Mercurial > repos > iuc > umi_tools_count
annotate umi-tools_counts.xml @ 7:8250ea3a1501 draft
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author | iuc |
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date | Wed, 10 Feb 2021 19:29:55 +0000 |
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1 <tool id="umi_tools_count" name="UMI-tools count" version="@VERSION@.1"> |
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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 <requirement type="package" version="4.7">sed</requirement> |
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13 </expand> |
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14 <command detect_errors="exit_code"><![CDATA[ |
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15 #import re |
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16 |
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17 ln -s '${input_bam}' 'input.bam' && |
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18 ln -s '${input_bam.metadata.bam_index}' 'input.bam.bai' && |
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19 |
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20 umi_tools count |
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21 -I input.bam |
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22 '$paired' |
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23 --extract-umi-method='$barcodes.extract_umi_method.value' |
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24 #if str($barcodes.extract_umi_method) == 'read_id': |
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25 --umi-separator='$barcodes.umi_separator.value' |
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26 #else if str($barcodes.extract_umi_method) == 'tag': |
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27 --umi-tag='$barcodes.umi_tag.value' |
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28 --cell-tag='$barcodes.cell_tag.value' |
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29 #end if |
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30 --method='$method.value' |
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31 --edit-distance-threshold='$edit_distance_threshold' |
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32 --mapping-quality='$advanced.mapping_quality' |
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33 --per-gene |
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34 '$wide_format_cell_counts' |
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35 '$advanced.per_contig' |
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36 '$advanced.per_cell' |
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37 |
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38 #if str($advanced.gene_tag) != "": |
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39 --gene-tag='$advanced.gene_tag.value' |
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40 #end if |
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41 #if str($advanced.skip_tags_regex) != "": |
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42 --skip-tags-regex='$advanced.skip_tags_regex.value' |
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43 #end if |
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44 #if '$advanced.random_seed' != 0: |
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45 --random-seed='$advanced.random_seed' |
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46 #end if |
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47 -S '$out_counts' |
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48 |
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49 |
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50 #if str($cond_extra.prepender) != "none": |
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51 #set $replacer = re.sub('[^\w\_]+', '_', str($input_bam.element_identifier.rsplit('.',1)[0])) |
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52 #if str($cond_extra.prepender) == "string": |
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53 #set $replacer = str($cond_extra.custom_label) |
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54 #end if |
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55 |
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56 && sed -i -r '1s|\b([ACGT]+)\b|'"$replacer"'_\1|g' '$out_counts' |
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57 #end if |
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58 |
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59 ]]></command> |
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60 <inputs> |
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61 <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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62 <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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63 <conditional name="barcodes" > |
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64 <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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65 <option value="read_id" selected="true">Barcodes are contained at the end of the read seperated by a delimiter</option> |
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66 <option value="tag" >Barcodes are contained in tags</option> |
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67 <option value="umis" >Barcodes were extracted using umis</option> |
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68 </param> |
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69 <when value="read_id" > |
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70 <param argument="--umi-separator" name="umi_separator" type="text" label="Delimiter between read id and the UMI" value="_" > |
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71 <sanitizer invalid_char="" > |
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72 <valid initial="string.punctuation" /> |
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73 </sanitizer> |
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74 </param> |
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75 </when> |
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76 <when value="tag" > |
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77 <param argument="--umi-tag" name="umi_tag" type="text" label="Tag which contains the UMI" > |
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78 <expand macro="sanitize_tag" /> |
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79 </param> |
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80 <param argument="--cell-tag" name="cell_tag" type="text" label="Tag which contains the cell barcode" > |
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81 <expand macro="sanitize_tag" /> |
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82 </param> |
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83 </when> |
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84 <when value="umis"></when> |
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85 </conditional> |
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86 <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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87 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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88 counts < 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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89 <option value="unique" >Unique</option> |
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90 <option value="percentile">Percentile</option> |
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91 <option value="cluster">Cluster</option> |
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92 <option value="adjacency">Adjacency</option> |
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93 <option value="directional" selected="true" >Directional</option> |
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94 </param> |
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95 <param argument="--edit-distance-threshold" name="edit_distance_threshold" type="integer" label="Edit distance threshold" min="0" value="1" /> |
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96 <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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97 <section name="advanced" title="Extra parameters" > |
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98 <param argument="--mapping-quality" name="mapping_quality" type="integer" min="0" value="0" label="Minimum mapping quality" /> |
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99 <!-- Currently hard-coded parameter. Leave here if useful to future wrapper --> |
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100 <!-- <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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101 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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102 -\-gene-tag or -\-per-contig option" /> --> |
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103 <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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104 <expand macro="sanitize_tag" /> |
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105 </param> |
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106 <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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107 <expand macro="barcode_sanitizer" /> |
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108 </param> |
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109 <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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110 <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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111 <param argument="--random-seed" name="random_seed" type="integer" min="0" value="0" label="Random Seed" /> |
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112 </section> |
