Mercurial > repos > iuc > umi_tools_extract

annotate macros.xml @ 15:27ac32a22ad2 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
author iuc
date Mon, 13 Sep 2021 14:52:06 +0000
parents d5ff68d2d5ff
children 7accf7407811
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79436b3019e9 planemo upload commit c8e46ecad0b1473097517e582ed6c43eb0635b36
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1 <?xml version="1.0"?>
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2 <macros>
15
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4 <!-- macros applying to all umi_tools -->
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5
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6 <token name="@TOOL_VERSION@">1.1.2</token>
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7 <token name="@VERSION_SUFFIX@">0</token>
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8 <token name="@PROFILE@">21.01</token>
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9 <xml name="requirements">
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10 <requirements>
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11 <requirement type="package" version="@TOOL_VERSION@">umi_tools</requirement>
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12 <yield />
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13 </requirements>
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14 </xml>
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15 <xml name="citations">
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16 <citations>
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17 <citation type="doi">10.1101/gr.209601.116</citation>
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18 <citation type="bibtex">
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19 @misc{githubUMI-tools,
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20 title = {UMI-tools},
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21 publisher = {GitHub},
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22 journal = {GitHub repository},
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23 url = {https://github.com/CGATOxford/UMI-tools},
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24 }
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25 </citation>
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26 </citations>
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27 </xml>
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28 <xml name="advanced_options_macro">
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29 <section name="advanced" title="Extra parameters" expanded="false">
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30 <param argument="--random-seed" type="integer" min="0" optional="true" label="Random Seed" />
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31 </section>
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32 </xml>
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33 <token name="@ADVANCED_OPTIONS@"><![CDATA[
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34 #if str($advanced.random_seed) != ''
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35 --random-seed='$advanced.random_seed'
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36 #end if
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37 ]]></token>
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38
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39 <!-- macros for extract and whitelist-->
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40
11
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41 <macro name="barcode_sanitizer" >
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42 <sanitizer invalid_char="">
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43 <valid initial="string.letters,string.digits">
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44 <add value="&#42;" /><!-- asterisk -->
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45 <add value="&#44;" /><!-- comma -->
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46 <add value="&#46;" /><!-- period -->
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47 <add value="&#60;" /><!-- less than -->
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48 <add value="&#61;" /><!-- equals sign -->
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49 <add value="&#62;" /><!-- greater than -->
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50 <add value="&#63;" /><!-- question mark -->
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51 <add value="&#95;" /><!-- underscore -->
12
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52 <add value="&#40;" /><!-- left bracket -->
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53 <add value="&#41;" /><!-- right bracket -->
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54 <add value="&#91;"/> <!-- left square bracket -->
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55 <add value="&#93;"/> <!-- right square bracket -->
11
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56 <add value="&#123;"/><!-- left brace -->
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57 <add value="&#125;"/><!-- right brace -->
12
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58 <add value="&#94;"/> <!-- caret -->
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59 <add value="-"/>
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60 <add value="!"/>
11
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61 </valid>
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62 </sanitizer>
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63 </macro>
15
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64 <xml name="sanitize_tag" >
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65 <sanitizer invalid_char="">
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66 <valid initial="string.letters,string.digits" />
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67 </sanitizer>
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68 </xml>
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69 <macro name="barcode1_macro" >
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70 <param argument="--bc-pattern" type="text" label="Barcode pattern for first read"
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71 help="Use this option to specify the format of the UMI/barcode. Use Ns to
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72 represent the random positions and Xs to indicate the bc positions.
