Mercurial > repos > iuc > umi_tools_extract

annotate macros.xml @ 18:015cf18f4a15 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit be699fdf0360f0535f52564e5b59be9b84712b14
author iuc
date Sat, 28 Sep 2024 16:39:41 +0000
parents f3759eec3018
children 7a7e33d28f62
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1 <?xml version="1.0"?>
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2 <macros>
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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@">1.1.5</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 -->
17
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59 <add value="&#36;"/> <!-- dollar sign-->
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60 <add value="&#43;" /><!-- plus sign -->
12
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61 <add value="-"/>
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62 <add value="!"/>
11
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63 </valid>
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64 </sanitizer>
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65 </macro>
15
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66 <xml name="sanitize_tag" >
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67 <sanitizer invalid_char="">
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68 <valid initial="string.letters,string.digits" />
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69 </sanitizer>
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70 </xml>
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71 <macro name="barcode1_macro" >
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72 <param argument="--bc-pattern" type="text" label="Barcode pattern for first read"
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73 help="Use this option to specify the format of the UMI/barcode. Use Ns to
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74 represent the random positions and Xs to indicate the bc positions.
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75 Bases with Ns will be extracted and added to the read name. Remaining
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76 bases, marked with an X will be reattached to the read">
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77 <validator type="empty_field" />
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78 <expand macro="barcode_sanitizer" />
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79 </param>
4
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80 </macro>
15
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81 <macro name="barcode2_macro" >
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82 <param argument="--bc-pattern2" type="text" value="" label="Barcode pattern for second read"
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83 help="Use this option to specify the format of the UMI/barcode for
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84 the second read pair if required" >
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85 <expand macro="barcode_sanitizer" />
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86 </param>
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87 </macro>
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88 <!-- not just fastq because this would allow also fastqcsanger -->
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89 <token name="@FASTQ_FORMATS@">fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz</token>
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90 <xml name="bio_tools">
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91 <xrefs>
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92 <xref type="bio.tools">umi-tools</xref>
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93 </xrefs>
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94 </xml>
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95 <xml name="input_types">
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96 <conditional name="input_type_cond">
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97 <param name="input_type" type="select" label="Library type">
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98 <option value="single">Single-end</option>
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99 <option value="paired">Paired-end</option>
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100 <option value="paired_collection">Paired-end Dataset Collection</option>
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101 </param>
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102 <when value="single">
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103 <param name="input_read1" type="data" format="@FASTQ_FORMATS@" label="Reads in FASTQ format" />
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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104 <expand macro="barcode1_macro"/>
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105 </when>
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106 <when value="paired">
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107 <param name="input_read1" type="data" format="@FASTQ_FORMATS@" label="Reads in FASTQ format" />
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108 <param name="input_read2" type="data" format="@FASTQ_FORMATS@" label="Reads in FASTQ format" />
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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109 <expand macro="barcode1_macro"/>
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110 <expand macro="barcode2_macro"/>
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111 <yield/>
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112 </when>
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113 <when value="paired_collection">
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114 <param name="input_readpair" type="data_collection" collection_type="paired" format="@FASTQ_FORMATS@" label="Reads in FASTQ format" />
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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115 <expand macro="barcode1_macro"/>
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116 <expand macro="barcode2_macro"/>
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117 <yield/>
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118 </when>
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119 </conditional>
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120 </xml>
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121 <token name="@COMMAND_LINK@"><![CDATA[
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122 #set $gz = False
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123 #if $input_type_cond.input_type == 'single':
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124 #if $input_type_cond.input_read1.is_of_type("fastq.gz", "fastqsanger.gz"):
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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125 ln -s '$input_type_cond.input_read1' input_single.gz &&
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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126 #set $gz = True
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127 #else
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128 ln -s '$input_type_cond.input_read1' input_single.txt &&
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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129 #end if
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130 #elif $input_type_cond.input_type == 'paired':
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131 #if $input_type_cond.input_read1.is_of_type("fastq.gz", "fastqsanger.gz"):
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132 ln -s '$input_type_cond.input_read1' input_read1.gz &&
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133 ln -s '$input_type_cond.input_read2' input_read2.gz &&
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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134 #set $gz = True
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135 #else
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136 ln -s '$input_type_cond.input_read1' input_read1.txt &&
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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137 ln -s '$input_type_cond.input_read2' input_read2.txt &&
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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138 #end if
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139 #else ## paired_collection
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140 #if $input_type_cond.input_readpair.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