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113 <conditional name="cond_extra" > |
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114 <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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115 <option value="none" selected="true" >No modifications</option> |
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116 <option value="string">Custom Label</option> |
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117 <option value="dataset name">Dataset Name</option> |
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118 </param> |
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119 <when value="none"></when> |
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120 <when value="dataset name"></when> |
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121 <when value="string"> |
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122 <param name="custom_label" type="text" label="Label to Prepend" > |
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123 <sanitizer invalid_char=""> |
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124 <valid initial="string.letters,string.digits"> |
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125 <add value="-"/> |
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126 <add value="_"/> |
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127 <add value="."/> |
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128 </valid> |
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129 </sanitizer> |
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130 </param> |
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131 </when> |
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132 </conditional> |
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133 </inputs> |
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134 <outputs> |
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135 <data name="out_counts" format="tabular" /> |
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136 </outputs> |
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137 <tests> |
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138 <test><!--count_single_gene_tag:--> |
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139 <param name="input_bam" value="chr19_gene_tags.bam" /> |
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140 <param name="random_seed" value="123456789" /> |
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141 <param name="method" value="directional" /> |
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142 <param name="gene_tag" value="XF" /> |
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143 <param name="skip_tags_regex" value="^[__|Unassigned]" /> |
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144 <param name="extract_umi_method" value="umis" /> |
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145 <param name="wide_format_cell_counts" value="false" /> |
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146 <param name="per_cell" value="false" /> |
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147 <output name="out_counts" value="count_single_gene_tag.tsv" /> |
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148 </test> |
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149 <test><!--count_single_cells_gene_tag:--> |
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150 <param name="input_bam" value="chr19_gene_tags.bam" /> |
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151 <param name="random_seed" value="123456789" /> |
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152 <param name="method" value="directional" /> |
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153 <param name="gene_tag" value="XF" /> |
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154 <param name="skip_tags_regex" value="^[__|Unassigned]" /> |
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155 <param name="per_cell" value="true" /> |
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156 <param name="extract_umi_method" value="umis" /> |
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157 <param name="wide_format_cell_counts" value="false" /> |
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158 <output name="out_counts" value="count_single_cells_gene_tag.tsv" /> |
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159 </test> |
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160 <test><!--count_single_cells_wide_gene_tag:--> |
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161 <param name="input_bam" value="chr19_gene_tags.bam" /> |
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162 <param name="random_seed" value="123456789" /> |
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163 <param name="method" value="directional" /> |
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164 <param name="gene_tag" value="XF" /> |
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165 <param name="skip_tags_regex" value="^[__|Unassigned]" /> |
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166 <param name="per_cell" value="true" /> |
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167 <param name="extract_umi_method" value="umis" /> |
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168 <param name="wide_format_cell_counts" value="true" /> |
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169 <output name="out_counts" value="count_single_cells_gene_tag_wide.tsv" /> |
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170 </test> |
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171 <test><!-- count ENSDARG00000019692, with defaults --> |
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172 <param name="input_bam" value="fc.ENSDARG00000019692.bam" /> |
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173 <param name="method" value="unique" /> |
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174 <output name="out_counts" value="fc.ENSDARG00000019692.counts" /> |
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175 </test> |
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176 <test><!-- count ENSDARG00000019692, relabel string --> |
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177 <param name="input_bam" value="fc.ENSDARG00000019692.bam" /> |
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178 <param name="method" value="unique" /> |
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179 <conditional name="cond_extra" > |
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180 <param name="prepender" value="string" /> |
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181 <param name="custom_label" value="test" /> |
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182 </conditional> |
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183 <output name="out_counts" value="fc.ENSDARG00000019692.counts.test" /> |
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184 </test> |
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185 <test><!-- count ENSDARG00000019692, relabel filename --> |
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186 <param name="input_bam" value="fc.ENSDARG00000019692.bam" /> |
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187 <param name="method" value="unique" /> |
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188 <conditional name="cond_extra" > |
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189 <param name="prepender" value="dataset name" /> |
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190 </conditional> |
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191 <output name="out_counts" value="fc.ENSDARG00000019692.counts.name" /> |
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192 </test> |
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193 </tests> |
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194 <help><![CDATA[ |
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195 |
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196 UMI Tools count - Count reads per gene from BAM using UMIs |
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197 ---------------------------------------------------------- |
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198 |
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199 Purpose |
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200 ------- |
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201 |
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202 The purpose of this command is to count the number of reads per gene based |
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203 on the mapping co-ordinate and the UMI attached to the read. |
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204 |
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205 |
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206 It is assumed that the FASTQ files were processed with extract_umi.py |
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207 before mapping and thus the UMI is the last word of the read name. e.g: |
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208 |
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209 @HISEQ:87:00000000_AATT |
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210 |
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211 where AATT is the UMI sequeuence. |
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212 |
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213 If you have used an alternative method which does not separate the |
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214 read id and UMI with a "_", such as bcl2fastq which uses ":", you can |
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215 specify the separator, or if your UMIs are encoded in a tag you can also specify this. |
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216 |
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217 ]]></help> |
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218 <expand macro="citations" /> |
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219 </tool> |