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73 Bases with Ns will be extracted and added to the read name. Remaining
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74 bases, marked with an X will be reattached to the read">
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75 <validator type="empty_field" />
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76 <expand macro="barcode_sanitizer" />
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77 </param>
4
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78 </macro>
15
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79 <macro name="barcode2_macro" >
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80 <param argument="--bc-pattern2" type="text" value="" label="Barcode pattern for second read"
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81 help="Use this option to specify the format of the UMI/barcode for
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82 the second read pair if required" >
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83 <expand macro="barcode_sanitizer" />
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84 </param>
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85 </macro>
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86 <!-- not just fastq because this would allow also fastqcsanger -->
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87 <token name="@FASTQ_FORMATS@">fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz</token>
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88 <xml name="bio_tools">
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89 <xrefs>
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90 <xref type="bio.tools">umi-tools</xref>
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91 </xrefs>
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92 </xml>
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93 <xml name="input_types">
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94 <conditional name="input_type_cond">
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95 <param name="input_type" type="select" label="Library type">
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96 <option value="single">Single-end</option>
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97 <option value="paired">Paired-end</option>
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98 <option value="paired_collection">Paired-end Dataset Collection</option>
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99 </param>
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100 <when value="single">
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101 <param name="input_read1" type="data" format="@FASTQ_FORMATS@" label="Reads in FASTQ format" />
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102 <expand macro="barcode1_macro"/>
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103 </when>
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104 <when value="paired">
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105 <param name="input_read1" type="data" format="@FASTQ_FORMATS@" label="Reads in FASTQ format" />
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106 <param name="input_read2" type="data" format="@FASTQ_FORMATS@" label="Reads in FASTQ format" />
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107 <expand macro="barcode1_macro"/>
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108 <expand macro="barcode2_macro"/>
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109 <yield/>
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110 </when>
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111 <when value="paired_collection">
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112 <param name="input_readpair" type="data_collection" collection_type="paired" format="@FASTQ_FORMATS@" label="Reads in FASTQ format" />
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113 <expand macro="barcode1_macro"/>
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114 <expand macro="barcode2_macro"/>
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115 <yield/>
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116 </when>
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117 </conditional>
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118 </xml>
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119 <token name="@COMMAND_LINK@"><![CDATA[
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120 #set $gz = False
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121 #if $input_type_cond.input_type == 'single':
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122 #if $input_type_cond.input_read1.is_of_type("fastq.gz", "fastqsanger.gz"):
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123 ln -s '$input_type_cond.input_read1' input_single.gz &&
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124 #set $gz = True
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125 #else
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126 ln -s '$input_type_cond.input_read1' input_single.txt &&
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127 #end if
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128 #elif $input_type_cond.input_type == 'paired':
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129 #if $input_type_cond.input_read1.is_of_type("fastq.gz", "fastqsanger.gz"):
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130 ln -s '$input_type_cond.input_read1' input_read1.gz &&
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131 ln -s '$input_type_cond.input_read2' input_read2.gz &&
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132 #set $gz = True
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133 #else
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134 ln -s '$input_type_cond.input_read1' input_read1.txt &&
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135 ln -s '$input_type_cond.input_read2' input_read2.txt &&
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136 #end if
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137 #else ## paired_collection
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138 #if $input_type_cond.input_readpair.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
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139 ln -s '$input_type_cond.input_readpair.forward' input_read1.gz &&
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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140 ln -s '$input_type_cond.input_readpair.reverse' input_read2.gz &&
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141 #set $gz = True
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142 #else
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143 ln -s '$input_type_cond.input_readpair.forward' input_read1.txt &&
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144 ln -s '$input_type_cond.input_readpair.reverse' input_read2.txt &&
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145 #end if
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146 #end if
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147 ]]></token>
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148
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149 <!-- macros for count, dedup, and group -->
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150
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151 <token name="@LINK_SAM_BAM_INPUT@"><![CDATA[
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152 #if $input.is_of_type("sam"):
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153 ## TODO dedup has problems with SAM input in some cases
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154 ## https://github.com/CGATOxford/UMI-tools/issues/483
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155 ## so convert it to sorted BAM for now
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156 ## #set $input_file = $input
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157 samtools sort --no-PG '$input' > 'input.bam' &&
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158 samtools index -b 'input.bam' &&
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159 #set $input_file = 'input.bam'
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160 #else:
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161 ln -sf '${input}' 'input.bam' &&
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162 ln -sf '$input.metadata.bam_index' 'input.bam.bai' &&
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163 #set $input_file = 'input.bam'
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164 #end if
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165 ]]></token>
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166 <token name="@SET_INPUT_TYPE@"><![CDATA[
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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167 ## TODO see comment in LINK_SAM_BAM_INPUT
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168 ## #if $input.is_of_type("sam"):
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169 ## --in-sam
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170 ## #end if
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171 ]]></token>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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172
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173 <xml name="fastq_barcode_extraction_options_macro">
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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174 <conditional name="extract_method_cond">
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175 <param argument="--extract-method" type="select" label="Barcode Extraction Method"
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176 help="If bracketed expressions are used in the above barcode pattern, then set this to 'regex'. Otherwise leave as 'string'" >
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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177 <option value="string" selected="true" />
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178 <option value="regex" />
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179 </param>
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180 <when value="string">
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181 <param argument="--3prime" name="prime3" type="boolean" label="Is barcode on 3' end of the read?"
