annotate macros.xml @ 2:95e88f407e86 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit dcb5fdc6a89563af33a1783e4f70754d6611585c
author iuc
date Thu, 10 Oct 2024 18:28:25 +0000
parents a09398bc953a
children 16331f8cff98
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
dda5772507b2 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"?>
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
2 <macros>
2
95e88f407e86 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit dcb5fdc6a89563af33a1783e4f70754d6611585c
iuc
parents: 1
diff changeset
3 <token name="@TOOL_VERSION@">1.5.1</token>
0
dda5772507b2 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>
dda5772507b2 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>
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
6 <xml name="biotools">
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
7 <xrefs>
dda5772507b2 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>
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
9 </xrefs>
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
10 </xml>
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
11 <xml name="requirements">
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
12 <requirements>
dda5772507b2 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>
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
14 <yield/>
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
15 </requirements>
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
16 </xml>
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
17 <xml name="version">
dda5772507b2 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>
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
19 </xml>
dda5772507b2 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[
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
21 #if $usher_update_option.choice == 'update'
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
22 freyja update &&
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
23 #end if
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
24 ]]></token>
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
25 <token name="@PREPROCESS_VCF_INPUT@"><![CDATA[
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
26 ln -s '$variants_file' 'variants_file.vcf' &&
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
27 ]]></token>
dda5772507b2 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[
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
29 #if $variants_file.ext == 'vcf'
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
30 'variants_file.vcf'
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
31 #else
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
32 '$variants_file'
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
33 #end if
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
34 '$depth_file'
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
35 #if $eps
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
36 --eps '${eps}'
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
37 #end if
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
38 #if $meta
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
39 --meta '${meta}'
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
40 #end if
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
41 $confirmedonly
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
42 ]]></token>
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
43 <token name="@CUSTOM_BARCODES_COMMAND@"><![CDATA[
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
44 #if $usher_update_option.choice == 'custom'
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
45 --barcodes '${usher_update_option.usher_barcodes}'
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
46 #end if
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
47 ]]></token>
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
48 <token name="@DASH_COMMAND@"><![CDATA[
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
49 echo '${plot_format.plot_title}' > plot_title.txt &&
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
50 echo '${plot_format.plot_intro}' > plot_intro.txt &&
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
51 freyja dash
1
a09398bc953a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
iuc
parents: 0
diff changeset
52 --mincov $plot_format.mincov
0
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
53 #if $need_aggregation.choice == 'no'
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
54 '$tsv_aggregated'
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
55 #else
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
56 'aggregated.tsv'
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
57 #end if
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
58 '$plot_format.csv_meta'
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
59 plot_title.txt
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
60 plot_intro.txt
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
61 --output abundances_dashboard.html
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
62 ]]></token>
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
63 <token name="@PLOT_COMMAND@"><![CDATA[
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
64 freyja plot
1
a09398bc953a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
iuc
parents: 0
diff changeset
65 $plot_format.lineages
a09398bc953a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
iuc
parents: 0
diff changeset
66 --mincov $plot_format.mincov
0
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
67 #if $need_aggregation.choice == 'no'
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
68 '$tsv_aggregated'
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
69 #else
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
70 'aggregated.tsv'
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
71 #end if
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
72 --output abundances_plot.pdf
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
73 #if $plot_format.csv_meta
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
74 --times '${plot_format.csv_meta}'
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
75 #end if
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
76 #if $plot_format.interval == 'MS'
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
77 --interval MS
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
78 #else
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
79 --interval D
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
80 --windowsize 70
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
81 #end if
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
82 ]]></token>
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
83 <token name="@PLOT_AND_DASH_COMMAND@"><![CDATA[
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
84 #if $plot_format.choice == 'dash'
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
85 @DASH_COMMAND@
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
86 #else if $plot_format.choice == 'plot'
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
87 freyja plot
1
a09398bc953a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
iuc
parents: 0
diff changeset
88 $plot_format.lineages
a09398bc953a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
iuc
parents: 0
diff changeset
89 --mincov $plot_format.mincov
0
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
90 #if $need_aggregation.choice == 'no'
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
91 $tsv_aggregated
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
92 #else
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
