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author itaxotools
date Sun, 29 Jan 2023 16:24:30 +0000
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1 <tool id="ASAP" name="ASAP" version="0.2.1+galaxy0" python_template_version="3.8" profile="22.05">
2 <description>Agglomerate Specimens by Automatic Processing</description>
3 <requirements></requirements>
4 <command detect_errors="exit_code"><![CDATA[
5 cp '$input1' '${os.path.splitext(os.path.basename($input1.name))[0]}' &&
6 $__tool_directory__/asap
7 #if $opts.isMega:
8 -m
9 #end if
10 #if $opts.output_all:
11 -a
12 #end if
13 #* broken
14 #if $distance=="-d 0":
15 -t $opts.transition
16 #end if
17 *#
18 $distance
19 #if $opts.replicates!=1000:
20 -r $opts.replicates
21 #end if
22 #if $opts.results!=10:
23 -n $opts.results
24 #end if
25 #if $opts.pvalue!=0.001:
26 -b $opts.pvalue
27 #end if
28 #* broken
29
30 #if $seed!=-1:
31 -x $opts.seed
32 #end if
33
34 *#
35
36 '${os.path.splitext(os.path.basename($input1.name))[0]}'
37 #if $spart_only:
38 -u &>'$output1'&&
39 #else
40 &>'$output1'&&
41 #end if
42 cp *.spart '$output2' &&
43 cp *.xml '$output3'
44
45 #*
46 #if $spart_only:
47 &&
48 rm -f *.txt *.svg *.all
49 #end if
50 *#
51
52 ]]></command>
53 <inputs>
54 <param type="data" name="input1" label="Source file" format="fasta,phylip,csv" />
55 <param name="spart_only" type="boolean" label="Only spart files" checked="true" help="Only the spart output is collected" />
56 <param name="distance" type="select" label="Distance">
57 <option value="-d 1">Jukes-Cantor</option>
58 <option value="-d 0">Kimura-2P</option>
59 <option value="-d 3">simple distance</option>
60 </param>
61 <section name="opts" title="Advanced options">
62 <param name="output_all" type="boolean" label="Output all files" help="all probabilities, tree and graph files (default only graph files and 10 best agglomerations)" />
63 <param name="transition" type="float" label="transition/transversion" value="2" help="(not used/broken) for Kimura (default is 2) " />
64 <param name="replicates" type="integer" label="number of replicates" value="1000" help="for statistical tests (default is 10^3) " />
65 <param name="pvalue" type="float" label="Pvalue" value="0.001" help="Threshold for results to be reported (default is 0.001)"/>
66 <param name="seed" type="float" label="Seed" value="-1" help="(not used/broken) Fixed seed for random generator (default -1 = random seed)"/>
67 <param name="results" type="integer" label="number of results" value="10" help="best results to be reported (default is 10)" />
68 <param name="isMega" type="boolean" label="MEGA distance file" help="see MEGA information below" />
69
70 </section>
71 </inputs>
72 <outputs>
73 <data name="output1" label="${os.path.splitext(os.path.basename($input1.name))[0]}.log" format="txt">
74 <filter> spart_only is False</filter>
75 </data>
76 <data name="output2" label="${os.path.splitext(os.path.basename($input1.name))[0]}.spart" format="spart"/>
77 <data name="output3" label="${os.path.splitext(os.path.basename($input1.name))[0]}.xml" format="xml"/>
78 <data name="report" label="ASAP: ${os.path.splitext($input1.name)[0]}" format="svg" metadata_source="$input1">
79 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.svg" ext="svg" visible="true" />
80 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.csv" ext="csv" visible="true" />
81 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" ext="txt" visible="true" />
82 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.all" ext="tsv" visible="true" />
83 <discover_datasets pattern="partition" ext="txt" visible="true" />
84 <filter> spart_only is False</filter>
85 </data>
86 </outputs>
87 <tests>
88 <test>
89 <param name="input1" value="ASAP_examplefile1_LophiotomaCOI_iTaxoTools_0_1.fas"/>
90 <param name="replicates" value="1000"/>
91 <param name="results" value="10"/>
92 <param name="distance" value="-d 1"/>
93 <param name="spart_only" value="false"/>
94 <param name="output_all" value="false"/>
95 <output name="output1">
96 <assert_contents>
97 <has_text text="asap has finished building and testing all partitions"/>
98 </assert_contents>
99 </output>
100 </test>
101 </tests>
102
103
104
105 <help><![CDATA[
106 **About ASAP:**
107
108 *This Galaxy version is based on the ASAP version from October 2022.*
109
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.*
111
112 Standalone executables with graphical user interface of the newest version of ASAP are available for Windows and Mac from:
113
114 http://itaxotools.org/
115
116 https://github.com/iTaxoTools/iTaxoTools-Executables/releases
117
118 For detailed instructions on the use of ASAP and interpretation of results, see the iTaxoTools manual available at:
119 http://itaxotools.org/
120
121
122 **Source files:**
123 ASAP accepts three kinds of source files:
124
125 - fasta alignment
126 - phylip distance file
127 - MEGA distance file (see MEGA information below)
128
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.*
130
131 **Purpose and results of ASAP analyses:**
132
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.
134 Each species partition consists of various subsets of individuals (sequences) that can be considered as primary species hypotheses.
135
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).*
137
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.*
139
140 **Output:**
141
142 ASAP outputs a variety of files:
143
144 - Several graphs in SVG format. These cannot be visualized in Galaxy, but can be downloaded and opened in a browser or graphics program.
145 - A log file.
146 - The calculated species partitions in SPART and SPART-XML format (Miralles et al. 2021)
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).
148
149
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.*
151
152 ]]>
153 </help>
154 <citations>
155 <citation type="doi">
156 10.1111/1755-0998.13470
157 </citation>
158 <citation type="doi">
159 10.1111/1755-0998.13281
160 </citation>
161 <citation type="doi">
162 10.11646/megataxa.6.2.1
163 </citation>
164 </citations>
165 </tool>