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comparison abyss-pe.xml @ 7:841084c5fc46 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit e14b8554ee2a7d00b98c7cb863a07245d29ab93f"
author iuc
date Wed, 20 Oct 2021 12:50:40 +0000
parents 0e93176640ac
children 553bfe8bd0b5
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6:0e93176640ac 7:841084c5fc46
2 <description>de novo sequence assembler</description> 2 <description>de novo sequence assembler</description>
3 <xrefs> 3 <xrefs>
4 <xref type="bio.tools">abyss</xref> 4 <xref type="bio.tools">abyss</xref>
5 </xrefs> 5 </xrefs>
6 <macros> 6 <macros>
7 <token name="@TOOL_VERSION@">2.3.1</token> 7 <token name="@TOOL_VERSION@">2.3.2</token>
8 <xml name="reads_conditional"> 8 <xml name="reads_conditional">
9 <conditional name="reads"> 9 <conditional name="reads">
10 <param name="reads_selector" type="select" label="Type of paired-end datasets"> 10 <param name="reads_selector" type="select" label="Type of paired-end datasets">
11 <option value="paired">2 separate datasets</option> 11 <option value="paired">2 separate datasets</option>
12 <option value="paired_collection">1 paired dataset collection</option> 12 <option value="paired_collection">1 paired dataset collection</option>
35 <!-- In case the return code has not been set propery check stderr too --> 35 <!-- In case the return code has not been set propery check stderr too -->
36 <regex match="Error:" /> 36 <regex match="Error:" />
37 <regex match="Exception:" /> 37 <regex match="Exception:" />
38 </stdio> 38 </stdio>
39 <version_command>ABYSS --version | head -n 1</version_command> 39 <version_command>ABYSS --version | head -n 1</version_command>
40 <command> 40 <command><![CDATA[
41 abyss-pe 41 abyss-pe
42 name=abyss 42 name=abyss
43 j=\${GALAXY_SLOTS:-1} 43 j=\${GALAXY_SLOTS:-1}
44 B=\${GALAXY_MEMORY_MB:-2048}M
44 k=$k 45 k=$k
45 46
46 #if str($K) 47 #if str($K)
47 K=$K 48 K=$K
48 #end if 49 #end if
89 n=$n 90 n=$n
90 #end if 91 #end if
91 #if str($d) 92 #if str($d)
92 d=$d 93 d=$d
93 #end if 94 #end if
94 #if str($S) 95 #if $S
95 S=$S 96 S='$S'
96 #end if 97 #end if
97 #if str($N) 98 #if $N
98 N=$N 99 N='$N'
99 #end if 100 #end if
100 #if $lib_repeat 101 #if $lib_repeat
101 lib=' 102 lib='
102 #for $i in range(len($lib_repeat)) 103 #for $i in range(len($lib_repeat))
103 lib$i 104 lib$i
144 ' 145 '
145 #for $i, $v in enumerate($long_seqs) 146 #for $i, $v in enumerate($long_seqs)
146 long${i}='$v' 147 long${i}='$v'
147 #end for 148 #end for
148 #end if 149 #end if
149 </command> 150 ]]></command>
150 151
151 <inputs> 152 <inputs>
152 <repeat name="lib_repeat" title="Paired-end library" help="(lib)"> 153 <repeat name="lib_repeat" title="Paired-end library" help="(lib)">
153 <expand macro="reads_conditional" /> 154 <expand macro="reads_conditional" />
154 </repeat> 155 </repeat>
165 <param argument="E" type="integer" value="" min="0" optional="true" label="Minimum erosion k-mer coverage per strand" help="Erode bases at the ends of blunt contigs with coverage less than this value on either strand. Defaults to 1 if sqrt(median) &gt; 2 else 0" /> 166 <param argument="E" type="integer" value="" min="0" optional="true" label="Minimum erosion k-mer coverage per strand" help="Erode bases at the ends of blunt contigs with coverage less than this value on either strand. Defaults to 1 if sqrt(median) &gt; 2 else 0" />
166 <param argument="t" type="integer" value="" optional="true" label="Maximum length of blunt contigs to trim" help="Defaults to the value of k" /> 167 <param argument="t" type="integer" value="" optional="true" label="Maximum length of blunt contigs to trim" help="Defaults to the value of k" />
