Mercurial > repos > jdv > porechop

annotate porechop.xml @ 9:e3ad639c692a draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 83364d7d78ca5524a08065daef995bfcd54a379d-dirty
author jdv
date Fri, 01 Dec 2017 21:27:15 -0500
parents 852b3fe95c20
children 0cb1ba651e9e
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15e64c5938e6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 083a08f96c17f3116dce1dc1573192860f41ed70-dirty
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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>
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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/$filename"
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36 #end if
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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38 --threads \${GALAXY_SLOTS:-1}
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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40 ##--Demultiplex Options--------------------------
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42 #if str($demux_section.demux_options.demux) == "yes":
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44 --barcode_threshold $demux_section.demux_options.barcode_threshold
6b572c4f2ce1 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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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 $demux_section.demux_options.discard_unassigned
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49 #end if
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51 ##--Adapter Trim Options--------------------------
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52
8
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53 #if str($trim_section.trim) == "no":
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54 --untrimmed
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55 #end if
0
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8
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57 --adapter_threshold $adapter_section.adapter_threshold
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58 --check_reads $adapter_section.check_reads
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59 --scoring_scheme $adapter_section.scoring_scheme
0
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61 --end_size $adapter_section.end_size
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62 --end_threshold $adapter_section.end_threshold
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63 --min_trim_size $adapter_section.min_trim_size
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64 --extra_end_trim $adapter_section.extra_end_trim
0
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65
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66 $adapter_section.discard_middle
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67 --middle_threshold $adapter_section.middle_threshold
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68 --extra_middle_trim_good_side $adapter_section.extra_middle_trim_good_side
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69 --extra_middle_trim_bad_side $adapter_section.extra_middle_trim_bad_side
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70 --min_split_read_size $adapter_section.min_split_read_size
0
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72
3
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73 | perl $__tool_directory__/porechop_summarize.pl
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74 > $result_table
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75
0
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76 ]]>
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77 </command>
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79 <!-- ***************************************************************** -->
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81 <inputs>
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83 <param argument="--input" type="data" format="fastq,fasta" label="Input reads" />
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84
2
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85 <param name="out_format" type="select" label="Output format">
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86 <option value="fastq" selected="true">fastq</option>
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87 <option value="fasta">fasta</option>
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88 </param>
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89
0
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90 <section name="demux_section" title="Demultiplexing Options" expanded="True">
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91 <conditional name="demux_options">
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92 <param name="demux" type="select" label="Perform demultiplexing" help="">
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93 <option value="no" selected="true">no</option>
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94 <option value="yes">yes</option>
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95 </param>
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96 <when value="no" />
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97 <when value="yes">
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98 <param argument="--barcode_threshold" size="5" type="float" value="75.0" min="0" max="100" label="Barcode threshold identity" />
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99 <param argument="--barcode_diff" size="5" type="float" value="5.0" min="0" max="100" label="Barcode threshold difference" />
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100 <param argument="--require_two_barcodes" type="boolean" truevalue="--require_two_barcodes" falsevalue="" checked="false" label="Require two barcodes" />
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101 <param argument="--discard_unassigned" type="boolean" truevalue="--discard_unassigned" falsevalue="" checked="false" label="Discard unassigned reads" />
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102 </when>
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103 </conditional>
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104 </section>
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105
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106 <section name="trim_section" title="Trimming Options" expanded="True">
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107 <param name="trim" type="select" label="Perform adapter trimming" help="">
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108 <option value="no" selected="true">no</option>
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109 <option value="yes">yes</option>
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110 </param>
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111 </section>
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112 <section name="adapter_section" title="Adapter Options" expanded="False">
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113 <param argument="--adapter_threshold" size="4" type="float" value="90.0" min="0" max="100" label="Adapter set threshold identity" />
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114 <param argument="--check_reads" size="7" type="integer" value="10000" label="Number of reads to check to determine adapter sets" />
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115 <param argument="--scoring_scheme" type="text" value="3,-6,-5,-2" label="Scoring scheme" />
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116 <param argument="--end_size" size="4" type="integer" value="150" label="Number of terminal bases to search" />
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117 <param argument="--min_trim_size" size="4" type="integer" value="4" label="Minimum adapter match length" />
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118 <param argument="--extra_end_trim" size="4" type="integer" value="2" label="Adjacent bases to trim " />
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119 <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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120
8
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121 <param argument="--discard_middle" type="boolean" truevalue="--discard_middle" falsevalue="" checked="false" label="Discard reads with middle adapters" />
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122 <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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123 <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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124 <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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125 <param argument="--min_split_read_size" size="4" type="integer" value="1000" label="Minimum length of split reads to keep" />
