Mercurial > repos > iuc > freyja_demix

annotate freyja_demix.xml @ 0:fc6252e78d5b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
author iuc
date Thu, 28 Jul 2022 09:26:02 +0000
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children c0a0e79d7196
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0
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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1 <tool id="freyja_demix" name="Freyja: Demix" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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2 profile="@PROFILE@">
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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3 <description>
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4 lineage abundances
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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5 </description>
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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6 <macros>
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7 <import>macros.xml</import>
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8 </macros>
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9 <expand macro="biotools"/>
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10 <expand macro="requirements">
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11 <requirement type="package" version="4.7">sed</requirement>
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12 </expand>
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13 <expand macro="version"/>
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14 <command detect_errors="exit_code"><![CDATA[
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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15 @RUN_FREYJA_UPDATE_COMMAND@
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16 #if str($sample_name.source) == 'auto':
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17 #set $sn = $variants_in.element_identifier
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18 #else:
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19 #set $sn = str($sample_name.name)
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20 #end if
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21 #set $in_file = $sn.replace(' ', '_') + '.' + $variants_in.ext
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22 ln -s '$variants_in' $in_file &&
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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23 freyja demix
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24 '$in_file'
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25 '$depth_file'
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26 #if $eps
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27 --eps $eps
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28 #end if
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29 #if $meta
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30 --meta '$meta'
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31 #end if
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32 $confirmedonly
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33 @CUSTOM_BARCODES_COMMAND@
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34 --covcut $depth_cutoff
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35 --output abundances_raw.tsv &&
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36 sed 's/$in_file/$sn/' abundances_raw.tsv > abundances.tsv
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37 ]]></command>
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38 <inputs>
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39 <param name="variants_in" type="data" format="tabular"
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40 label="Dataset with input variant calls"
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41 help="This can be a VCF dataset, or the tabular calls output of freayja call or ivar variants."/>
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42 <conditional name="sample_name">
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43 <param name="source" type="select" label="Set sample name"
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44 help="Select autodetect to have the dataset or collection element name used as the sample name, or, for a single input dataset, provide an explicit sample name.">
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45 <option value="auto">Autodetect sample name</option>
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46 <option value="manual">Specify sample name explicitly</option>
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47 </param>
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48 <when value="auto"/>
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49 <when value="manual">
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50 <param name="name" type="text" label="Name of the sample"/>
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51 </when>
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52 </conditional>
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53 <expand macro="demixing_common_options"/>
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54 <param name="depth_cutoff" argument="--covcut" type="integer" min="0" value="10"
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55 multiple="true"
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56 label="Depth cutoff for coverage estimate"
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57 help="In the result file the coverage value will provide the 10x coverage estimate (percent of sites with 10 or greater reads- 10 is the default but can be modfied in this field. "/>
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58 </inputs>
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59 <outputs>
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60 <data name="abundances" format="tabular"
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61 label="${tool.name} on ${on_string}: Lineages abundances summary"
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62 from_work_dir="abundances.tsv"/>
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63 </outputs>
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64 <tests>
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65 <!-- Test 01: manual name sample -->
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66 <test expect_num_outputs="1">
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67 <param name="variants_in" value="variants.tsv"/>
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68 <param name="depth_file" value="depths.tsv"/>
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69 <conditional name="usher_update_option">
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70 <param name="choice" value="repo"/>
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71 </conditional>
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72 <conditional name="sample_name">
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73 <param name="source" value="manual"/>
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74 <param name="name" value="samplename"/>
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75 </conditional>
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76 <output name="abundances" ftype="tabular">
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77 <assert_contents>
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78 <has_text text="samplename"/>
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79 </assert_contents>
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80 </output>
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81 </test>
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82 <!-- Test 02: autoname sample -->
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83 <test expect_num_outputs="1">
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84 <param name="variants_in" value="variants.tsv"/>
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85 <param name="depth_file" value="depths.tsv"/>
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86 <conditional name="usher_update_option">
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87 <param name="choice" value="repo"/>
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88 </conditional>
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89 <conditional name="sample_name">
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90 <param name="source" value="auto"/>
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91 </conditional>
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92 <output name="abundances" ftype="tabular">
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93 <assert_contents>
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94 <has_text text="summarized"/>
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95 </assert_contents>
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96 </output>
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97 </test>
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98 </tests>
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99 <help><![CDATA[
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100 @HELP_HEADER@
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101
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102 **Freyja demix** estimates lineage abundances in a potentially multi-lineage input sample.
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103
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104 Inputs
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105 ======
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106
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107 The tool requires as input a dataset with called variants and a dataset with genome-wide sequencing depth information.
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108 Both types of data can be produced with *Freyja call*, but the tool accepts variant calls also in VCF format.
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109
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110 Note
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111 ----
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112
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113 For single samples it is recommended to select "Specify sample name explicitly"
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114 under "Set sample name".
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115
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116 To use this tool on multiple samples in parallel, please provide two
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117 collections in the same sample sort order - one with the variant calls, the
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118 other one with the sequencing depths - and select "Autodetect sample name",
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119 which will use collection element identifiers as the names of the samples.
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120 This will produce a new collection of demixing reports that can be passed to
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121 *Freyja: Aggregate and visualize* with sample names preserved.
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122
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123 Selection of multiple regular called variants and depth datasets is discouraged
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124 since proper dataset pairing cannot be guaranteed!
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125
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126 Outputs
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127 =======
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128
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129 The tool produces tabular output that includes the lineages detected in the sample, their corresponding abundances, and a lineage summary by constellation.
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130
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131 Example output:
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132
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133 ========== ===================================================
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134 filename
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135 summarized [('Delta', 0.65), ('Other', 0.25), ('Alpha', 0.1')]
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136 lineages ['B.1.617.2' 'B.1.2' 'AY.6' 'Q.3']
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137 abundances "[0.5 0.25 0.15 0.1]"
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138 resid 3.14159
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139 coverage 95.8
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140 ========== ===================================================
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141
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142
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143 Where *summarized* denotes a sum of all lineage abundances in a particular WHO designation (i.e. B.1.617.2 and AY.6 abundances are summed in the above example), otherwise they are grouped into "Other". The *lineage* array lists the identified lineages in descending order, and *abundances* contains the corresponding abundances estimates. The value of *resid* corresponds to the residual of the weighted least absolute devation problem used to estimate lineage abundances. The *coverage* value provides the 10x coverage estimate (percent of sites with 10 or greater reads- 10 is the default but can be modfied using the *--covcut* option).
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144 ]]></help>
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145 <expand macro="citations"/>
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146 </tool>