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182 truevalue="--3prime" falsevalue=""
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183 help="By default the barcode is assumed to be on the 5' end of the read, but
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184 use this option to specify that it is on the 3' end instead.
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185 This option only works with ``--extract-method=string``
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186 since 3' encoding can be specified explicitly with a regex, e.g
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187 ``.*(?P&lt;umi_1&gt;.{5})$``" />
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188 </when>
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189 <when value="regex">
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190 <param name="filtered_out_bool" type="boolean" label="Write out reads not matching regex pattern"/>
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191 </when>
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192 </conditional>
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193 <param argument="--ignore-read-pair-suffixes" type="boolean" truevalue="--ignore-read-pair-suffixes" falsevalue="" label="Ignore '\1' and '\2' read name suffixes"/>
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194 </xml>
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195 <token name="@FASTQ_BARCODE_EXTRACTION_OPTIONS@"><![CDATA[
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196 ## fastq barcode extraction options:
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197 --extract-method='$extract_method_cond.extract_method'
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198 --bc-pattern='$input_type_cond.bc_pattern'
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199 #if $input_type_cond.input_type != 'single' and $input_type_cond.bc_pattern2 != ''
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200 --bc-pattern2='$input_type_cond.bc_pattern2'
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201 #end if
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202 #if $extract_method_cond.extract_method == 'string'
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203 $extract_method_cond.prime3
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204 #else if $extract_method_cond.filtered_out_bool
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205 #if $input_type_cond.input_type == 'single':
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206 --filtered-out='$filtered_out'
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207 #else if $input_type_cond.input_type == 'paired':
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208 --filtered-out='$filtered_out'
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209 --filtered-out2='$filtered_out_paired'
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210 #else
15
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211 --filtered-out='$filtered_out_paired_collection.forward'
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212 --filtered-out2='$filtered_out_paired_collection.reverse'
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213 #end if
15
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214 #end if
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215 $ignore_read_pair_suffixes
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216 ]]></token>
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217 <token name="@FASTQ_BARCODE_EXTRACTION_HELP@"><![CDATA[
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218 There are two methods enabled to extract the umi barcode (+/-
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219 cell barcode). For both methods, the patterns should be provided
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220 using the ``--bc-pattern`` and ``--bc-pattern2`` options.x
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221
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222 - ``string``
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223 This should be used where the barcodes are always in the same
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224 place in the read.
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225
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226 - N = UMI position (required)
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227 - C = cell barcode position (optional)
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228 - X = sample position (optional)
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229
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230 Bases with Ns and Cs will be extracted and added to the read
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231 name. The corresponding sequence qualities will be removed from
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232 the read. Bases with an X will be reattached to the read.
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233
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234 E.g. If the pattern is `NNNNCC`,
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235 Then the read::
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236
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237 @HISEQ:87:00000000 read1
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238 AAGGTTGCTGATTGGATGGGCTAG
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239 +
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240 DA1AEBFGGCG01DFH00B1FF0B
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241
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242 will become::
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243
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244 @HISEQ:87:00000000_TT_AAGG read1
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245 GCTGATTGGATGGGCTAG
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246 +
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247 1AFGGCG01DFH00B1FF0B
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248
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249 where 'TT' is the cell barcode and 'AAGG' is the UMI.
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250
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251 - ``regex``
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252 This method allows for more flexible barcode extraction and
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253 should be used where the cell barcodes are variable in
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254 length. Alternatively, the regex option can also be used to
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255 filter out reads which do not contain an expected adapter
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256 sequence. UMI-tools uses the regex module rather than the more
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257 standard re module since the former also enables fuzzy matching
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258
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259 The regex must contain groups to define how the barcodes are
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260 encoded in the read. The expected groups in the regex are:
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261
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262 umi_n = UMI positions, where n can be any value (required)
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263 cell_n = cell barcode positions, where n can be any value (optional)
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264 discard_n = positions to discard, where n can be any value (optional)
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265
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266 UMI positions and cell barcode positions will be extracted and
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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267 added to the read name. The corresponding sequence qualities
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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268 will be removed from the read.
