Mercurial > repos > iuc > freyja_demix

annotate macros.xml @ 3:c5f2ce99da69 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 79a21a9a4a63e538f2ba0bc29384593df2c65859
author iuc
date Fri, 15 Nov 2024 16:44:54 +0000
parents 53b22b7dff19
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
2 <macros>
3
c5f2ce99da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 79a21a9a4a63e538f2ba0bc29384593df2c65859
iuc
parents: 2
diff changeset
3 <token name="@TOOL_VERSION@">1.5.2</token>
0
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
4 <token name="@VERSION_SUFFIX@">0</token>
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
5 <token name="@PROFILE@">21.01</token>
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
6 <xml name="biotools">
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
7 <xrefs>
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
8 <xref type="bio.tools">freyja</xref>
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
9 </xrefs>
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
10 </xml>
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
11 <xml name="requirements">
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
12 <requirements>
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
13 <requirement type="package" version="@TOOL_VERSION@">freyja</requirement>
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
14 <yield/>
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
15 </requirements>
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
16 </xml>
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
17 <xml name="version">
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
18 <version_command>freyja --version</version_command>
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
19 </xml>
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
20 <token name="@RUN_FREYJA_UPDATE_COMMAND@"><![CDATA[
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
21 #if $usher_update_option.choice == 'update'
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
22 freyja update &&
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
23 #end if
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
24 ]]></token>
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
25 <token name="@PREPROCESS_VCF_INPUT@"><![CDATA[
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
26 ln -s '$variants_file' 'variants_file.vcf' &&
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
27 ]]></token>
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
28 <token name="@STANDARD_INPUT_FOR_BOOT@"><![CDATA[
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
29 #if $variants_file.ext == 'vcf'
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
30 'variants_file.vcf'
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
31 #else
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
32 '$variants_file'
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
33 #end if
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
34 '$depth_file'
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
35 #if $eps
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
36 --eps '${eps}'
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
37 #end if
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
38 #if $meta
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
39 --meta '${meta}'
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
40 #end if
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
41 $confirmedonly
3
c5f2ce99da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 79a21a9a4a63e538f2ba0bc29384593df2c65859
iuc
parents: 2
diff changeset
42 --pathogen '$pathogen'
0
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
43 ]]></token>
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
44 <token name="@CUSTOM_BARCODES_COMMAND@"><![CDATA[
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
45 #if $usher_update_option.choice == 'custom'
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
46 --barcodes '${usher_update_option.usher_barcodes}'
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
47 #end if
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
48 ]]></token>
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
49 <token name="@DASH_COMMAND@"><![CDATA[
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
50 echo '${plot_format.plot_title}' > plot_title.txt &&
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
51 echo '${plot_format.plot_intro}' > plot_intro.txt &&
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
52 freyja dash
1
c0a0e79d7196 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
iuc
parents: 0
diff changeset
53 --mincov $plot_format.mincov
0
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
54 #if $need_aggregation.choice == 'no'
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
55 '$tsv_aggregated'
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
56 #else
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
57 'aggregated.tsv'
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
58 #end if
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
59 '$plot_format.csv_meta'
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
60 plot_title.txt
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
61 plot_intro.txt
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
62 --output abundances_dashboard.html
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
63 ]]></token>
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
64 <token name="@PLOT_COMMAND@"><![CDATA[
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
65 freyja plot
1
c0a0e79d7196 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
iuc
parents: 0
diff changeset
66 $plot_format.lineages
c0a0e79d7196 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
iuc
parents: 0
diff changeset
67 --mincov $plot_format.mincov
0
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
68 #if $need_aggregation.choice == 'no'
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
69 '$tsv_aggregated'
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
70 #else
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
71 'aggregated.tsv'
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
72 #end if
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
73 --output abundances_plot.pdf