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141 ln -s '$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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142 ln -s '$input_type_cond.input_readpair.reverse' input_read2.gz &&
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143 #set $gz = True
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144 #else
15
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145 ln -s '$input_type_cond.input_readpair.forward' input_read1.txt &&
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146 ln -s '$input_type_cond.input_readpair.reverse' input_read2.txt &&
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147 #end if
15
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148 #end if
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149 ]]></token>
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150
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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151 <!-- macros for count, dedup, and group -->
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152
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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153 <token name="@LINK_SAM_BAM_INPUT@"><![CDATA[
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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154 #if $input.is_of_type("sam"):
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155 ## TODO dedup has problems with SAM input in some cases
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156 ## https://github.com/CGATOxford/UMI-tools/issues/483
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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157 ## so convert it to sorted BAM for now
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158 ## #set $input_file = $input
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159 samtools sort --no-PG '$input' > 'input.bam' &&
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160 samtools index -b 'input.bam' &&
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161 #set $input_file = 'input.bam'
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162 #else:
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163 ln -sf '${input}' 'input.bam' &&
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164 ln -sf '$input.metadata.bam_index' 'input.bam.bai' &&
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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165 #set $input_file = 'input.bam'
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166 #end if
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167 ]]></token>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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168 <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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169 ## TODO see comment in LINK_SAM_BAM_INPUT
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170 ## #if $input.is_of_type("sam"):
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171 ## --in-sam
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172 ## #end if
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173 ]]></token>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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174
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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175 <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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176 <conditional name="extract_method_cond">
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177 <param argument="--extract-method" type="select" label="Barcode Extraction Method"
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178 help="If bracketed expressions are used in the above barcode pattern, then set this to 'regex'. Otherwise leave as 'string'" >
17
f3759eec3018 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit 31bad8c5bf75981eafcd19ec6b00593f184fdeb8"
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179 <option value="string" selected="true">String</option>
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180 <option value="regex">Regex</option>
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181 </param>
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182 <when value="string">
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183 <param argument="--3prime" name="prime3" type="boolean" label="Is barcode on 3' end of the read?"
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184 truevalue="--3prime" falsevalue=""
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185 help="By default the barcode is assumed to be on the 5' end of the read, but
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186 use this option to specify that it is on the 3' end instead.
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187 This option only works with ``--extract-method=string``
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188 since 3' encoding can be specified explicitly with a regex, e.g
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189 ``.*(?P&lt;umi_1&gt;.{5})$``" />
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190 </when>
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191 <when value="regex">
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192 <param name="filtered_out_bool" type="boolean" label="Write out reads not matching regex pattern"/>
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193 </when>
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194 </conditional>
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195 <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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196 </xml>
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197 <token name="@FASTQ_BARCODE_EXTRACTION_OPTIONS@"><![CDATA[
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198 ## fastq barcode extraction options:
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199 --extract-method='$extract_method_cond.extract_method'
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200 --bc-pattern='$input_type_cond.bc_pattern'
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201 #if $input_type_cond.input_type != 'single' and $input_type_cond.bc_pattern2 != ''
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202 --bc-pattern2='$input_type_cond.bc_pattern2'
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203 #end if
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204 #if $extract_method_cond.extract_method == 'string'
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205 $extract_method_cond.prime3
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206 #else if $extract_method_cond.filtered_out_bool
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207 #if $input_type_cond.input_type == 'single':
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208 --filtered-out='$filtered_out'
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209 #else if $input_type_cond.input_type == 'paired':
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210 --filtered-out='$filtered_out'
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211 --filtered-out2='$filtered_out_paired'
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212 #else
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213 --filtered-out='$filtered_out_paired_collection.forward'
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214 --filtered-out2='$filtered_out_paired_collection.reverse'
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215 #end if
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216 #end if
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217 $ignore_read_pair_suffixes
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218 ]]></token>
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219 <token name="@FASTQ_BARCODE_EXTRACTION_HELP@"><![CDATA[
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220 There are two methods enabled to extract the umi barcode (+/-
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221 cell barcode). For both methods, the patterns should be provided
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222 using the ``--bc-pattern`` and ``--bc-pattern2`` options.x
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223
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224 - ``string``
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225 This should be used where the barcodes are always in the same
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226 place in the read.