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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269
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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270 Discard bases and the corresponding quality scores will be
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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271 removed from the read. All bases matched by other groups or
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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diff changeset
272 components of the regex will be reattached to the read sequence
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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273
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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274 For example, the following regex can be used to extract reads
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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275 from the Klein et al inDrop data::
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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276
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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277 (?P<cell_1>.{8,12})(?P<discard_1>GAGTGATTGCTTGTGACGCCTT)(?P<cell_2>.{8})(?P<umi_1>.{6})T{3}.*
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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278
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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279 Where only reads with a 3' T-tail and `GAGTGATTGCTTGTGACGCCTT` in
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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280 the correct position to yield two cell barcodes of 8-12 and 8bp
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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281 respectively, and a 6bp UMI will be retained.
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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282
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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283 You can also specify fuzzy matching to allow errors. For example if
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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284 the discard group above was specified as below this would enable
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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285 matches with up to 2 errors in the discard_1 group.
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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286
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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287 ::
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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288
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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289 (?P<discard_1>GAGTGATTGCTTGTGACGCCTT){s<=2}
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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290
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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291 Note that all UMIs must be the same length for downstream
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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292 processing with dedup, group or count commands]]></token>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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293
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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294 <xml name="barcode_options_macro">
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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295 <conditional name="bc" >
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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296 <param argument="--extract-umi-method" type="select" label="Umi Extract Method" help="How are the barcodes encoded in the read?" >
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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297 <option value="read_id" selected="true">Barcodes are contained at the end of the read seperated by a delimiter</option>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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298 <option value="tag" >Barcodes are contained in tags</option>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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299 <option value="umis" >Barcodes were extracted using umis</option>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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300 </param>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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301 <when value="read_id" >
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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302 <param argument="--umi-separator" type="text" label="Delimiter between read id and the UMI" value="_" >
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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303 <sanitizer invalid_char="" >
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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304 <valid initial="string.punctuation" />
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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305 </sanitizer>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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306 </param>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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307 </when>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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308 <when value="tag" >
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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309 <param argument="--umi-tag" type="text" label="Tag which contains the UMI" value="RX" >
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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310 <expand macro="sanitize_tag" />
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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311 </param>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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312 <param argument="--umi-tag-split" type="text" label="Separate the UMI in tag by SPLIT" help="and take the first element"/>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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313 <param argument="--umi-tag-delimiter" type="text" label="Separate the UMI in tag by DELIMITER" help="and concatenate the elements"/>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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314 <param argument="--cell-tag" type="text" label="Tag which contains the cell barcode" >
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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315 <expand macro="sanitize_tag" />
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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316 </param>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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317 <param argument="--cell-tag-split" type="text" label="Separate the cell barcode in tag by SPLIT" help="and take the first element"/>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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318 <param argument="--cell-tag-delimiter" type="text" label="Separate the cell barcode in tag by DELIMITER" help="and concatenate the elements"/>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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319 </when>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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320 <when value="umis"/>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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321 </conditional>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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322 </xml>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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323 <token name="@BARCODE_OPTIONS@"><![CDATA[
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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324 --extract-umi-method $bc.extract_umi_method
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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325 #if str($bc.extract_umi_method) == 'read_id':
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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326 --umi-separator '$bc.umi_separator'
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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327 #else if str($bc.extract_umi_method) == 'tag':
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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328 --umi-tag '$bc.umi_tag'
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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329 #if $bc.umi_tag_split != ''
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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330 --umi-tag-split '$bc.umi_tag_split'
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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331 #end if
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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332 #if $bc.umi_tag_delimiter != ''
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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333 --umi-tag-delimiter '$bc.umi_tag_delimiter'
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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334 #end if
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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335 --cell-tag '$bc.cell_tag'
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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336 #if $bc.cell_tag_split != ''
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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337 --cell-tag-split '$bc.cell_tag_split'
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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338 #end if
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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339 #if $bc.cell_tag_delimiter != ''
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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340 --cell-tag-delimiter '$bc.cell_tag_delimiter'
4
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
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341 #end if
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
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342 #end if
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
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343 ]]></token>
15
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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344 <token name="@BARCODE_HELP@"><![CDATA[
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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345 Extracting barcodes
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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346 -------------------
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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347
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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348 It is assumed that the FASTQ files were processed with ``umi_tools
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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349 extract`` before mapping and thus the UMI is the last word of the read
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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350 name. e.g:
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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351
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352 @HISEQ:87:00000000_AATT
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353
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354 where ``AATT`` is the UMI sequeuence.
