Mercurial > repos > iuc > ppanggolin_rarefaction

annotate ppanggolin_rarefaction.xml @ 1:f484ad86a4f2 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/main/tools/ppanggolin commit 29098ae57dcc42db8f9adf321d31ed37fb999d17
author iuc
date Mon, 24 Nov 2025 12:54:50 +0000
parents d848a49b3303
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
1 <tool id="ppanggolin_rarefaction" name="PPanGGOLiN rarefaction" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
2 <description>computes the rarefaction curve of the pangenome</description>
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
3 <macros>
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
4 <import>macros.xml</import>
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
5 </macros>
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
6 <expand macro="xrefs"/>
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
7 <expand macro="requirements"/>
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
8
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
9 <command detect_errors="exit_code"><![CDATA[
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
10 mkdir -p ./tmp_ppanggolin/rarefaction &&
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
11 mkdir -p ./tmp_ppanggolin/tmpdir_rarefaction &&
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
12
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
13 ppanggolin rarefaction
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
14 --pangenome '$pangenome_h5'
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
15 --output ./tmp_ppanggolin/rarefaction
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
16 --tmpdir ./tmp_ppanggolin/tmpdir_rarefaction
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
17 --force
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
18 --cpu "\${GALAXY_SLOTS:-4}"
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
19 --disable_prog_bar
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
20
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
21 --depth $depth
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
22 --min $min
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
23 --max $max
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
24
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
25 #if str($nb_of_partitions) != "":
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
26 --nb_of_partitions $nb_of_partitions
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
27 #end if
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
28
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
29 #if "output_rarefaction_csv" in $advanced_pangenome_optional_files:
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
30 && cat ./tmp_ppanggolin/rarefaction/rarefaction.csv > '${rarefaction_csv}'
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
31 #end if
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
32 #if "output_rarefaction_parameters_csv" in $advanced_pangenome_optional_files:
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
33 && cat ./tmp_ppanggolin/rarefaction/rarefaction_parameters.csv > '${rarefaction_parameters_csv}'
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
34 #end if
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
35 && cat ./tmp_ppanggolin/rarefaction/rarefaction_curve.html > '${rarefaction_curve_html}'
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
36
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
37 ]]></command>
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
38
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
39 <inputs>
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
40
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
41 <expand macro="inputs_pangenome"/>
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
42
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
43 <param argument="--depth" type="integer" value="30" min="1" max="100" label="The number of sampling for each genome" help="Default=30 ; min=1 ; max=100. Warning: if this value is greater than 30, the computation will be VERY intensive and it will take a long time.">
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
44 </param>
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
45
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
46 <param argument="--min" type="integer" value="1" min="1" max="499" label="The minimal number of genomes in a sample" help="Default=1 ; min=1 ; max=499. The min value must be lower than the max value.">
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
47 </param>
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
48
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
49 <param argument="--max" type="integer" value="100" min="1" max="500" label="The maximal number of genomes in a sample" help="Default=1 ; min=1 ; max=500. The min value must be lower than the max value. Warning: if if this value is greater than 100, the computation will be VERY intensive and it will take a long time.">
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
50 </param>
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
51
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
52 <expand macro="inputs_nb_of_partitions"/>
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
53
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
54 <param name="advanced_pangenome_optional_files" type="select" label="Add the following output files in the Galaxy history" multiple="true" optional="true" display="checkboxes" >
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
55 <option value="output_rarefaction_csv" selected="true">Rarefaction data in tabular format (csv)</option>
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
56 <option value="output_rarefaction_parameters_csv" selected="true">Rarefaction parameters in tabular format (csv)</option>
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
57 </param>
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
58
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
59 </inputs>
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
60
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
61 <outputs>
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
62
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
63 <data name="rarefaction_csv" format="csv" label="PPanGGOLiN rarefaction on ${on_string}: Rarefaction data (csv)" >
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
64 <filter>advanced_pangenome_optional_files and "output_rarefaction_csv" in advanced_pangenome_optional_files</filter>
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
65 </data>
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
66 <data name="rarefaction_parameters_csv" format="csv" label="PPanGGOLiN rarefaction on ${on_string}: Rarefaction parameters (csv)" >
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
67 <filter>advanced_pangenome_optional_files and "output_rarefaction_parameters_csv" in advanced_pangenome_optional_files</filter>
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
68 </data>
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
69
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
70 <data name="rarefaction_curve_html" format="html" label="PPanGGOLiN rarefaction on ${on_string}: Rarefaction curve" />
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
71
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
72 </outputs>
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
73
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
74 <tests>
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
75 <test expect_num_outputs="3">
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
76 <param name="pangenome_h5" value="h5/test_data.h5" ftype="h5"/>
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
77 <param name="depth" value="30"/>
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
78 <param name="min" value="1"/>
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
79 <param name="max" value="100"/>
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
80 <output name="rarefaction_csv" >
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
81 <assert_contents>
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
82 <has_size value="4045" delta="100"/>
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
83 </assert_contents>
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
84 </output>
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
85 <output name="rarefaction_parameters_csv" >
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
86 <assert_contents>
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
87 <has_size value="324" delta="50"/>
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
88 </assert_contents>
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
89 </output>
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
90 <output name="rarefaction_curve_html" >
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
91 <assert_contents>
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
92 <has_size value="4575692" delta="100"/>
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
93 </assert_contents>
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
94 </output>
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
95 </test>
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
96 </tests>
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
97
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
98 <help><![CDATA[
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
99
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
100 PPanGGOLiN_ (Gautreau et al. 2020) is a software suite used to create and manipulate prokaryotic pangenomes from a set of either assembled
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
101 genomic DNA sequences or provided genome annotations. PPanGGOLiN builds pangenomes through a graphical model and a statistical method to partition gene
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
102 families in persistent, shell and cloud genomes. It integrates both information on protein-coding genes and their genomic neighborhood to build a graph
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
103 of gene families where each node is a gene family, and each edge is a relation of genetic contiguity.
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
104
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
105 The `ppanggolin rarefaction` command generates a rarefaction curve. It represents the evolution of the number of gene families for each partition as you add more genomes to the pangenome. It has been used a lot in the literature as an indicator of the diversity that you are missing with your dataset on your taxonomic group (Tettelin et al., 2005). The idea is that if at some point when you keep adding genomes to your pangenome you do not add any more gene families, you might have access to your entire taxonomic group’s diversity. On the contrary, if you are still adding a lot of genes you may be still missing a lot of gene families.
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
106
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
107 There are 8 partitions represented. For each of the partitions, there are multiple representations of the observed data. You can find the observed means, medians, 1st and 3rd quartiles of the number of gene families per number of genome used. You can also find the best fitting of the data by the Heaps’ law, which is usually used to represent this evolution of the diversity in terms of gene families in each of the partitions.
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
108
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
109 .. _PPanGGOLiN: https://github.com/labgem/PPanGGOLiN
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
110 .. _documentation: https://ppanggolin.readthedocs.io/en/latest/user/PangenomeAnalyses/pangenomeAnalyses.html#rarefaction-curve
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
111
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
112 ]]></help>
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
113
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
114 <expand macro="citation"/>
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
115
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
116 </tool>
d848a49b3303 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
iuc
parents:
diff changeset
117