167 <param argument="c" type="float" value="" optional="true" label="Minimum mean k-mer coverage of a unitig" help="Defaults to sqrt(median)" /> 168 <param argument="c" type="float" value="" optional="true" label="Minimum mean k-mer coverage of a unitig" help="Defaults to sqrt(median)" />
168 <param argument="b" type="integer" value="" optional="true" label="Maximum length of a bubble (in bp)" help="abyss-pe has two bubble popping stages. The default limits are 3*k bp for ABYSS and 10000 bp for PopBubbles" /> 169 <param argument="b" type="integer" value="" optional="true" label="Maximum length of a bubble (in bp)" help="abyss-pe has two bubble popping stages. The default limits are 3*k bp for ABYSS and 10000 bp for PopBubbles" />
169 <param argument="SS" type="boolean" label="Assemble in strand-specific mode" help="Requires that all libraries are strand-specific RNA-Seq libraries. Assumes that the first read in a read pair is reveresed with respect to the transcripts sequenced" /> 170 <param argument="SS" type="boolean" label="Assemble in strand-specific mode" help="Requires that all libraries are strand-specific RNA-Seq libraries. Assumes that the first read in a read pair is reveresed with respect to the transcripts sequenced" />
170 <param argument="m" type="integer" value="50" min="0" optional="true" label="Minimum overlap of two unitigs (in bp)" /> 171 <param argument="m" type="integer" value="" min="0" optional="true" label="Minimum overlap of two unitigs (in bp)" help="Defaults to 0 (interpreted as k - 1) if mate-pair libraries are provided or if k&lt;=50, otherwise 50" />
171 <param argument="p" type="float" value="0.9" optional="true" label="Minimum sequence identity of a bubble" /> 172 <param argument="p" type="float" value="0.9" optional="true" label="Minimum sequence identity of a bubble" />
172 <param argument="a" type="integer" value="2" min="0" optional="true" label="Maximum number of branches of a bubble" /> 173 <param argument="a" type="integer" value="2" min="0" optional="true" label="Maximum number of branches of a bubble" />
173 <param argument="l" type="integer" value="" min="1" optional="true" label="Minimum alignment length of a read (in bp)" help="Defaults to the value of k" /> 174 <param argument="l" type="integer" value="" min="1" optional="true" label="Minimum alignment length of a read (in bp)" help="Defaults to the value of k" />
174 <param argument="s" type="integer" value="200" min="0" optional="true" label="Minimum unitig length required for building contigs (in bp)" help="The seed length should be at least twice the value of k. If more sequence is assembled than the expected genome size, try increasing this value" /> 175 <param argument="s" type="integer" value="200" min="0" optional="true" label="Minimum unitig length required for building contigs (in bp)" help="The seed length should be at least twice the value of k. If more sequence is assembled than the expected genome size, try increasing this value" />
175 <param argument="n" type="integer" value="10" min="0" optional="true" label="Minimum number of pairs required for building contigs" /> 176 <param argument="n" type="integer" value="10" min="0" optional="true" label="Minimum number of pairs required for building contigs" />
176 <param argument="d" type="integer" value="6" min="0" optional="true" label="Allowable error of a distance estimate (in bp)" /> 177 <param argument="d" type="integer" value="6" min="0" optional="true" label="Allowable error of a distance estimate (in bp)" />