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355
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356 If you have used an alternative method which does not separate the
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357 read id and UMI with a "_", such as bcl2fastq which uses ":", you can
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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358 specify the separator with the option ``--umi-separator=<sep>``,
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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359 replacing <sep> with e.g ":".
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360
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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361 Alternatively, if your UMIs are encoded in a tag, you can specify this
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362 by setting the option --extract-umi-method=tag and set the tag name
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363 with the --umi-tag option. For example, if your UMIs are encoded in
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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364 the 'UM' tag, provide the following options:
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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365 ``--extract-umi-method=tag`` ``--umi-tag=UM``
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366
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367 Finally, if you have used umis to extract the UMI +/- cell barcode,
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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368 you can specify ``--extract-umi-method=umis``
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369
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370 The start position of a read is considered to be the start of its alignment
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371 minus any soft clipped bases. A read aligned at position 500 with
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372 cigar 2S98M will be assumed to start at position 498.]]></token>
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373
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374
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375 <xml name="umi_grouping_options_macro">
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376 <section name="umi" title="UMI grouping options">
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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377 <param argument="--method" type="select" label="Method used to identify PCR duplicates within reads" help="All methods start by identifying the reads with the same mapping position">
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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378 <option value="unique">Reads group share the exact same UMI</option>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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379 <option value="percentile">Reads group share the exact same UMI. UMIs with counts less than 1% of the median counts for UMIs at the same position are ignored</option>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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380 <option value="cluster">Identify clusters based on hamming distance</option>
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381 <option value="adjacency">Identify clusters based on hamming distance and resolve networks by using the node counts</option>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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382 <option value="directional">Identify clusters based on distance and counts, restrict network expansion by threshold</option>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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383 </param>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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384 <param argument="--edit-distance-threshold" type="integer" value="1" label="Edit distance threshold" help="For the adjacency and cluster methods the threshold for the edit distance to connect two UMIs in the network can be increased. The default value of 1 works best unless the UMI is very long (&gt;14bp)" />
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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385 <param argument="--spliced-is-unique" type="boolean" truevalue="--spliced-is-unique" falsevalue="" label="Spliced reads are unique" help="Causes two reads that start in the same position on the same strand and having the same UMI to be considered unique if one is spliced and the other is not. (Uses the 'N' cigar operation to test for splicing)" />
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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386 <param argument="--soft-clip-threshold" type="integer" value="4" label="Soft clip threshold" help="Mappers that soft clip, will sometimes do so rather than mapping a spliced read if there is only a small overhang over the exon junction. By setting this option, you can treat reads with at least this many bases soft-clipped at the 3' end as spliced" />
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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387 <param argument="--read-length" type="boolean" truevalue="--read-length" falsevalue="" label="Use the read length as as a criterion when deduping" />
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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388 </section>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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389 </xml>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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390 <token name="@UMI_GROUPING_OPTIONS@"><![CDATA[
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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391 --method $umi.method
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392 --edit-distance-threshold $umi.edit_distance_threshold
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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393 $umi.spliced_is_unique
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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394 --soft-clip-threshold $umi.soft_clip_threshold
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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395 $umi.read_length
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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396 ]]></token>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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397 <token name="@UMI_GROUPING_HELP@"><![CDATA[
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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398 UMI grouping options
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399 --------------------
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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400
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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401 Grouping Method
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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402 ...............
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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403
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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404 What method to use to identify group of reads with the same (or
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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405 similar) UMI(s)?
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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406
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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407 All methods start by identifying the reads with the same mapping position.
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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408
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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409 The simplest methods, unique and percentile, group reads with
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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410 the exact same UMI. The network-based methods, cluster, adjacency and
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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411 directional, build networks where nodes are UMIs and edges connect UMIs
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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412 with an edit distance <= threshold (usually 1). The groups of reads
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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413 are then defined from the network in a method-specific manner. For all
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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414 the network-based methods, each read group is equivalent to one read
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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415 count for the gene.
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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416
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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417 - unique
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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418 Reads group share the exact same UMI
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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419
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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420 - percentile
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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421 Reads group share the exact same UMI. UMIs with counts < 1% of the
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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422 median counts for UMIs at the same position are ignored.
