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comparison spades.xml @ 3:6dff6ed33cd7 draft

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planemo upload commit b8b20b735c418c2f2086a6aa48a7e36e34f80753
author nml
date Wed, 06 Jul 2016 16:01:02 -0400
parents e37014a072e9
children 35cb17bd8bf9
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2:e37014a072e9 3:6dff6ed33cd7
1 <tool id="spades" name="spades" version="1.3.1"> 1 <tool id="spades" name="spades" version="1.3.2">
2 <description>SPAdes genome assembler for regular and single-cell projects</description> 2 <description>SPAdes genome assembler for regular and single-cell projects</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="3.8.0">spades</requirement> 4 <requirement type="package" version="3.8.0">spades</requirement>
5 </requirements> 5 </requirements>
6 <command interpreter="perl">spades.pl 6 <command interpreter="perl">spades.pl
22 --disable-gzip-output 22 --disable-gzip-output
23 $sc 23 $sc
24 $onlyassembler 24 $onlyassembler
25 $careful 25 $careful
26 -t \${GALAXY_SLOTS:-16} 26 -t \${GALAXY_SLOTS:-16}
27 -k "$kmers" 27
28 #if str($kmer_choice.auto_kmer_choice) == 'False':
29 -k "$kmer_choice.kmers"
30 #else
31
32 #end if
28 33
29 #if $cov.state == "auto": 34 #if $cov.state == "auto":
30 --cov-cutoff 'auto' 35 --cov-cutoff 'auto'
31 #elif $cov.state == "value": 36 #elif $cov.state == "value":
32 --cov-cutoff '$cov.cutoff' 37 --cov-cutoff '$cov.cutoff'
86 <option value="false">No</option> 91 <option value="false">No</option>
87 <option value="true">Yes</option> 92 <option value="true">Yes</option>
88 </param> 93 </param>
89 <param name="onlyassembler" type="boolean" truevalue="--only-assembler" falsevalue="" checked="False" label="Run only assembly? (without read error correction)" /> 94 <param name="onlyassembler" type="boolean" truevalue="--only-assembler" falsevalue="" checked="False" label="Run only assembly? (without read error correction)" />
90 <param name="careful" type="boolean" truevalue="--careful" falsevalue="" checked="True" label="Careful correction?" help="Tries to reduce number of mismatches and short indels. Also runs MismatchCorrector – a post processing tool, which uses BWA tool (comes with SPAdes)." /> 95 <param name="careful" type="boolean" truevalue="--careful" falsevalue="" checked="True" label="Careful correction?" help="Tries to reduce number of mismatches and short indels. Also runs MismatchCorrector – a post processing tool, which uses BWA tool (comes with SPAdes)." />
91 <param name="kmers" type="text" label="K-mers to use, separated by commas" value="21,33,55" help="Comma-separated list of k-mer sizes to be used (all values must be odd, less than 128, listed in ascending order, and smaller than the read length). The default value is 21,33,55." > 96 <conditional name="kmer_choice">
92 97 <param name="auto_kmer_choice" type="boolean" checked="False" truevalue="true" falsevalue="false" label="Automatically choose k-mer values" help="k-mer choices can be chosen by SPAdes instead of being entered manually" />
93 </param> 98 <when value="false">
99 <param name="kmers" type="text" label="K-mers to use, separated by commas" value="21,33,55" help="Comma-separated list of k-mer sizes to be used (all values must be odd, less than 128, listed in ascending order, and smaller than the read length). The default value is 21,33,55." />
100 </when>
101 <when value="true"> </when>
102 </conditional>
94 <conditional name="cov"> 103 <conditional name="cov">
95 <param name="state" type="select" label="Coverage Cutoff"> 104 <param name="state" type="select" label="Coverage Cutoff">
96 <option value="off">Off</option> 105 <option value="off">Off</option>
97 <option value="value">User Specific</option> 106 <option value="value">User Specific</option>
98 <option value="auto">Auto</option> 107 <option value="auto">Auto</option>
208 </outputs> 217 </outputs>
209 <tests> 218 <tests>
210 <test> 219 <test>
211 <param name="sc" value="false" /> 220 <param name="sc" value="false" />
212 <param name="careful" value="false" /> 221 <param name="careful" value="false" />
213 <param name="kmers" value="33,55" /> 222 <param name="kmers" value="33" />
214 <param name="lib_type" value="paired_end" /> 223 <param name="lib_type" value="paired_end" />
215 <param name="fwd_reads" value="ecoli_1K_1.fq" ftype="fastq" /> 224 <param name="fwd_reads" value="ecoli_1K_1.fq" ftype="fastq" />
216 <param name="rev_reads" value="ecoli_1K_2.fq" ftype="fastq" /> 225 <param name="rev_reads" value="ecoli_1K_2.fq" ftype="fastq" />
217 <output name="out_contigs" file="reference_1K.fa" ftype="fasta" compare="re_match" lines_diff="1" /> 226 <output name="out_contigs" file="kmer_33_output.fa" ftype="fasta" compare="re_match" lines_diff="1" />
227 </test>
228 <test>
229 <param name="sc" value="false" />
230 <param name="careful" value="false" />
231 <param name="auto_kmer_choice" value="true" />
232 <param name="lib_type" value="paired_end" />
233 <param name="fwd_reads" value="ecoli_1K_1.fq" ftype="fastq" />
234 <param name="rev_reads" value="ecoli_1K_2.fq" ftype="fastq" />
235 <output name="out_contigs" file="auto_kmer_output.fa" ftype="fasta" compare="re_match" lines_diff="1" />
236 </test>
237 <test>
238 <param name="sc" value="false" />
239 <param name="careful" value="false" />
240 <param name="kmers" value="77" />
241 <param name="lib_type" value="paired_end" />
242 <param name="fwd_reads" value="ecoli_1K_1.fq" ftype="fastq" />
243 <param name="rev_reads" value="ecoli_1K_2.fq" ftype="fastq" />
244 <output name="out_contigs" file="kmer_77_output.fa" ftype="fasta" compare="re_match" lines_diff="1" />
218 </test> 245 </test>
219 </tests> 246 </tests>
220 <help> 247 <help>
221 **What it does** 248 **What it does**
222 249