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126 </section>
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127
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128 </inputs>
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129
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130 <!-- ***************************************************************** -->
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131
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132 <outputs>
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133
2
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134 <collection type="list" name="output_collection_fastq" label="${tool.name} on ${on_string}">
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135 <filter>out_format == 'fastq'</filter>
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136 <filter>demux_section['demux_options']['demux'] == 'yes'</filter>
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137 <discover_datasets pattern="__designation_and_ext__" directory="out" format="fastqsanger" />
2
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138 </collection>
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139 <collection type="list" name="output_collection_fasta" label="${tool.name} on ${on_string}">
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140 <filter>out_format == 'fasta'</filter>
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141 <filter>demux_section['demux_options']['demux'] == 'yes'</filter>
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142 <discover_datasets pattern="__designation_and_ext__" directory="out" format="fasta" />
2
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143 </collection>
9
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144 <data format="fastq" name="ouput_fastq">
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145 <discover_datasets directory='out' pattern="(?P&lt;designation&gt;.+)" ext="fastq" visible="true" assign_primary_output="true" />
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146 <filter>out_format == 'fastq'</filter>
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147 <filter>demux_section['demux_options']['demux'] == 'no'</filter>
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148 </data>
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149 <data format="fasta" name="ouput_fasta">
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150 <discover_datasets directory='out' pattern="(?P&lt;designation&gt;.+)" ext="fasta" visible="true" assign_primary_output="true" />
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151 <filter>out_format == 'fasta'</filter>
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152 <filter>demux_section['demux_options']['demux'] == 'no'</filter>
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153 </data>
2
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154
7
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155 <data format="tabular" name="result_table" label="${tool.name} on ${on_string} (summary)" />
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156 </outputs>
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157
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158 <!-- ***************************************************************** -->
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159
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160 <tests>
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161 <test>
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162 <param name="input" value="test_barcodes.fastq" ftype="fastq" />
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163 <param name="demux" value="yes" />
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164 <output_collection name="output_collection_fastq" type="list" count="4">
8
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165 <element name="BC01" file="bar1/BC01.fastq" compare="diff" decompress="true"/>
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166 <element name="BC02" file="bar1/BC02.fastq" compare="diff" decompress="true"/>
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167 <element name="BC03" file="bar1/BC03.fastq" compare="diff" decompress="true"/>
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168 <element name="none" file="bar1/none.fastq" compare="diff" decompress="true"/>
0
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169 </output_collection>
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170 </test>
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171 <test>
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172 <param name="input" value="test_barcodes.fastq" ftype="fastq" />
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173 <param name="demux" value="yes" />
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174 <param name="require_two_barcodes" value="True" />
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175 <output_collection name="output_collection_fastq" type="list" count="4">
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176 <element name="BC01" file="bar2/BC01.fastq" compare="diff" decompress="true"/>
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177 <element name="BC02" file="bar2/BC02.fastq" compare="diff" decompress="true"/>
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178 <element name="BC03" file="bar2/BC03.fastq" compare="diff" decompress="true"/>
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179 <element name="none" file="bar2/none.fastq" compare="diff" decompress="true"/>
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180 </output_collection>
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181 </test>
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182 <test>
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183 <param name="input" value="test_barcodes.fastq" ftype="fastq" />
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184 <param name="demux" value="yes" />
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185 <param name="trim" value="yes" />
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186 <param name="discard_unassigned" value="yes" />
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187 <output_collection name="output_collection_fastq" type="list" count="3">
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188 <element name="BC01" file="bar1_trim/BC01.fastq" compare="diff" decompress="true"/>
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189 <element name="BC02" file="bar1_trim/BC02.fastq" compare="diff" decompress="true"/>
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190 <element name="BC03" file="bar1_trim/BC03.fastq" compare="diff" decompress="true"/>
0
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191 </output_collection>
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192 </test>
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193 <test>
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194 <param name="input" value="test_barcodes.fastq" ftype="fastq" />
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195 <param name="demux" value="no" />
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196 <param name="trim" value="yes" />
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197 <param name="out_format" value="fasta" />
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198 <output name="output_fasta" file="no_demux.fasta" compare="diff" />
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199 </test>
0
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200 </tests>
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201
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202 <!-- ***************************************************************** -->
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203
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204 <help>
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205 <![CDATA[
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206
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207 **Description**
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208
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209 Porechop is a tool for finding and removing adapters from Oxford Nanopore
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210 reads. Adapters on the ends of reads are trimmed off, and when a read has an
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211 adapter in its middle, it is treated as chimeric and chopped into separate
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212 reads. Porechop performs thorough alignments to effectively find adapters,
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213 even at low sequence identity.