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227
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228 - N = UMI position (required)
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229 - C = cell barcode position (optional)
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230 - X = sample position (optional)
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231
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232 Bases with Ns and Cs will be extracted and added to the read
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233 name. The corresponding sequence qualities will be removed from
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234 the read. Bases with an X will be reattached to the read.
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235
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236 E.g. If the pattern is `NNNNCC`,
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237 Then the read::
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238
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239 @HISEQ:87:00000000 read1
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240 AAGGTTGCTGATTGGATGGGCTAG
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241 +
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242 DA1AEBFGGCG01DFH00B1FF0B
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243
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244 will become::
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245
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246 @HISEQ:87:00000000_TT_AAGG read1
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247 GCTGATTGGATGGGCTAG
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248 +
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249 1AFGGCG01DFH00B1FF0B
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250
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251 where 'TT' is the cell barcode and 'AAGG' is the UMI.
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252
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253 - ``regex``
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254 This method allows for more flexible barcode extraction and
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255 should be used where the cell barcodes are variable in
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256 length. Alternatively, the regex option can also be used to
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257 filter out reads which do not contain an expected adapter
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258 sequence. UMI-tools uses the regex module rather than the more
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259 standard re module since the former also enables fuzzy matching
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260
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261 The regex must contain groups to define how the barcodes are
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262 encoded in the read. The expected groups in the regex are:
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263
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264 umi_n = UMI positions, where n can be any value (required)
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265 cell_n = cell barcode positions, where n can be any value (optional)
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266 discard_n = positions to discard, where n can be any value (optional)
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267
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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268 UMI positions and cell barcode positions will be extracted and
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269 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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270 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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271
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272 Discard bases and the corresponding quality scores will be
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273 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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274 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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275
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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276 For example, the following regex can be used to extract reads
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277 from the Klein et al inDrop data::
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278
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279 (?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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280
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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281 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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282 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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283 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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284
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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285 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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286 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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287 matches with up to 2 errors in the discard_1 group.
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288
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289 ::
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 (?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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292
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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293 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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294 processing with dedup, group or count commands]]></token>
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295
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296 <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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297 <conditional name="bc" >
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298 <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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299 <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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300 <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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301 <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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302 </param>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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303 <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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304 <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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305 <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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306 <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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307 </sanitizer>
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308 </param>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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309 </when>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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310 <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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311 <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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312 <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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313 </param>
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="--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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315 <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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316 <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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317 <expand macro="sanitize_tag" />
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318 </param>
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319 <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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320 <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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321 </when>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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322 <when value="umis"/>
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323 </conditional>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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324 </xml>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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325 <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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326 --extract-umi-method $bc.extract_umi_method
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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327 #if str($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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328 --umi-separator '$bc.umi_separator'
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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329 #else if str($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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330 --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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331 #if $bc.umi_tag_split != ''
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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332 --umi-tag-split '$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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333 #end if
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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334 #if $bc.umi_tag_delimiter != ''
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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335 --umi-tag-delimiter '$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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336 #end if
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 '$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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338 #if $bc.cell_tag_split != ''
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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339 --cell-tag-split '$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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340 #end if
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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341 #if $bc.cell_tag_delimiter != ''
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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342 --cell-tag-delimiter '$bc.cell_tag_delimiter'
4
e73a22ff585c planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0
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343 #end if
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344 #end if
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345 ]]></token>
15
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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346 <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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347 Extracting barcodes
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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348 -------------------
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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349
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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350 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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351 extract`` before mapping and thus the UMI is the last word of the read
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352 name. e.g:
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353
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354 @HISEQ:87:00000000_AATT
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355
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356 where ``AATT`` is the UMI sequeuence.
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357
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358 If you have used an alternative method which does not separate the
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359 read id and UMI with a "_", such as bcl2fastq which uses ":", you can
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360 specify the separator with the option ``--umi-separator=<sep>``,
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361 replacing <sep> with e.g ":".
