Mercurial > repos > iuc > freyja_aggregate_plot

annotate macros.xml @ 1:1f89eeba299a 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 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
author iuc
date Fri, 07 Jul 2023 05:51:06 +0000
parents 0ceb9fb0f4ce
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
0ceb9fb0f4ce 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"?>
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
2 <macros>
1
1f89eeba299a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
iuc
parents: 0
diff changeset
3 <token name="@TOOL_VERSION@">1.4.4</token>
0
0ceb9fb0f4ce 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>
0ceb9fb0f4ce 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>
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
6 <xml name="biotools">
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
7 <xrefs>
0ceb9fb0f4ce 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>
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
9 </xrefs>
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
10 </xml>
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
11 <xml name="requirements">
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
12 <requirements>
0ceb9fb0f4ce 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>
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
14 <yield/>
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
15 </requirements>
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
16 </xml>
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
17 <xml name="version">
0ceb9fb0f4ce 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>
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
19 </xml>
0ceb9fb0f4ce 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[
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
21 #if $usher_update_option.choice == 'update'
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
22 freyja update &&
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
23 #end if
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
24 ]]></token>
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
25 <token name="@PREPROCESS_VCF_INPUT@"><![CDATA[
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
26 ln -s '$variants_file' 'variants_file.vcf' &&
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
27 ]]></token>
0ceb9fb0f4ce 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[
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
29 #if $variants_file.ext == 'vcf'
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
30 'variants_file.vcf'
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
31 #else
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
32 '$variants_file'
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
33 #end if
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
34 '$depth_file'
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
35 #if $eps
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
36 --eps '${eps}'
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
37 #end if
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
38 #if $meta
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
39 --meta '${meta}'
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
40 #end if
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
41 $confirmedonly
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
42 ]]></token>
0ceb9fb0f4ce 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[
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
44 #if $usher_update_option.choice == 'custom'
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
45 --barcodes '${usher_update_option.usher_barcodes}'
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
46 #end if
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
47 ]]></token>
0ceb9fb0f4ce 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[
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
49 echo '${plot_format.plot_title}' > plot_title.txt &&
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
50 echo '${plot_format.plot_intro}' > plot_intro.txt &&
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
51 freyja dash
1
1f89eeba299a 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
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
53 #if $need_aggregation.choice == 'no'
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
54 '$tsv_aggregated'
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
55 #else
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
56 'aggregated.tsv'
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
57 #end if
0ceb9fb0f4ce 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'
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
59 plot_title.txt
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
60 plot_intro.txt
0ceb9fb0f4ce 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
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
62 ]]></token>
0ceb9fb0f4ce 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[
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
64 freyja plot
1
1f89eeba299a 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
1f89eeba299a 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
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
67 #if $need_aggregation.choice == 'no'
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
68 '$tsv_aggregated'
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
69 #else
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
70 'aggregated.tsv'
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
71 #end if
0ceb9fb0f4ce 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
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
73 #if $plot_format.csv_meta
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
74 --times '${plot_format.csv_meta}'
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
75 #end if
0ceb9fb0f4ce 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'
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
77 --interval MS
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
78 #else
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
79 --interval D
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
80 --windowsize 70
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
81 #end if
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
82 ]]></token>
0ceb9fb0f4ce 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[
0ceb9fb0f4ce 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'
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
85 @DASH_COMMAND@
0ceb9fb0f4ce 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'
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
87 freyja plot
1
1f89eeba299a 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
1f89eeba299a 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
0ceb9fb0f4ce 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'
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
91 $tsv_aggregated
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
92 #else
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
93 aggregated.tsv
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
94 #end if
0ceb9fb0f4ce 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
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
96 #if $plot_format.need_metadata.choice == 'yes'
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
97 --times '${plot_format.need_metadata.csv_meta}'
0ceb9fb0f4ce 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'
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
99 --interval MS
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
100 #else
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
101 --interval D
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
102 --windowsize 70
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
103 #end if
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
104 #end if
0ceb9fb0f4ce 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'
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
106 @DASH_COMMAND@ &&
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
107 @PLOT_COMMAND@
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
108 #end if
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
109 ]]></token>
0ceb9fb0f4ce 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">
0ceb9fb0f4ce 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"/>
0ceb9fb0f4ce 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">
0ceb9fb0f4ce 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"
0ceb9fb0f4ce 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.">
0ceb9fb0f4ce 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
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
116 outdated)
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
117 </option>
0ceb9fb0f4ce 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>
0ceb9fb0f4ce 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>-->
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
120 </param>
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
121 <when value="repo"/>
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
122 <when value="custom">
0ceb9fb0f4ce 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"/>
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
124 </when>
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
125 <!--<when value="update" />-->
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
126 </conditional>
0ceb9fb0f4ce 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"
0ceb9fb0f4ce 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"
0ceb9fb0f4ce 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."/>
0ceb9fb0f4ce 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"
0ceb9fb0f4ce 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"
0ceb9fb0f4ce 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."/>
0ceb9fb0f4ce 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=""
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
134 checked="false"
0ceb9fb0f4ce 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"
0ceb9fb0f4ce 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
1f89eeba299a 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=""
1f89eeba299a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
iuc
parents: 0
diff changeset
138 checked="false"
1f89eeba299a 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"
1f89eeba299a 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"/>
1f89eeba299a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
iuc
parents: 0
diff changeset
141 </xml>
1f89eeba299a 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">
1f89eeba299a 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=""
1f89eeba299a 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"/>
1f89eeba299a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
iuc
parents: 0
diff changeset
145 </xml>
1f89eeba299a 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">
1f89eeba299a 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"
1f89eeba299a 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"
1f89eeba299a 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
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
150 </xml>
0ceb9fb0f4ce 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[
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
152 What it does
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
153 ============
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
154
0ceb9fb0f4ce 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).
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
156
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
157 General information
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
158 ===================
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
159
0ceb9fb0f4ce 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.
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
161
0ceb9fb0f4ce 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.
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
163 ]]></token>
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
164 <xml name="citations">
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
165 <citations>
1
1f89eeba299a 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
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
167 </citations>
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
168 </xml>
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
parents:
diff changeset
169 </macros>