Mercurial > repos > iuc > umi_tools_count

annotate umi-tools_counts.xml @ 3:b557acca0b56 draft

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author iuc
date Fri, 20 Jul 2018 03:50:03 -0400
parents 3c932ad4a174
children 70cb5527defb
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1 <tool id="umi_tools_count" name="UMI-tools count" version="@VERSION@.2">
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2 <description>performs quantification of UMIs from BAM files</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <xml name="sanitize_tag" >
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6 <sanitizer invalid_char="">
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7 <valid initial="string.letters,string.digits" />
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8 </sanitizer>
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9 </xml>
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10 </macros>
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11 <expand macro="requirements" />
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12 <command detect_errors="exit_code"><![CDATA[
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13 #import re
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14
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15 ln -s '${input_bam}' 'input.bam' &&
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16 ln -s '${input_bam.metadata.bam_index}' 'input.bam.bai' &&
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17
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18 umi_tools count
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19 -I input.bam
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20 '$paired'
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21 --extract-umi-method='$barcodes.extract_umi_method.value'
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22 #if str($barcodes.extract_umi_method) == 'read_id':
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23 --umi-separator='$barcodes.umi_separator.value'
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24 #else if str($barcodes.extract_umi_method) == 'tag':
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25 --umi-tag='$barcodes.umi_tag.value'
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26 --cell-tag='$barcodes.cell_tag.value'
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27 #end if
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28 --method='$method.value'
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29 --edit-distance-threshold='$edit_distance_threshold'
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30 --mapping-quality='$advanced.mapping_quality'
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31 --per-gene
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32 '$wide_format_cell_counts'
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33 '$advanced.per_contig'
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34 '$advanced.per_cell'
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35
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36 #if str($advanced.gene_tag) != "":
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37 --gene-tag='$advanced.gene_tag.value'
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38 #end if
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39 #if str($advanced.skip_tags_regex) != "":
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40 --skip-tags-regex='$advanced.skip_tags_regex.value'
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41 #end if
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42 #if '$advanced.random_seed' != 0:
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43 --random-seed='$advanced.random_seed'
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44 #end if
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45 -S '$out_counts'
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46
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47
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48 #if str($cond_extra.prepender) != "none":
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49 #set $replacer = re.sub('[^\w\_]+', '_', str($input_bam.element_identifier.rsplit('.',1)[0]))
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50 #if str($cond_extra.prepender) == "string":
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51 #set $replacer = str($cond_extra.custom_label)
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52 #end if
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53
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54 && sed -i -r '1s|\b([ACGT]+)\b|'"$replacer"'_\1|g' '$out_counts'
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55 #end if
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56
0
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57 ]]></command>
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58 <inputs>
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59 <param name="input_bam" type="data" format="bam" label="Sorted BAM file" help="Please use the samtools sort tool to ensure a correct BAM input" />
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60 <param argument="--paired" type="boolean" truevalue="--paired" falsevalue="" checked="false" label="Bam is paired-end" help="both read pairs will be output. This will also force the use of the template length to determine reads with the same mapping coordinates." />
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61 <conditional name="barcodes" >
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62 <param argument="--extract-umi-method" name="extract_umi_method" type="select" label="Umi Extract Method" help="How are the barcodes encoded in the read?" >
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63 <option value="read_id" selected="true">Barcodes are contained at the end of the read seperated by a delimiter</option>
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64 <option value="tag" >Barcodes are contained in tags</option>
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65 <option value="umis" >Barcodes were extracted using umis</option>
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66 </param>
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67 <when value="read_id" >
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68 <param argument="--umi-separator" name="umi_separator" type="text" label="Delimiter between read id and the UMI" value="_" >
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69 <sanitizer invalid_char="" >
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70 <valid initial="string.punctuation" />
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71 </sanitizer>
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72 </param>
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73 </when>
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74 <when value="tag" >
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75 <param argument="--umi-tag" name="umi_tag" type="text" label="Tag which contains the UMI" >
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76 <expand macro="sanitize_tag" />
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77 </param>
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78 <param argument="--cell-tag" name="cell_tag" type="text" label="Tag which contains the cell barcode" >
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79 <expand macro="sanitize_tag" />
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80 </param>
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81 </when>
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82 <when value="umis"></when>
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83 </conditional>
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84 <param argument="--method" type="select" label="Method to identify group of reads" help="UMIs with the same (or similar) codes can be grouped together. The simplest methods 'unique' and 'percentile' group identical