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
74 #if $plot_format.csv_meta
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
75 --times '${plot_format.csv_meta}'
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
76 #end if
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
77 #if $plot_format.interval == 'MS'
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
78 --interval MS
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
79 #else
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
80 --interval D
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
81 --windowsize 70
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
82 #end if
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
83 ]]></token>
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
84 <token name="@PLOT_AND_DASH_COMMAND@"><![CDATA[
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
85 #if $plot_format.choice == 'dash'
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
86 @DASH_COMMAND@
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
87 #else if $plot_format.choice == 'plot'
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
88 freyja plot
1
c0a0e79d7196 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
iuc
parents: 0
diff changeset
89 $plot_format.lineages
c0a0e79d7196 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
iuc
parents: 0
diff changeset
90 --mincov $plot_format.mincov
0
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
91 #if $need_aggregation.choice == 'no'
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
92 $tsv_aggregated
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
93 #else
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
94 aggregated.tsv
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
95 #end if
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
96 --output abundances_plot.pdf
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
97 #if $plot_format.need_metadata.choice == 'yes'
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
98 --times '${plot_format.need_metadata.csv_meta}'
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
99 #if $plot_format.need_metadata.interval == 'MS'
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
100 --interval MS
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
101 #else
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
102 --interval D
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
103 --windowsize 70
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
104 #end if
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
105 #end if
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
106 #else if $plot_format.choice == 'plot_and_dash'
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
107 @DASH_COMMAND@ &&
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
108 @PLOT_COMMAND@
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
109 #end if
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
110 ]]></token>
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
111 <xml name="demixing_common_options">
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
112 <param name="depth_file" type="data" format="tabular" label="Sequencing depth file"/>
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
113 <conditional name="usher_update_option">
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
114 <param name="choice" type="select" label="Source of UShER barcodes data"
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
115 help="Freyja ships with an usher_barcodes.csv file, which the tool can access internally. Since this file gets updated rather frequently, you can also download the latest version of the file from https://github.com/andersen-lab/Freyja/raw/main/freyja/data/usher_barcodes.csv, set the dataset's datatype to csv and use it as a custom barcodes file.">
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
116 <option value="repo" selected="true">Use data shipped with the tool (can be
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
117 outdated)
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
118 </option>
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
119 <option value="custom">Provide a custom barcodes file</option>
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
120 <!--<option value="update">Get updated versions of the curated lineage file as well as the UShER global phylogenetic tree (can cause tool to run slowly)</option>-->
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
121 </param>
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
122 <when value="repo"/>
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
123 <when value="custom">
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
124 <param name="usher_barcodes" type="data" format="csv" label="UShER barcodes file"/>
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
125 </when>
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
126 <!--<when value="update" />-->
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
127 </conditional>
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
128 <param argument="--meta" type="data" format="json" optional="true"
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
129 label="Custom lineage metadata file"
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
130 help="For additional flexibility and reproducibility of analyses, a custom lineage-to-contellation mapping metadata file can be provided."/>
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
131 <param argument="--eps" type="float" optional="true"
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
132 label="Minimum lineage abundance tp include"
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
133 help="e.g. 0.0001."/>
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
134 <param argument="--confirmedonly" type="boolean" truevalue="--confirmedonly" falsevalue=""
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
135 checked="false"
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
136 label="Remove unconfirmed lineages from the analysis"
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
137 help="If the UShER tree includes proposed lineages, the --confirmedonly flag removes unconfirmed lineages from the analysis."/>
1
c0a0e79d7196 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