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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423
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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424 - cluster
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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425 Identify clusters of connected UMIs (based on hamming distance
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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426 threshold). Each network is a read group
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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427
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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428 - adjacency
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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429 Cluster UMIs as above. For each cluster, select the node (UMI)
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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430 with the highest counts. Visit all nodes one edge away. If all
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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431 nodes have been visited, stop. Otherwise, repeat with remaining
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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432 nodes until all nodes have been visted. Each step
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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433 defines a read group.
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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diff changeset
434
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
435 - directional (default)
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
436 Identify clusters of connected UMIs (based on hamming distance
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
437 threshold) and umi A counts >= (2* umi B counts) - 1. Each
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
438 network is a read group.
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
439
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
440 ]]></token>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
441
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
442 <xml name="sambam_options_macro">
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
443 <section name="sambam" title="SAM/BAM options">
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
444 <param argument="--mapping-quality" type="integer" value="0" label="Minimum mapping quality for a read to be retained"/>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
445 <param argument="--unmapped-reads" type="select" label="How to handle unmapped reads">
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
446 <option value="discard">discard</option>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
447 <option value="use">use</option>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
448 <option value="correct">correct</option>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
449 </param>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
450 <param argument="--chimeric-pairs" type="select" optional="true" label="How to handle chimeric read pairs (default: use)">
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
451 <option value="discard">discard</option>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
452 <option value="use">use</option>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
453 <option value="correct">correct</option>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
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454 </param>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
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455 <param argument="--unpaired-reads" type="select" optional="true" label="How to handle unpaired reads (default: use)">
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
456 <option value="discard">discard</option>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
457 <option value="use">use</option>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
458 <option value="correct">correct</option>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
459 </param>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
460 <param argument="--ignore-umi" type="boolean" truevalue="--ignore-umi" falsevalue="" label="Ignore UMI and dedup only on position"/>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
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461 <param argument="--ignore-tlen" type="boolean" truevalue="--ignore-tlen" falsevalue="" label="Dedup paired end reads based solely on read1" help="whether or not the template length is the same"/>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
462 <param argument="--chrom" type="text" value="" label="Consider only chromosome" help="If a value is given only a single chromosome with the given name is considered"/>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
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463 <param argument="--subset" type="float" min="0.0" max="1.0" value="1.0" label="Only consider a random selection of the reads" />
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
464 <!--in-sam is set automatically-->
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
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465 <param argument="--paired" type="boolean" truevalue="--paired" falsevalue="" label="BAM is paired end" help="This will also force the use of the template length to determine reads with the same mapping coordinates" />
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
466 </section>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
467 </xml>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
468 <token name="@SAMBAM_OPTIONS@"><![CDATA[
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
469 --mapping-quality $sambam.mapping_quality
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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470 --unmapped-reads $sambam.unmapped_reads
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
471 #if $sambam.chimeric_pairs
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
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472 --chimeric-pairs $sambam.chimeric_pairs
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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473 #end if
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
474 #if $sambam.unpaired_reads
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
475 --unpaired-reads $sambam.unpaired_reads
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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diff changeset
476 #end if
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
477 $sambam.ignore_umi
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
478 $sambam.ignore_tlen
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
479 #if str($sambam.chrom) != ''
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
480 --chrom '$sambam.chrom'
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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481 #end if
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
482 --subset $sambam.subset
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
483 $sambam.paired
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
484 @SET_INPUT_TYPE@
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
485 ]]></token>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
486
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
487 <!-- per-gene is hard coded in count https://github.com/CGATOxford/UMI-tools/blob/c3ead0792ad590822ca72239ef01b8e559802da9/umi_tools/count.py#L92
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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diff changeset
488 hence we need a specialized macro here
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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489 TODO count used XF as default for gene-tag now I set it explicitly for the tests but we could as well parametrize the macro and set tool specific defaults
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
490 -->
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
491
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
492 <xml name="fullsc_options_macro">
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
493 <expand macro="sc_options_macro">
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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494 <param argument="--per-gene" type="boolean" truevalue="--per-gene" falsevalue="" label="Deduplicate per gene"