177 <param argument="S" type="integer" value="" min="0" optional="true" label="Minimum contig length required for building scaffolds (in bp)" help="Defaults to the value of s" /> 178 <param argument="S" type="text" value="" label="Minimum contig size required for building scaffolds (in bp)" help="It can be an interval. Defaults to 100-5000">
178 <param argument="N" type="integer" value="" min="0" optional="true" label="Minimum number of pairs required for building scaffolds" help="Defaults to the value of n" /> 179 <validator type="regex" message="Must be a an integer or an interval">^([0-9]+(-[0-9]+)?)?$</validator>
180 </param>
181 <param argument="N" type="text" value="" label="Minimum number of pairs required for building scaffolds" help="It can be an interval. Defaults to 15-20">
182 <validator type="regex" message="Must be a an integer or an interval">^([0-9]+(-[0-9]+)?)?$</validator>
183 </param>
179 </inputs> 184 </inputs>
180 185
181 <outputs> 186 <outputs>
182 <data name="unitigs" format="fasta" label="${tool.name} on ${on_string}: unitigs" from_work_dir="abyss-unitigs.fa" /> 187 <data name="unitigs" format="fasta" label="${tool.name} on ${on_string}: unitigs" from_work_dir="abyss-unitigs.fa" />
183 <data name="contigs_outfile" format="fasta" label="${tool.name} on ${on_string}: contigs" from_work_dir="abyss-contigs.fa"> 188 <data name="contigs_outfile" format="fasta" label="${tool.name} on ${on_string}: contigs" from_work_dir="abyss-contigs.fa">
187 <filter>lib_repeat or mp_repeat</filter> 192 <filter>lib_repeat or mp_repeat</filter>
188 </data> 193 </data>
189 <data name="long_scaffolds" format="fasta" label="${tool.name} on ${on_string}: scaffolds" from_work_dir="abyss-long-scaffs.fa"> 194 <data name="long_scaffolds" format="fasta" label="${tool.name} on ${on_string}: scaffolds" from_work_dir="abyss-long-scaffs.fa">
190 <filter>long_seqs</filter> 195 <filter>long_seqs</filter>
191 </data> 196 </data>
192 <data name="bubbles" format="fasta" label="${tool.name} on ${on_string}: bubbles" from_work_dir="abyss-bubbles.fa" />
193 <data name="indels" format="fasta" label="${tool.name} on ${on_string}: indels" from_work_dir="abyss-indel.fa" /> 197 <data name="indels" format="fasta" label="${tool.name} on ${on_string}: indels" from_work_dir="abyss-indel.fa" />
194 <data name="coverage_histogram_outfile" format="tabular" label="${tool.name} on ${on_string}: coverage histogram" from_work_dir="coverage.hist" />
195 <data name="stats" format="tabular" label="${tool.name} on ${on_string}: stats" from_work_dir="abyss-stats.tab" /> 198 <data name="stats" format="tabular" label="${tool.name} on ${on_string}: stats" from_work_dir="abyss-stats.tab" />
196 </outputs> 199 </outputs>
197 200
198 <tests> 201 <tests>
199 <test> 202 <test>
206 </repeat> 209 </repeat>
207 <param name="k" value="50" /> 210 <param name="k" value="50" />
208 <output name="unitigs" file="abyss-unitigs1.fa" /> 211 <output name="unitigs" file="abyss-unitigs1.fa" />
209 <output name="contigs_outfile" file="abyss-contigs1.fa" /> 212 <output name="contigs_outfile" file="abyss-contigs1.fa" />
210 <output name="scaffolds" file="abyss-scaffolds1.fa" /> 213 <output name="scaffolds" file="abyss-scaffolds1.fa" />
211 <output name="bubbles" file="empty_file.fasta" />
212 <output name="indels" file="empty_file.fasta" /> 214 <output name="indels" file="empty_file.fasta" />
213 <output name="coverage_histogram_outfile" file="coverage1.hist" />
214 <output name="stats" file="abyss-stats1.tab" /> 215 <output name="stats" file="abyss-stats1.tab" />
215 </test> 216 </test>