iuc
parents: 0
diff changeset
138 <param argument="--wgisaid" type="boolean" truevalue="--wgisaid" falsevalue=""
c0a0e79d7196 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
iuc
parents: 0
diff changeset
139 checked="false"
c0a0e79d7196 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
iuc
parents: 0
diff changeset
140 label="Use larger library with non-public lineages"
c0a0e79d7196 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
iuc
parents: 0
diff changeset
141 help="Allows to use larger UShER barcodes library extended with GISAID non-public lineages"/>
3
c5f2ce99da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 79a21a9a4a63e538f2ba0bc29384593df2c65859
iuc
parents: 2
diff changeset
142 <param argument="--pathogen" type="select" label="Pathogen of interest">
c5f2ce99da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 79a21a9a4a63e538f2ba0bc29384593df2c65859
iuc
parents: 2
diff changeset
143 <option value="SARS-CoV-2" selected="true">SARS-CoV-2</option>
c5f2ce99da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 79a21a9a4a63e538f2ba0bc29384593df2c65859
iuc
parents: 2
diff changeset
144 <option value="MPXV" selected="true">MPXV</option>
c5f2ce99da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 79a21a9a4a63e538f2ba0bc29384593df2c65859
iuc
parents: 2
diff changeset
145 <option value="H5NX" selected="true">H5NX</option>
c5f2ce99da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 79a21a9a4a63e538f2ba0bc29384593df2c65859
iuc
parents: 2
diff changeset
146 <option value="H1N1pdm" selected="true">H1N1pdm</option>
c5f2ce99da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 79a21a9a4a63e538f2ba0bc29384593df2c65859
iuc
parents: 2
diff changeset
147 <option value="FLU-B-VIC" selected="true">FLU-B-VIC</option>
c5f2ce99da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 79a21a9a4a63e538f2ba0bc29384593df2c65859
iuc
parents: 2
diff changeset
148 <option value="MEASLESN450" selected="true">MEASLESN450</option>
c5f2ce99da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 79a21a9a4a63e538f2ba0bc29384593df2c65859
iuc
parents: 2
diff changeset
149 <option value="MEASLES" selected="true">MEASLES</option>
c5f2ce99da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 79a21a9a4a63e538f2ba0bc29384593df2c65859
iuc
parents: 2
diff changeset
150 <option value="RSVa" selected="true">RSVa</option>
c5f2ce99da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 79a21a9a4a63e538f2ba0bc29384593df2c65859
iuc
parents: 2
diff changeset
151 <option value="RSVb" selected="true">RSVb</option>
c5f2ce99da69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 79a21a9a4a63e538f2ba0bc29384593df2c65859
iuc
parents: 2
diff changeset
152 </param>
1
c0a0e79d7196 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
iuc
parents: 0
diff changeset
153 </xml>
c0a0e79d7196 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
iuc
parents: 0
diff changeset
154 <xml name="plot_lineages">
c0a0e79d7196 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
iuc
parents: 0
diff changeset
155 <param argument="--lineages" type="boolean" truevalue="--lineages" falsevalue=""
c0a0e79d7196 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
iuc
parents: 0
diff changeset
156 checked="false" label="Use lineage specific breakdown"/>
c0a0e79d7196 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
iuc
parents: 0
diff changeset
157 </xml>
c0a0e79d7196 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
iuc
parents: 0
diff changeset
158 <xml name="plot_mincov">
c0a0e79d7196 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
iuc
parents: 0
diff changeset
159 <param argument="--mincov" type="float" min="0" max="100" value="60"
c0a0e79d7196 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
iuc
parents: 0
diff changeset
160 label="Minimum genome coverage"
c0a0e79d7196 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
iuc
parents: 0
diff changeset
161 help="Include in the plot only samples where the 'coverage' value is greater than the specified --mincov parameter. It excludes samples with coverage values below the minimum coverage threshold. By default, the minimum genome coverage is set at 60 percent."/>
0
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
162 </xml>
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
163 <token name="@HELP_HEADER@"><![CDATA[
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
164 What it does
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
165 ============
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
166
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
167 Freyja is a tool to recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset (BAM aligned to the Hu-1 reference).
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
168
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
169 General information
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
170 ===================
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
171
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
172 Freyja is a tool to recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset (BAM aligned to the Hu-1 reference). The method uses lineage-determining mutational "barcodes" derived from the UShER global phylogenetic tree as a basis set to solve the constrained (unit sum, non-negative) de-mixing problem.
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
173
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
174 Freyja is intended as a post-processing step after primer trimming and variant calling in iVar (Grubaugh and Gangavaparu et al., 2019). From measurements of SNV freqency and sequencing depth at each position in the genome, Freyja returns an estimate of the true lineage abundances in the sample.
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
175 ]]></token>
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
176 <xml name="citations">
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
177 <citations>
1
c0a0e79d7196 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
iuc
parents: 0
diff changeset
178 <citation type="doi">10.1038/s41586-022-05049-6</citation>
0
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
179 </citations>
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
180 </xml>
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
181 </macros>