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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495 help="Must combine with either --gene-tag or --per-contig. As for --per-contig except with this option you can align to a reference transcriptome with more than one transcript per gene. You need to also provide a map of genes to transcripts. This will also add a metacontig ('MC') tag to the output BAM file" />
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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496 </expand>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
497 </xml>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
498 <token name="@FULLSC_OPTIONS@"><![CDATA[
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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499 $sc.per_gene
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
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500 @SC_OPTIONS@
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
501 ]]></token>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
502
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
503 <xml name="sc_options_macro">
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
504 <section name="sc" title="Single-cell RNA-Seq options">
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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diff changeset
505 <yield/>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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506 <param argument="--gene-tag" type="text" optional="true" label="Deduplicate by this gene tag" help="As --per-gene except here the gene information is encoded in the bam read tag specified so you do not need to supply the mapping file">
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
507 <expand macro="sanitize_tag" />
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
508 </param>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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509 <param argument="--assigned-status-tag" type="text" optional="true" label="Bam tag describing whether read is assigned to a gene" help="By default, this is set as the same tag as --gene-tag">
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
510 <expand macro="sanitize_tag" />
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
511 </param>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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512 <param argument="--skip-tags-regex" name="skip_tags_regex" type="text" label="Skip any reads where the gene matches this tag" value="" >
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
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513 <expand macro="barcode_sanitizer" />
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
514 </param>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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diff changeset
515 <param argument="--per-contig" type="boolean" truevalue="--per-contig" falsevalue="" label="Deduplicate per contig" help="Field 3 in BAM; RNAME. All reads with the same contig will be considered to have the same alignment position. This is useful if your library prep generates PCR duplicates with non identical alignment positions such as CEL-Seq. In this case, you would align to a reference transcriptome with one transcript per gene" />
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
516 <param argument="--gene-transcript-map" type="data" format="tabular" optional="true" label="Tabular file mapping genes to transripts" />
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
517 <param argument="--per-cell" name="per_cell" type="boolean" truevalue="--per-cell" falsevalue="" label="Group reads only if they have the same cell barcode" />
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
518 </section>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
519 </xml>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
520 <token name="@SC_OPTIONS@"><![CDATA[
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
521 #if str($sc.gene_tag) != "":
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
522 --gene-tag '$sc.gene_tag'
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
523 #end if
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
524 #if str($sc.assigned_status_tag) != "":
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
525 --assigned-status-tag '$sc.assigned_status_tag'
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
526 #end if
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
527 #if str($sc.skip_tags_regex) != "":
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
528 --skip-tags-regex '$sc.skip_tags_regex'
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
529 #end if
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
530 $sc.per_contig
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
531 #if $sc.gene_transcript_map:
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
532 --gene-transcript-map '$sc.gene_transcript_map'
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
533 #end if
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
534 $sc.per_cell
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
535 ]]></token>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
536
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
537 <xml name="groupdedup_options_macro">
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
538 <section name="gd" title="group/dedup specific options">
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
539 <param argument="--buffer-whole-contig" type="boolean" truevalue="--buffer-whole-contig" falsevalue="" label="Read whole contig before outputting bundles" help="Guarantees that no reads are missed, but increases memory usage" />
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
540 <!-- TODO this option is hidden on the CLI. Should we expose it? -->
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
541 <param argument="--whole-contig" type="boolean" truevalue="--whole-contig" falsevalue="" label="Consider all alignments to a single contig together" help="This is useful if you have aligned to a transcriptome multi-fasta" />
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
542 <param argument="--multimapping-detection-method" type="select" optional="true" label="BAM Tag indicating multimapping " help="Some aligners identify multimapping using bam tags. Setting this option to NH, X0 or XT will use these tags when selecting the best read amongst reads with the same position and umi">
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
543 <option value="NH">NH</option>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
544 <option value="X0">X0</option>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
545 <option value="XT">XT</option>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
546 </param>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
547 </section>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
548 </xml>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
549 <token name="@GROUPDEDUP_OPTIONS@"><![CDATA[
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
550 $gd.buffer_whole_contig
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
551 $gd.whole_contig
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
552 $gd.multimapping_detection_method
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
553 ]]></token>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
554
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
555 <xml name="log_input_macro">
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
556 <param argument="--log" type="boolean" label="Output log?" truevalue="--log" falsevalue="" help="Choose if you want to generate a text file containing logging information" />
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
557 </xml>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
558 <xml name="log_output_macro">
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
559 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: logfile" >
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
560 <filter>log</filter>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
561 </data>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
562 </xml>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
563 <token name="@LOG@"><![CDATA[
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
564 #if $log:
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
565 --log='$out_log'
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
566 #end if
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
567 --log2stderr
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
568 ]]></token>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
569
1
79436b3019e9 planemo upload commit c8e46ecad0b1473097517e582ed6c43eb0635b36
iuc
parents:
diff changeset
570 </macros>