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comparison abyss-pe.xml @ 5:fa5259cc561b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
author iuc
date Fri, 19 Mar 2021 21:37:30 +0000
parents 3ce74eab308b
children 0e93176640ac
comparison
equal deleted inserted replaced
4:3ce74eab308b 5:fa5259cc561b
1 <tool id="abyss-pe" name="ABySS" version="@TOOL_VERSION@"> 1 <tool id="abyss-pe" name="ABySS" version="@TOOL_VERSION@+galaxy1">
2 <description>de novo sequence assembler</description> 2 <description>de novo sequence assembler</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">2.2.3</token> 4 <token name="@TOOL_VERSION@">2.2.3</token>
5 <xml name="reads_conditional"> 5 <xml name="reads_conditional">
6 <conditional name="reads"> 6 <conditional name="reads">
8 <option value="paired">2 separate datasets</option> 8 <option value="paired">2 separate datasets</option>
9 <option value="paired_collection">1 paired dataset collection</option> 9 <option value="paired_collection">1 paired dataset collection</option>
10 <option value="paired_il">1 dataset of interleaved reads</option> 10 <option value="paired_il">1 dataset of interleaved reads</option>
11 </param> 11 </param>
12 <when value="paired"> 12 <when value="paired">
13 <param name="reads1" type="data" format="fasta,fastq,fastqsanger,fastqillumina" label="Paired-end reads 1" /> 13 <param name="reads1" type="data" format="fasta,fastq,fastq.gz" label="Paired-end reads 1" />
14 <param name="reads2" type="data" format="fasta,fastq,fastqsanger,fastqillumina" label="Paired-end reads 2" /> 14 <param name="reads2" type="data" format="fasta,fastq,fastq.gz" label="Paired-end reads 2" />
15 </when> 15 </when>
16 <when value="paired_collection"> 16 <when value="paired_collection">
17 <param name="reads_coll" type="data_collection" collection_type="paired" format="fasta,fastq,fastqsanger,fastqillumina" label="Paired-end reads collection" /> 17 <param name="reads_coll" type="data_collection" collection_type="paired" format="fasta,fastq,fastqsanger,fastqillumina" label="Paired-end reads collection" />
18 </when> 18 </when>
19 <when value="paired_il"> 19 <when value="paired_il">
20 <param name="reads_il" type="data" format="fasta,fastq,fastqsanger,fastqillumina" label="Interleaved paired-end reads" /> 20 <param name="reads_il" type="data" format="fasta,fastq,fastq.gz" label="Interleaved paired-end reads" />
21 </when> 21 </when>
22 </conditional> 22 </conditional>
23 </xml> 23 </xml>
24 </macros> 24 </macros>
25 <requirements> 25 <requirements>
147 147
148 <inputs> 148 <inputs>
149 <repeat name="lib_repeat" title="Paired-end library" help="(lib)"> 149 <repeat name="lib_repeat" title="Paired-end library" help="(lib)">
150 <expand macro="reads_conditional" /> 150 <expand macro="reads_conditional" />
151 </repeat> 151 </repeat>
152 <param name="se_reads" argument="se" type="data" multiple="true" optional="true" format="fasta,fastq,fastqsanger,fastqillumina" label="Single-end reads" /> 152 <param name="se_reads" argument="se" type="data" multiple="true" optional="true" format="fasta,fastq,fastq.gz" label="Single-end reads" />
153 <repeat name="mp_repeat" title="Mate-pair library" help="The mate-pair libraries are used only for scaffolding and do not contribute towards the consensus sequence (mp)"> 153 <repeat name="mp_repeat" title="Mate-pair library" help="The mate-pair libraries are used only for scaffolding and do not contribute towards the consensus sequence (mp)">
154 <expand macro="reads_conditional" /> 154 <expand macro="reads_conditional" />
155 </repeat> 155 </repeat>
156 <param name="long_seqs" argument="long" type="data" multiple="true" optional="true" format="fasta,fastq,fastqsanger,fastqillumina" label="Long sequences" help="Long sequence libraries are used only for rescaffolding and do not contribute towards the consensus sequence" /> 156 <param name="long_seqs" argument="long" type="data" multiple="true" optional="true" format="fasta,fastq,fastq.gz" label="Long sequences" help="Long sequence libraries are used only for rescaffolding and do not contribute towards the consensus sequence" />
157 <param argument="k" type="integer" value="41" label="K-mer length (in bp)" help="The length of a k-mer (when -K is not set) or the span of a k-mer pair (when K is set)" /> 157 <param argument="k" type="integer" value="41" label="K-mer length (in bp)" help="The length of a k-mer (when -K is not set) or the span of a k-mer pair (when K is set)" />