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85 UMIs, however 'cluster', 'adjacency', and 'directional' can group similar umis with edit distances less than some threshold. Unique: Reads group share the exact same UMI. Percentile: Reads group share the same UMI, and UMIs with
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86 counts &lt; 1% of the median counts for UMIs at the same position are ignored. Cluster: Identify clusters of connected UMIs (based on hamming distance threshold). Adjacency: Same as cluster, but considers only directly ajacent UMIs in the cluster. Directional: Identify cluster of connected UMIs based on hamming distance and umi." >
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87 <option value="unique" >Unique</option>
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88 <option value="percentile">Percentile</option>
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89 <option value="cluster">Cluster</option>
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90 <option value="adjacency">Adjacency</option>
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91 <option value="directional" selected="true" >Directional</option>
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92 </param>
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93 <param argument="--edit-distance-threshold" name="edit_distance_threshold" type="integer" label="Edit distance threshold" min="0" value="1" />
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94 <param argument="--wide-format-cell-counts" name="wide_format_cell_counts" type="boolean" truevalue="--wide-format-cell-counts" falsevalue="" checked="true" label="Output a matrix of genes and cells, instead of a flat file" />
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95 <section name="advanced" title="Extra parameters" >
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96 <param argument="--mapping-quality" name="mapping_quality" type="integer" min="0" value="0" label="Minimum mapping quality" />
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97 <!-- Currently hard-coded parameter. Leave here if useful to future wrapper -->
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98 <!-- <param argument="-\-per-gene" name="per_gene" type="text" label="Group reads together if they have the same gene" help="Reads will be grouped together if they have the same gene. This is useful if your library
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99 prep generates PCR duplicates with non-identical alignment positions such as CEL-Seq. Note this option is hardcoded to be on with the count command. I.e counting is always performed per-gene. Must be combined with either
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100 -\-gene-tag or -\-per-contig option" /> -->
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101 <param argument="--gene-tag" name="gene_tag" type="text" label="Deduplicate per gene." value="XT" help="The gene information is encoded in the bam read tag." >
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102 <expand macro="sanitize_tag" />
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103 </param>
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104 <param argument="--skip-tags-regex" name="skip_tags_regex" type="text" label="Skip any reads where the gene matches this tag" value="" >
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105 <sanitizer invalid_char="">
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106 <valid initial="string.letters,string.digits">
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107 <add value="!="/>
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108 <add value="-"/>
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109 <add value="_"/>
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110 <add value="."/>
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111 <add value="?"/>
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112 <add value="&lt;"/><!-- left triangle bracket -->
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113 <add value="&gt;"/><!-- right triangle bracket -->
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114 <add value="&#91;"/> <!-- left square bracket -->
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115 <add value="&#93;"/> <!-- right square bracket -->
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116 <add value="&#94;"/> <!-- caret -->
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117 <add value="&#123;"/> <!-- left curly -->
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118 <add value="&#125;"/> <!-- right curly -->
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119 <add value="&#40;"/> <!-- left parenthesis -->
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120 <add value="&#41;"/> <!-- right parenthesis -->
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121 </valid>
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122 </sanitizer>
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123 </param>
1
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124 <param argument="--per-contig" name="per_contig" type="boolean" truevalue="--per-contig" falsevalue="" checked="false" label="Deduplicate per contig (field 3 in BAM; RNAME)" help="All reads with the same contig will be considered to have the same alignment position. This is useful if you have aligned to a reference transcriptome with one transcript per gene." />
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125 <param argument="--per-cell" name="per_cell" type="boolean" truevalue="--per-cell" falsevalue="" checked="true" label="Group reads only if they have the same cell barcode." />
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126 <param argument="--random-seed" name="random_seed" type="integer" min="0" value="0" label="Random Seed" />
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127 </section>
3
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128 <conditional name="cond_extra" >
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129 <param name="prepender" type="select" label="Prepend a label to all column headers" help="This preserves uniqueness when merging with other files with the same headers. Note: filename must not contain a '.' character" >
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130 <option value="none" selected="true" >No modifications</option>
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131 <option value="string">Custom Label</option>
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132 <option value="dataset name">Dataset Name</option>
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133 </param>
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134 <when value="none"></when>
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135 <when value="dataset name"></when>
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136 <when value="string">
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137 <param name="custom_label" type="text" label="Label to Prepend" >
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138 <sanitizer invalid_char="">
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139 <valid initial="string.letters,string.digits">
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140 <add value="-"/>
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141 <add value="_"/>
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142 <add value="."/>
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143 </valid>
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144 </sanitizer>
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145 </param>
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146 </when>
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147 </conditional>
0
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148 </inputs>
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149 <outputs>