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362
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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363 Alternatively, if your UMIs are encoded in a tag, you can specify this
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364 by setting the option --extract-umi-method=tag and set the tag name
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365 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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366 the 'UM' tag, provide the following options:
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367 ``--extract-umi-method=tag`` ``--umi-tag=UM``
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368
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369 Finally, if you have used umis to extract the UMI +/- cell barcode,
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370 you can specify ``--extract-umi-method=umis``
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371
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372 The start position of a read is considered to be the start of its alignment
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373 minus any soft clipped bases. A read aligned at position 500 with
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374 cigar 2S98M will be assumed to start at position 498.]]></token>
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375
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376
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377 <xml name="umi_grouping_options_macro">
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378 <section name="umi" title="UMI grouping options">
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379 <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">
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380 <option value="unique">Reads group share the exact same UMI</option>
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381 <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>
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382 <option value="cluster">Identify clusters based on hamming distance</option>
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383 <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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384 <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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385 </param>
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386 <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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387 <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)" />
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388 <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" />
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389 <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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390 </section>
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391 </xml>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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392 <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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393 --method $umi.method
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394 --edit-distance-threshold $umi.edit_distance_threshold
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395 $umi.spliced_is_unique
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396 --soft-clip-threshold $umi.soft_clip_threshold
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397 $umi.read_length
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398 ]]></token>
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399 <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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400 UMI grouping options
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401 --------------------
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402
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403 Grouping Method
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404 ...............
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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405
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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406 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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407 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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408
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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409 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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410
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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411 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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412 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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413 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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414 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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415 are then defined from the network in a method-specific manner. For all
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416 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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417 count for the gene.
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418
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419 - unique
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420 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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421
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422 - percentile
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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423 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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424 median counts for UMIs at the same position are ignored.
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425
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426 - cluster
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427 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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428 threshold). Each network is a read group
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429
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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430 - adjacency
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431 Cluster UMIs as above. For each cluster, select the node (UMI)
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432 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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433 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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diff changeset
434 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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parents: 12
diff changeset
435 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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parents: 12
diff changeset
436
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
437 - 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
438 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
439 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
440 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
441
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
442 ]]></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
443
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 <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
445 <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
446 <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
447 <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"
iuc
parents: 12
diff changeset
448 <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
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449 <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
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450 <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
451 </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
452 <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"
iuc
parents: 12
diff changeset
453 <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
454 <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
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455 <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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456 </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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457 <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"
iuc
parents: 12
diff changeset
458 <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
459 <option value="use">use</option>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
460 <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
461 </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
462 <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
diff changeset
463 <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
464 <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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465 <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
466 <!--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
diff changeset
467 <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
468 </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
469 </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
470 <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
471 --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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parents: 12
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472 --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
473 #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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474 --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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475 #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
476 #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
477 --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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478 #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
479 $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
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480 $sambam.ignore_tlen
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 12
diff changeset
481 #if str($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
482 --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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483 #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
484 --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
485 $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
486 @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
487 ]]></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
488
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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489 <!-- 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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490 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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491 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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492 -->
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
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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494 <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
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495 <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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496 <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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497 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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498 </expand>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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499 </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
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500 <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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501 $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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502 @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
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503 ]]></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
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504
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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505 <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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506 <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
507 <yield/>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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508 <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
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509 <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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510 </param>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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511 <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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512 <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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513 </param>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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514 <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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515 <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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diff changeset
516 </param>
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-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
518 <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
519 <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
520 </section>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
521 </xml>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
522 <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
523 #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
524 --gene-tag '$sc.gene_tag'
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
525 #end if
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
526 #if str($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
527 --assigned-status-tag '$sc.assigned_status_tag'
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
528 #end if
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
529 #if str($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
530 --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
531 #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
532 $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
533 #if $sc.gene_transcript_map:
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
534 --gene-transcript-map '$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
535 #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
536 $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
537 ]]></token>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
538
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
539 <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
540 <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
541 <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
542 <!-- 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
543 <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
544 <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
545 <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
546 <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
547 <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
548 </param>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
549 </section>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
550 </xml>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
551 <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
552 $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
553 $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
554 $gd.multimapping_detection_method
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
555 ]]></token>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
556
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
557 <xml name="log_input_macro">
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
558 <param argument="--log" type="boolean" label="Output log?" truevalue="--log" falsevalue="" help="Choose if you want to generate a text file containing logging information" />
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
559 </xml>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
560 <xml name="log_output_macro">
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
561 <data name="out_log" format="txt" label="${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
562 <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
563 </data>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
564 </xml>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
565 <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
566 #if $log:
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
567 --log='$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
568 #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
569 --log2stderr
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
570 ]]></token>
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 12
diff changeset
571
1
79436b3019e9 planemo upload commit c8e46ecad0b1473097517e582ed6c43eb0635b36
iuc
parents:
diff changeset
572 </macros>