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