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150 <data name="out_counts" format="tabular" />
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151 </outputs>
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152 <tests>
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153 <test><!--count_single_gene_tag:-->
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154 <param name="input_bam" value="chr19_gene_tags.bam" />
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155 <param name="random_seed" value="123456789" />
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156 <param name="method" value="directional" />
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157 <param name="gene_tag" value="XF" />
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158 <param name="skip_tags_regex" value="^[__|Unassigned]" />
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159 <param name="extract_umi_method" value="umis" />
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160 <param name="wide_format_cell_counts" value="false" />
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161 <param name="per_cell" value="false" />
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162 <output name="out_counts" value="count_single_gene_tag.tsv" />
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163 </test>
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164 <test><!--count_single_cells_gene_tag:-->
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165 <param name="input_bam" value="chr19_gene_tags.bam" />
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166 <param name="random_seed" value="123456789" />
1
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167 <param name="method" value="directional" />
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168 <param name="gene_tag" value="XF" />
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169 <param name="skip_tags_regex" value="^[__|Unassigned]" />
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170 <param name="per_cell" value="true" />
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171 <param name="extract_umi_method" value="umis" />
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172 <param name="wide_format_cell_counts" value="false" />
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173 <output name="out_counts" value="count_single_cells_gene_tag.tsv" />
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174 </test>
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175 <test><!--count_single_cells_wide_gene_tag:-->
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176 <param name="input_bam" value="chr19_gene_tags.bam" />
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177 <param name="random_seed" value="123456789" />
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178 <param name="method" value="directional" />
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179 <param name="gene_tag" value="XF" />
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180 <param name="skip_tags_regex" value="^[__|Unassigned]" />
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181 <param name="per_cell" value="true" />
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182 <param name="extract_umi_method" value="umis" />
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183 <param name="wide_format_cell_counts" value="true" />
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184 <output name="out_counts" value="count_single_cells_gene_tag_wide.tsv" />
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185 </test>
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186 <test><!-- count ENSDARG00000019692, with defaults -->
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187 <param name="input_bam" value="fc.ENSDARG00000019692.bam" />
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188 <param name="method" value="unique" />
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189 <output name="out_counts" value="fc.ENSDARG00000019692.counts" />
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190 </test>
3
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191 <test><!-- count ENSDARG00000019692, relabel string -->
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192 <param name="input_bam" value="fc.ENSDARG00000019692.bam" />
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193 <param name="method" value="unique" />
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194 <conditional name="cond_extra" >
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195 <param name="prepender" value="string" />
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196 <param name="custom_label" value="test" />
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197 </conditional>
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198 <output name="out_counts" value="fc.ENSDARG00000019692.counts.test" />
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199 </test>
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200 <test><!-- count ENSDARG00000019692, relabel filename -->
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201 <param name="input_bam" value="fc.ENSDARG00000019692.bam" />
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202 <param name="method" value="unique" />
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203 <conditional name="cond_extra" >
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204 <param name="prepender" value="dataset name" />
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205 </conditional>
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206 <output name="out_counts" value="fc.ENSDARG00000019692.counts.name" />
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207 </test>
0
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208 </tests>
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209 <help><![CDATA[
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210
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211 UMI Tools count - Count reads per gene from BAM using UMIs
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212 ----------------------------------------------------------
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213
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214 Purpose
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215 -------
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216
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217 The purpose of this command is to count the number of reads per gene based
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218 on the mapping co-ordinate and the UMI attached to the read.
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219
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220
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221 It is assumed that the FASTQ files were processed with extract_umi.py
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222 before mapping and thus the UMI is the last word of the read name. e.g:
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223
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224 @HISEQ:87:00000000_AATT
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225
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226 where AATT is the UMI sequeuence.
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227
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228 If you have used an alternative method which does not separate the
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229 read id and UMI with a "_", such as bcl2fastq which uses ":", you can
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230 specify the separator, or if your UMIs are encoded in a tag you can also specify this.
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231
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232 ]]></help>
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233 <expand macro="citations" />
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234 </tool>