158 <param argument="K" type="integer" value="" optional="true" label="The length (in bp) of a single k-mer in a k-mer pair" help="Optional" /> 158 <param argument="K" type="integer" value="" optional="true" label="The length (in bp) of a single k-mer in a k-mer pair" help="Optional" />
159 <param argument="q" type="integer" value="3" max="40" optional="true" label="Minimum base quality when trimming" help="Trim bases from the ends of reads whose quality is less than this value" /> 159 <param argument="q" type="integer" value="3" max="40" optional="true" label="Minimum base quality when trimming" help="Trim bases from the ends of reads whose quality is less than this value" />
160 <param argument="Q" type="integer" value="0" max="40" optional="true" label="Minimum base quality" help="Mask all bases of reads whose quality is less than this value as 'N'" /> 160 <param argument="Q" type="integer" value="0" max="40" optional="true" label="Minimum base quality" help="Mask all bases of reads whose quality is less than this value as 'N'" />
161 <param argument="e" type="integer" value="" min="0" optional="true" label="Minimum erosion k-mer coverage" help="Erode bases at the ends of blunt contigs with coverage less than this value. Defaults to round(sqrt(median))" /> 161 <param argument="e" type="integer" value="" min="0" optional="true" label="Minimum erosion k-mer coverage" help="Erode bases at the ends of blunt contigs with coverage less than this value. Defaults to round(sqrt(median))" />
195 <tests> 195 <tests>
196 <test> 196 <test>
197 <repeat name="lib_repeat"> 197 <repeat name="lib_repeat">
198 <conditional name="reads"> 198 <conditional name="reads">
199 <param name="reads_selector" value="paired" /> 199 <param name="reads_selector" value="paired" />
200 <param name="reads1" ftype="fastqsanger" value="assembly_sample-R1.fastq" /> 200 <param name="reads1" ftype="fastqsanger" value="assembly_sample-R1.fastq.gz" />
201 <param name="reads2" ftype="fastqsanger" value="assembly_sample-R2.fastq" /> 201 <param name="reads2" ftype="fastqsanger" value="assembly_sample-R2.fastq.gz" />
202 </conditional> 202 </conditional>
203 </repeat> 203 </repeat>
204 <param name="k" value="50" /> 204 <param name="k" value="50" />
205 <output name="unitigs" file="abyss-unitigs1.fa" /> 205 <output name="unitigs" file="abyss-unitigs1.fa" />
206 <output name="contigs_outfile" file="abyss-contigs1.fa" /> 206 <output name="contigs_outfile" file="abyss-contigs1.fa" />
209 <output name="indels" file="empty_file.fasta" /> 209 <output name="indels" file="empty_file.fasta" />
210 <output name="coverage_histogram_outfile" file="coverage1.hist" /> 210 <output name="coverage_histogram_outfile" file="coverage1.hist" />
211 <output name="stats" file="abyss-stats1.tab" /> 211 <output name="stats" file="abyss-stats1.tab" />
212 </test> 212 </test>
213 <test> 213 <test>
214 <param name="se_reads" ftype="fastqsanger" value="assembly_sample-R1.fastq,assembly_sample-R2.fastq" /> 214 <param name="se_reads" ftype="fastqsanger" value="assembly_sample-R1.fastq.gz,assembly_sample-R2.fastq.gz" />
215 <param name="k" value="50" /> 215 <param name="k" value="50" />
216 <output name="unitigs" file="abyss-unitigs2.fa" /> 216 <output name="unitigs" file="abyss-unitigs2.fa" />
217 <output name="bubbles" file="empty_file.fasta" /> 217 <output name="bubbles" file="empty_file.fasta" />
218 <output name="indels" file="empty_file.fasta" /> 218 <output name="indels" file="empty_file.fasta" />
219 <output name="coverage_histogram_outfile" file="coverage2.hist" /> 219 <output name="coverage_histogram_outfile" file="coverage2.hist" />
220 <output name="stats" file="abyss-stats2.tab" /> 220 <output name="stats" file="abyss-stats2.tab" />
221 </test> 221 </test>
222 <test> 222 <test>
223 <param name="se_reads" ftype="fastqsanger" value="assembly_sample-R1.fastq,assembly_sample-R2.fastq" /> 223 <param name="se_reads" ftype="fastqsanger" value="assembly_sample-R1.fastq.gz,assembly_sample-R2.fastq.gz" />
224 <param name="long_seqs" ftype="fastqsanger" value="assembly_sample-R2.fastq" /> 224 <param name="long_seqs" ftype="fastqsanger" value="assembly_sample-R2.fastq.gz" />
225 <param name="k" value="50" /> 225 <param name="k" value="50" />
226 <output name="unitigs" file="abyss-unitigs3.fa" /> 226 <output name="unitigs" file="abyss-unitigs3.fa" />
227 <output name="long_scaffolds" file="abyss-long-scaffolds3.fa" /> 227 <output name="long_scaffolds" file="abyss-long-scaffolds3.fa" />
228 <output name="bubbles" file="empty_file.fasta" /> 228 <output name="bubbles" file="empty_file.fasta" />
229 <output name="indels" file="empty_file.fasta" /> 229 <output name="indels" file="empty_file.fasta" />