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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastga commit 6504da2141da78f7cadb90a2a00e8744b1e0377a
author iuc
date Fri, 20 Feb 2026 07:47:05 +0000
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1 <tool id="fastga" name="FastGA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>align whole genomes</description>
3 <macros>
4 <import>fastga_macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[
8 ## FastGA directly string matches the file extensions
9 ## symlinks are used to bypass that restriction
10 ln -s '$input1' 'input1.${input1.ext}' &&
11 ln -s '$input2' 'input2.${input2.ext}' &&
12 FastGA
13 '${output_settings.out.format}'
14 #if str( $output_settings.out.format ) == "-paf":
15 #if str( $output_settings.out.cigar_string ) != "no":
16 '${output_settings.out.cigar_string}'
17 #end if
18 #if str( $output_settings.out.cs_string ) != "no":
19 '${output_settings.out.cs_string}'
20 #end if
21 #end if
22 $use_soft_mask
23 $use_sym_seeding
24 -f${adaptive_seed_count_cutoff}
25 -c${minimum_seed_coverage}
26 -s${new_seed_threshold}
27 -l${minimum_alignment_length}
28 -i${minimum_alignment_identity}
29 'input1.${input1.ext}' 'input2.${input2.ext}'
30 #if str( $output_settings.out.format ) != "-1:output":
31 > output
32 #end if
33 ]]></command>
34 <inputs>
35 <param name="input1" type="data" label="FASTA sequence" format="fasta,fasta.gz"/>
36 <param name="input2" type="data" label="FASTA sequence" format="fasta,fasta.gz"/>
37 <param name="use_soft_mask" type="boolean" label="Use soft mask information if available (-M)" checked="false" truevalue="-M" falsevalue=""/>
38 <param name="use_sym_seeding" type="boolean" label="Use symmetric seeding (-S)" checked="false" truevalue="-S" falsevalue=""/>
39 <param name="adaptive_seed_count_cutoff" type="integer" label="Adaptive seed count cutoff (-f)" value="10" min="0" max="255"/>
40 <param name="minimum_seed_coverage" type="integer" label="Minimum seed chain coverage in both genomes (-c)" value="85" min="0"/>
41 <param name="new_seed_threshold" type="integer" label="Threshold for starting a new seed chain (-s)" value="1000" min="0"/>
42 <param name="minimum_alignment_length" type="integer" label="Minimum alignment length (-l)" value="100" min="0"/>
43 <param name="minimum_alignment_identity" type="float" label="Minimum alignment identity (-i)" value="0.7" min="0.55" max="0.99999999999999994"/>
44 <section name="output_settings" expanded="False" title="Output">
45 <conditional name="out">
46 <param name="format" type="select" label="Specify the output format">
47 <option value="-paf" selected="true">paf (-paf)</option>
48 <option value="-psl">psl (-psl)</option>
49 <option value="-1:output">1aln (-1)</option>
50 </param>
51 <when value="-paf">
52 <param name="cigar_string" type="select" label="Use CIGAR string?">
53 <option value="no" selected="true">No CIGAR string</option>
54 <option value="-pafx">CIGAR string with X's (-pafx)</option>
55 <option value="-pafm">CIGAR string with ='s (-pafm)</option>
56 </param>
57 <param name="cs_string" type="select" label="Use CS string?">
58 <option value="no" selected="true">No CS string</option>
59 <option value="-pafs">CS string in short form (-pafs)</option>
60 <option value="-pafS">CS string in long form (-pafS)</option>
61 </param>
62 </when>
63 <when value="-psl"/>
64 <when value="-1:output"/>
65 </conditional>
66 </section>
67 </inputs>
68 <outputs>
69 <data name="output" format="paf" from_work_dir="output">
70 <change_format>
71 <when input="output_settings.out.format" value="-paf" format="paf"/>
72 <when input="output_settings.out.format" value="-psl" format="psl"/>
73 <when input="output_settings.out.format" value="-1:output" format="txt"/>
74 </change_format>
75 </data>
76 </outputs>
77 <tests>
78 <test expect_num_outputs="1">
79 <param name="input1" value="chrM_hg38.fa.gz"/>
80 <param name="input2" value="chrM_mm39.fa.gz"/>
81 <section name="output_settings">
82 <conditional name="out">
83 <param name="format" value="-paf"/>
84 </conditional>
85 </section>
86 <output name="output" file="chrM_HGvMM.paf" ftype="paf"/>
87 </test>
88 <test expect_num_outputs="1">
89 <param name="input1" value="chrM_hg38.fa.gz"/>
90 <param name="input2" value="chrM_mm39.fa.gz"/>
91 <section name="output_settings">
92 <conditional name="out">
93 <param name="format" value="-psl"/>
94 </conditional>