216 <test> 217 <test>
217 <param name="se_reads" ftype="fastqsanger" value="assembly_sample-R1.fastq.gz,assembly_sample-R2.fastq.gz" /> 218 <param name="se_reads" ftype="fastqsanger" value="assembly_sample-R1.fastq.gz,assembly_sample-R2.fastq.gz" />
218 <param name="k" value="50" /> 219 <param name="k" value="50" />
219 <output name="unitigs" file="abyss-unitigs2.fa" /> 220 <output name="unitigs" file="abyss-unitigs2.fa" />
220 <output name="bubbles" file="empty_file.fasta" />
221 <output name="indels" file="empty_file.fasta" /> 221 <output name="indels" file="empty_file.fasta" />
222 <output name="coverage_histogram_outfile" file="coverage2.hist" />
223 <output name="stats" file="abyss-stats2.tab" /> 222 <output name="stats" file="abyss-stats2.tab" />
224 </test> 223 </test>
225 <test> 224 <test>
226 <param name="se_reads" ftype="fastqsanger" value="assembly_sample-R1.fastq.gz,assembly_sample-R2.fastq.gz" /> 225 <param name="se_reads" ftype="fastqsanger" value="assembly_sample-R1.fastq.gz,assembly_sample-R2.fastq.gz" />
227 <param name="long_seqs" ftype="fastqsanger" value="assembly_sample-R2.fastq.gz" /> 226 <param name="long_seqs" ftype="fastqsanger" value="assembly_sample-R2.fastq.gz" />
228 <param name="k" value="50" /> 227 <param name="k" value="50" />
229 <output name="unitigs" file="abyss-unitigs3.fa" /> 228 <output name="unitigs" file="abyss-unitigs3.fa" />
230 <output name="long_scaffolds" file="abyss-long-scaffolds3.fa" /> 229 <output name="long_scaffolds" file="abyss-long-scaffolds3.fa" />
231 <output name="bubbles" file="empty_file.fasta" />
232 <output name="indels" file="empty_file.fasta" /> 230 <output name="indels" file="empty_file.fasta" />
233 <output name="coverage_histogram_outfile" file="coverage3.hist" />
234 <output name="stats" file="abyss-stats3.tab" /> 231 <output name="stats" file="abyss-stats3.tab" />
235 </test> 232 </test>
236 </tests> 233 </tests>
237 <help> 234 <help><![CDATA[
238 **What it does** 235 **What it does**
239 236
240 `ABySS`_ is a de novo sequence assembler intended for short paired-end reads and large genomes. 237 `ABySS`_ is a de novo sequence assembler intended for short paired-end reads and large genomes.
241 238
242 **Input** 239 **Input**
253 250
254 This tool performs the complete ABySS pipeline using abyss-pe, described in https://github.com/bcgsc/abyss/blob/master/doc/flowchart.pdf . 251 This tool performs the complete ABySS pipeline using abyss-pe, described in https://github.com/bcgsc/abyss/blob/master/doc/flowchart.pdf .
255 252
256 **License and citation** 253 **License and citation**
257 254
258 This Galaxy tool is Copyright © 2015-2016 `Earlham Institute`_ and is released under the `MIT license`_. 255 This Galaxy tool is Copyright © 2015-2021 `Earlham Institute`_ and is released under the `MIT license`_.
259 256
260 .. _Earlham Institute: http://www.earlham.ac.uk/ 257 .. _Earlham Institute: http://www.earlham.ac.uk/
261 .. _MIT license: https://opensource.org/licenses/MIT 258 .. _MIT license: https://opensource.org/licenses/MIT
262 259
263 You can use this tool only if you agree to the license terms of: `ABySS`_. 260 You can use this tool only if you agree to the license terms of: `ABySS`_.
264 261
265 .. _ABySS: https://github.com/bcgsc/abyss 262 .. _ABySS: https://github.com/bcgsc/abyss
266 </help> 263 ]]></help>
267 <citations> 264 <citations>
265 <citation type="doi">doi:10.1101/gr.214346.116</citation>
268 <citation type="doi">10.1101/gr.089532.108</citation> 266 <citation type="doi">10.1101/gr.089532.108</citation>
269 </citations> 267 </citations>
270 </tool> 268 </tool>