Mercurial > repos > itaxotools > asap

annotate ASAP.xml @ 0:33ffef234008 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
author itaxotools
date Sun, 29 Jan 2023 16:24:30 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
1 <tool id="ASAP" name="ASAP" version="0.2.1+galaxy0" python_template_version="3.8" profile="22.05">
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
2 <description>Agglomerate Specimens by Automatic Processing</description>
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
3 <requirements></requirements>
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
4 <command detect_errors="exit_code"><![CDATA[
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
5 cp '$input1' '${os.path.splitext(os.path.basename($input1.name))[0]}' &&
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
6 $__tool_directory__/asap
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
7 #if $opts.isMega:
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
8 -m
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
9 #end if
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
10 #if $opts.output_all:
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
11 -a
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
12 #end if
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
13 #* broken
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
14 #if $distance=="-d 0":
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
15 -t $opts.transition
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
16 #end if
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
17 *#
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
18 $distance
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
19 #if $opts.replicates!=1000:
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
20 -r $opts.replicates
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
21 #end if
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
22 #if $opts.results!=10:
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
23 -n $opts.results
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
24 #end if
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
25 #if $opts.pvalue!=0.001:
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
26 -b $opts.pvalue
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
27 #end if
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
28 #* broken
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
29
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
30 #if $seed!=-1:
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
31 -x $opts.seed
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
32 #end if
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
33
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
34 *#
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
35
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
36 '${os.path.splitext(os.path.basename($input1.name))[0]}'
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
37 #if $spart_only:
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
38 -u &>'$output1'&&
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
39 #else
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
40 &>'$output1'&&
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
41 #end if
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
42 cp *.spart '$output2' &&
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
43 cp *.xml '$output3'
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
44
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
45 #*
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
46 #if $spart_only:
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
47 &&
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
48 rm -f *.txt *.svg *.all
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
49 #end if
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
50 *#
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
51
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
52 ]]></command>
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
53 <inputs>
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
54 <param type="data" name="input1" label="Source file" format="fasta,phylip,csv" />
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
55 <param name="spart_only" type="boolean" label="Only spart files" checked="true" help="Only the spart output is collected" />
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
56 <param name="distance" type="select" label="Distance">
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
57 <option value="-d 1">Jukes-Cantor</option>
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
58 <option value="-d 0">Kimura-2P</option>
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
59 <option value="-d 3">simple distance</option>
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
60 </param>
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
61 <section name="opts" title="Advanced options">
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
62 <param name="output_all" type="boolean" label="Output all files" help="all probabilities, tree and graph files (default only graph files and 10 best agglomerations)" />
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
63 <param name="transition" type="float" label="transition/transversion" value="2" help="(not used/broken) for Kimura (default is 2) " />
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
64 <param name="replicates" type="integer" label="number of replicates" value="1000" help="for statistical tests (default is 10^3) " />
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
65 <param name="pvalue" type="float" label="Pvalue" value="0.001" help="Threshold for results to be reported (default is 0.001)"/>
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
66 <param name="seed" type="float" label="Seed" value="-1" help="(not used/broken) Fixed seed for random generator (default -1 = random seed)"/>
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
67 <param name="results" type="integer" label="number of results" value="10" help="best results to be reported (default is 10)" />
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
68 <param name="isMega" type="boolean" label="MEGA distance file" help="see MEGA information below" />
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
69
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
70 </section>
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
71 </inputs>
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
72 <outputs>
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
73 <data name="output1" label="${os.path.splitext(os.path.basename($input1.name))[0]}.log" format="txt">
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
74 <filter> spart_only is False</filter>
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
75 </data>
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
76 <data name="output2" label="${os.path.splitext(os.path.basename($input1.name))[0]}.spart" format="spart"/>
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
77 <data name="output3" label="${os.path.splitext(os.path.basename($input1.name))[0]}.xml" format="xml"/>
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
78 <data name="report" label="ASAP: ${os.path.splitext($input1.name)[0]}" format="svg" metadata_source="$input1">
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
79 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.svg" ext="svg" visible="true" />
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
80 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.csv" ext="csv" visible="true" />
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
81 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" ext="txt" visible="true" />
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
82 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.all" ext="tsv" visible="true" />
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
83 <discover_datasets pattern="partition" ext="txt" visible="true" />
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
84 <filter> spart_only is False</filter>
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
85 </data>
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
86 </outputs>
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
87 <tests>
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