95 </section>
96 <output name="output" file="chrM_HGvMM.psl" ftype="psl"/>
97 </test>
98 <test expect_num_outputs="1">
99 <param name="input1" value="chrM_hg38.fa.gz"/>
100 <param name="input2" value="chrM_mm39.fa.gz"/>
101 <section name="output_settings">
102 <conditional name="out">
103 <param name="format" value="-paf"/>
104 <param name="cigar_string" value="-pafx"/>
105 </conditional>
106 </section>
107 <output name="output" file="pafx.paf" ftype="paf"/>
108 </test>
109 <test expect_num_outputs="1">
110 <param name="input1" value="chrM_hg38.fa.gz"/>
111 <param name="input2" value="chrM_mm39.fa.gz"/>
112 <param name="use_soft_mask" value="True"/>
113 <param name="use_sym_seeding" value="True"/>
114 <param name="adaptive_seed_count_cutoff" value="9"/>
115 <param name="minimum_seed_coverage" value="100"/>
116 <param name="new_seed_threshold" value="750"/>
117 <param name="minimum_alignment_length" value="90"/>
118 <param name="minimum_alignment_identity" value="0.6"/>
119 <section name="output_settings">
120 <conditional name="out">
121 <param name="format" value="-paf"/>
122 <param name="cigar_string" value="-pafm"/>
123 <param name="cs_string" value="-pafS"/>
124 </conditional>
125 </section>
126 <output name="output" file="pafmS_options.paf" ftype="paf"/>
127 </test>
128 <test expect_num_outputs="1">
129 <param name="input1" value="chrM_hg38.fa.gz"/>
130 <param name="input2" value="chrM_mm39.fa.gz"/>
131 <section name="output_settings">
132 <conditional name="out">
133 <param name="format" value="-1:output"/>
134 </conditional>
135 </section>
136 </test>
137 </tests>
138 <help><![CDATA[
139
140 FastGA compares two high-quality genomes and outputs a ``.1aln``, ``.paf``, or ``.psl`` file containing all local alignments found.
141
142 It is based on a novel adaptive seed finding algorithm as well as the first wave-based local aligner developed for daligner (2012).
143
144 FastGA uses a number of temporary, hidden files such as ONEcode genome databases (.1gdb) and genome indices (.gix) to achieve its high speed and space efficiency.
145
146 -----
147
148 Input
149 *****
150
151 This tool takes two ``fasta`` or ``fasta.gz`` input files to align.
152
153 It is a core assumption of FastGA that the input genomes are nearly complete and are of high quality (Q40 or better).
154
155 FastGA is not commutative by default (see *Use symmetric seeding* below).
156
157 -----
158
159 Options
160 *******
161
162 =============================== ======== =========== ===========================
163 **Option** **Flag** **Default** **Description**
164 ------------------------------- -------- ----------- ---------------------------
165 Use soft mask information -M False Use soft-masked regions if
166 present in the input FASTA
167 Use symmetric seeding -S False Enables symmetric seeding
168 (not recommended)
169 Adaptive seed count cutoff -f 10 Range: 0–255
170 Minimum seed chain coverage -c 85 Range: ≥ 0
171 Threshold for new seed chain -s 1000 Range: ≥ 0
172 Minimum alignment length -l 100 Range: ≥ 0
173 Minimum alignment identity -i 0.7 Range: 0.55–<1.0
174 =============================== ======== =========== ===========================
175
176 -----
177
178 Output
179 ******
180
181 **Output format**
182
183 ========== ======== =========== ===============================
184 **Format** **Flag** **Default** **Notes**
185 ---------- -------- ----------- -------------------------------
186 PAF -paf Yes
187 PSL -psl No
188 1ALN -1 No Output is nondeterministic
189 ========== ======== =========== ===============================
190
191 **CIGAR string options**
192
193 (available only when output format is PAF)
194
195 ============================== ======== ===========
196 **Option** **Flag** **Default**
197 ------------------------------ -------- -----------
198 No CIGAR string Yes
199 CIGAR string with X's -pafx No
200 CIGAR string with ='s -pafm No
201 ============================== ======== ===========
202
203 **CS string options**
204
205 (available only when output format is PAF)
206
207 ============================== ======== ===========
208 **Option** **Flag** **Default**
209 ------------------------------ -------- -----------
210 No CS string Yes
211 CS string (short form) -pafs No
212 CS string (long form) -pafS No
213 ============================== ======== ===========
214
215 ]]></help>
216 <expand macro="citations" />
217 </tool>