93 aggregated.tsv
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
94 #end if
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
95 --output abundances_plot.pdf
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
96 #if $plot_format.need_metadata.choice == 'yes'
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
97 --times '${plot_format.need_metadata.csv_meta}'
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
98 #if $plot_format.need_metadata.interval == 'MS'
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
99 --interval MS
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
100 #else
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
101 --interval D
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
102 --windowsize 70
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
103 #end if
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
104 #end if
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
105 #else if $plot_format.choice == 'plot_and_dash'
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
106 @DASH_COMMAND@ &&
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
107 @PLOT_COMMAND@
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
108 #end if
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
109 ]]></token>
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
110 <xml name="demixing_common_options">
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
111 <param name="depth_file" type="data" format="tabular" label="Sequencing depth file"/>
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
112 <conditional name="usher_update_option">
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
113 <param name="choice" type="select" label="Source of UShER barcodes data"
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
114 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.">
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
115 <option value="repo" selected="true">Use data shipped with the tool (can be
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
116 outdated)
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
117 </option>
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
118 <option value="custom">Provide a custom barcodes file</option>
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
119 <!--<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>-->
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
120 </param>
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
121 <when value="repo"/>
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
122 <when value="custom">
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
123 <param name="usher_barcodes" type="data" format="csv" label="UShER barcodes file"/>
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
124 </when>
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
125 <!--<when value="update" />-->
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
126 </conditional>
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
127 <param argument="--meta" type="data" format="json" optional="true"
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
128 label="Custom lineage metadata file"
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
129 help="For additional flexibility and reproducibility of analyses, a custom lineage-to-contellation mapping metadata file can be provided."/>
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
130 <param argument="--eps" type="float" optional="true"
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
131 label="Minimum lineage abundance tp include"
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
132 help="e.g. 0.0001."/>
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
133 <param argument="--confirmedonly" type="boolean" truevalue="--confirmedonly" falsevalue=""
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
134 checked="false"
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
135 label="Remove unconfirmed lineages from the analysis"
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
136 help="If the UShER tree includes proposed lineages, the --confirmedonly flag removes unconfirmed lineages from the analysis."/>
1
a09398bc953a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
iuc
parents: 0
diff changeset
137 <param argument="--wgisaid" type="boolean" truevalue="--wgisaid" falsevalue=""
a09398bc953a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
iuc
parents: 0
diff changeset
138 checked="false"
a09398bc953a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
iuc
parents: 0
diff changeset
139 label="Use larger library with non-public lineages"
a09398bc953a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
iuc
parents: 0
diff changeset
140 help="Allows to use larger UShER barcodes library extended with GISAID non-public lineages"/>
a09398bc953a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
iuc
parents: 0
diff changeset
141 </xml>
a09398bc953a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
iuc
parents: 0
diff changeset
142 <xml name="plot_lineages">
a09398bc953a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
iuc
parents: 0
diff changeset
143 <param argument="--lineages" type="boolean" truevalue="--lineages" falsevalue=""
a09398bc953a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
iuc
parents: 0
diff changeset
144 checked="false" label="Use lineage specific breakdown"/>
a09398bc953a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
iuc
parents: 0
diff changeset
145 </xml>
a09398bc953a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
iuc
parents: 0
diff changeset
146 <xml name="plot_mincov">
a09398bc953a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
iuc
parents: 0
diff changeset
147 <param argument="--mincov" type="float" min="0" max="100" value="60"
a09398bc953a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
iuc
parents: 0
diff changeset
148 label="Minimum genome coverage"
a09398bc953a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
iuc
parents: 0
diff changeset
149 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
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
150 </xml>
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
151 <token name="@HELP_HEADER@"><![CDATA[
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
152 What it does
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
153 ============
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
154
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
155 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).
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
156
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
157 General information
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
158 ===================
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
159
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
160 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.
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
161
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
162 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.
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
163 ]]></token>
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
164 <xml name="citations">
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
165 <citations>
1
a09398bc953a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
iuc
parents: 0
diff changeset
166 <citation type="doi">10.1038/s41586-022-05049-6</citation>
0
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
167 </citations>
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
168 </xml>
dda5772507b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
169 </macros>