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214
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215 Porechop also supports demultiplexing of Nanopore reads that were barcoded
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216 with the Native Barcoding Kit, PCR Barcoding Kit or Rapid Barcoding Kit.
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217
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218 **Options**
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219 ::
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220
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221 *** Barcode binning settings ***
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222
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223 -b BARCODE_DIR, --barcode_dir BARCODE_DIR
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224 Reads will be binned based on their barcode and saved to separate
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225 files in this directory (incompatible with --output)
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226 --barcode_threshold BARCODE_THRESHOLD
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227 A read must have at least this percent identity to a barcode to be
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228 binned (default: 75.0)
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229 --barcode_diff BARCODE_DIFF If the difference between a read's best barcode identity and its
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230 second-best barcode identity is less than this value, it will not be
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231 put in a barcode bin (to exclude cases which are too close to call)
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232 (default: 5.0)
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233 --require_two_barcodes Reads will only be put in barcode bins if they have a strong match for
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234 the barcode on both their start and end (default: a read can be binned
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235 with a match at its start or end)
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236 --untrimmed Bin reads but do not trim the ends (appropriate if reads are to be
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237 used with Nanopolish) (default: False)
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238
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239 *** Adapter search settings ***
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240
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241 --adapter_threshold ADAPTER_THRESHOLD
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242 An adapter set has to have at least this percent identity to be
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243 labelled as present and trimmed off (0 to 100) (default: 90.0)
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244 --check_reads CHECK_READS This many reads will be aligned to all possible adapters to determine
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245 which adapter sets are present (default: 10000)
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246 --scoring_scheme SCORING_SCHEME Comma-delimited string of alignment scores: match,mismatch, gap open,
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247 gap extend (default: 3,-6,-5,-2)
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248
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249 *** End adapter settings ***
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250
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251 --end_size END_SIZE The number of base pairs at each end of the read which will be
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252 searched for adapter sequences (default: 150)
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253 --min_trim_size MIN_TRIM_SIZE Adapter alignments smaller than this will be ignored (default: 4)
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254 --extra_end_trim EXTRA_END_TRIM This many additional bases will be removed next to adapters found at
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255 the ends of reads (default: 2)
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256 --end_threshold END_THRESHOLD Adapters at the ends of reads must have at least this percent identity
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257 to be removed (0 to 100) (default: 75.0)
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258
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259 *** Middle adapter settings ***
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260
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261 --discard_middle Reads with middle adapters will be discarded (default: reads with
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262 middle adapters are split) (this option is on by default when
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263 outputting reads into barcode bins)
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264 --middle_threshold MIDDLE_THRESHOLD
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265 Adapters in the middle of reads must have at least this percent
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266 identity to be found (0 to 100) (default: 85.0)
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267 --extra_middle_trim_good_side EXTRA_MIDDLE_TRIM_GOOD_SIDE
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268 This many additional bases will be removed next to middle adapters on
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269 their "good" side (default: 10)
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270 --extra_middle_trim_bad_side EXTRA_MIDDLE_TRIM_BAD_SIDE
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271 This many additional bases will be removed next to middle adapters on
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272 their "bad" side (default: 100)
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273 --min_split_read_size MIN_SPLIT_READ_SIZE
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274 Post-split read pieces smaller than this many base pairs will not be
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275 outputted (default: 1000)
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276
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277
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278 ]]>
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279 </help>
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280
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281 <!-- ***************************************************************** -->
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282
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283 <citations>
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284 </citations>
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285
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286 </tool>