme SCORING_SCHEME Comma-delimited string of alignment scores: match,mismatch, gap open,
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235 gap extend (default: 3,-6,-5,-2)
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236
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237 *** End adapter settings ***
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238
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239 --end_size END_SIZE The number of base pairs at each end of the read which will be
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240 searched for adapter sequences (default: 150)
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241 --min_trim_size MIN_TRIM_SIZE Adapter alignments smaller than this will be ignored (default: 4)
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242 --extra_end_trim EXTRA_END_TRIM This many additional bases will be removed next to adapters found at
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243 the ends of reads (default: 2)
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244 --end_threshold END_THRESHOLD Adapters at the ends of reads must have at least this percent identity
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245 to be removed (0 to 100) (default: 75.0)
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246
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247 *** Middle adapter settings ***
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248
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249 --discard_middle Reads with middle adapters will be discarded (default: reads with
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250 middle adapters are split) (this option is on by default when
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251 outputting reads into barcode bins)
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252 --middle_threshold MIDDLE_THRESHOLD
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253 Adapters in the middle of reads must have at least this percent
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254 identity to be found (0 to 100) (default: 85.0)
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255 --extra_middle_trim_good_side EXTRA_MIDDLE_TRIM_GOOD_SIDE
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256 This many additional bases will be removed next to middle adapters on
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257 their "good" side (default: 10)
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258 --extra_middle_trim_bad_side EXTRA_MIDDLE_TRIM_BAD_SIDE
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259 This many additional bases will be removed next to middle adapters on
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260 their "bad" side (default: 100)
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261 --min_split_read_size MIN_SPLIT_READ_SIZE
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262 Post-split read pieces smaller than this many base pairs will not be
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263 outputted (default: 1000)
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264
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265
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266 ]]>
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267 </help>
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268
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269 <!-- ***************************************************************** -->
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270
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271 <citations>
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272 </citations>
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273
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274 </tool>