88 <test>
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
89 <param name="input1" value="ASAP_examplefile1_LophiotomaCOI_iTaxoTools_0_1.fas"/>
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
90 <param name="replicates" value="1000"/>
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
91 <param name="results" value="10"/>
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
92 <param name="distance" value="-d 1"/>
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
93 <param name="spart_only" value="false"/>
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
94 <param name="output_all" value="false"/>
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
95 <output name="output1">
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
96 <assert_contents>
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
97 <has_text text="asap has finished building and testing all partitions"/>
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
98 </assert_contents>
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
99 </output>
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
100 </test>
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
101 </tests>
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
102
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
103
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
104
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
105 <help><![CDATA[
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
106 **About ASAP:**
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
107
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
108 *This Galaxy version is based on the ASAP version from October 2022.*
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
109
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
110 *Notes on Galaxy wrapper: Developed by F. Fischell in the framework of the iTaxoTools project in 2022/2023. Only tested for fasta alignment files. Transition and seed parameters are not currently supported. Tamura-Nei distance calculation is either really slow or broken, we recommend not using it.*
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
111
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
112 Standalone executables with graphical user interface of the newest version of ASAP are available for Windows and Mac from:
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
113
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
114 http://itaxotools.org/
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
115
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
116 https://github.com/iTaxoTools/iTaxoTools-Executables/releases
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
117
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
118 For detailed instructions on the use of ASAP and interpretation of results, see the iTaxoTools manual available at:
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
119 http://itaxotools.org/
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
120
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
121
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
122 **Source files:**
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
123 ASAP accepts three kinds of source files:
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
124
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
125 - fasta alignment
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
126 - phylip distance file
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
127 - MEGA distance file (see MEGA information below)
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
128
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
129 *Note: this Galaxy version has only been tested with fasta alignments which we assume are the most common input files used. Refer to the standalone version or the ASAP website if you experience problems with other kinds of input files in the Galaxy version.*
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
130
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
131 **Purpose and results of ASAP analyses:**
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
132
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
133 ASAP is a program for species delimitation that uses genetic distances derived from single-locus DNA sequence alignments to calculate species partitions. ASAP starts from genetic distances calculated between pairs of sequences, and successively groups them, first grouping the sequences with the least genetic distance, until all the sequences are clustered in a single group (i.e. following a hierarchical clustering approach). At each step where a new grouping occurs, ASAP will consider the corresponding partition and calculate a score, that is a combination of the probability of panmixia and the width of the barcode gap: the lower the score, the better the partition.
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
134 Each species partition consists of various subsets of individuals (sequences) that can be considered as primary species hypotheses.
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
135
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
136 *Note 1: ASAP results should not be used to draw final taxonomic conclusions; primary species hypotheses derived from an ASAP analysis should always be confronted with additional lines of evidence, and should be used for proposing changes in the taxonomy of a group of organisms only if confirmed by such additional evidence (secondary species hypotheses).*
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
137
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
138 *Note 2: Partitions can be ranked according to ASAP scores (the lowest score marks the best partition) but depending on other lines of evidence, users may favor/select any of the other partitions.*
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
139
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
140 **Output:**
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
141
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
142 ASAP outputs a variety of files:
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
143
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
144 - Several graphs in SVG format. These cannot be visualized in Galaxy, but can be downloaded and opened in a browser or graphics program.
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
145 - A log file.
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
146 - The calculated species partitions in SPART and SPART-XML format (Miralles et al. 2021)
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
147 - Separate text and table files for each species partition, with information on the assignment of individuals to subsets, andprobabilities and ASAP scores (the lowest ASAP score marks the best partition).
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
148
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
149
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
150 *Note: By default, the Galaxy version only outputs SPART and SPART-XML files to avoid cluttering the results panel with too many files. Change the sliding button for additional output. For additional detailed output and settings, use Advanced Options.*
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
151
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
152 ]]>
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
153 </help>
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
154 <citations>
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
155 <citation type="doi">
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
156 10.1111/1755-0998.13470
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
157 </citation>
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
158 <citation type="doi">
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
159 10.1111/1755-0998.13281
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
160 </citation>
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
161 <citation type="doi">
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
162 10.11646/megataxa.6.2.1
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
163 </citation>
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
164 </citations>
33ffef234008 planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
itaxotools
parents:
diff changeset
165 </tool>