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comparison bbduk.xml @ 9:7beb76ffbc0f draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb
author iuc
date Tue, 27 Aug 2024 10:15:37 +0000
parents d1f62024a08b
children
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8:d1f62024a08b 9:7beb76ffbc0f
152 <option value="files">files</option> 152 <option value="files">files</option>
153 <option value="keywords">keywords</option> 153 <option value="keywords">keywords</option>
154 </param> 154 </param>
155 <when value="no_reference"/> 155 <when value="no_reference"/>
156 <when value="files"> 156 <when value="files">
157 <param name="reference" type="data" format="fasta,fasta.gz" multiple="true" optional="false" label="Select one or more fasta file"/> 157 <param name="reference" type="data" format="fasta,fasta.gz" optional="false" label="Select one or more fasta file" multiple="true"/>
158 <expand macro="ktrim_cond"/> 158 <expand macro="ktrim_cond"/>
159 </when> 159 </when>
160 <when value="keywords"> 160 <when value="keywords">
161 <param name="reference" type="select" multiple="true" optional="false" label="Select one or more keywords"> 161 <param name="reference" type="select" optional="false" label="Select one or more keywords" multiple="true">
162 <option value="adapters">adapters</option> 162 <option value="adapters">adapters</option>
163 <option value="artifacts">artifacts</option> 163 <option value="artifacts">artifacts</option>
164 <option value="phix">phix</option> 164 <option value="phix">phix</option>
165 <option value="lambda">lambda</option> 165 <option value="lambda">lambda</option>
166 <option value="pjet">pjet</option> 166 <option value="pjet">pjet</option>
169 </param> 169 </param>
170 <expand macro="ktrim_cond"/> 170 <expand macro="ktrim_cond"/>
171 </when> 171 </when>
172 </conditional> 172 </conditional>
173 <section name="advanced_options" title="Advanced options" expanded="false"> 173 <section name="advanced_options" title="Advanced options" expanded="false">
174 <param argument="k" type="integer" value="27" min="1" label="Kmer length used for finding contaminants"/> 174 <param argument="k" type="integer" min="1" value="27" label="Kmer length used for finding contaminants"/>
175 <param argument="rcomp" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Look for reverse-complements of kmers in addition to forward kmers?"/> 175 <param argument="rcomp" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Look for reverse-complements of kmers in addition to forward kmers?"/>
176 <param argument="maskmiddle" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Treat the middle base of a kmer as a wildcard to increase sensitivity in the presence of errors?"/> 176 <param argument="maskmiddle" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Treat the middle base of a kmer as a wildcard to increase sensitivity in the presence of errors?"/>
177 <param argument="minkmerhits" type="integer" value="1" min="1" label="Reads need at least this many matching kmers to be considered as matching the reference"/> 177 <param argument="minkmerhits" type="integer" min="1" value="1" label="Reads need at least this many matching kmers to be considered as matching the reference"/>
178 <param argument="minkmerfraction" type="float" value="0" min="0" label="A read needs at least this fraction of its total kmers to hit a ref in order to be considered a match"/> 178 <param argument="minkmerfraction" type="float" min="0" value="0" label="A read needs at least this fraction of its total kmers to hit a ref in order to be considered a match"/>
179 <param argument="mincovfraction" type="float" value="0" min="0" label="A read needs at least this fraction of its total bases to be covered by ref kmers to be considered a match"/> 179 <param argument="mincovfraction" type="float" min="0" value="0" label="A read needs at least this fraction of its total bases to be covered by ref kmers to be considered a match"/>
180 <param argument="hammingdistance" type="integer" value="0" min="0" label="Maximum Hamming distance for ref kmers (subs only)"/> 180 <param argument="hammingdistance" type="integer" min="0" value="0" label="Maximum Hamming distance for ref kmers (subs only)"/>
181 <param argument="qhdist" type="integer" value="0" min="0" label="Hamming distance for query kmers"/> 181 <param argument="qhdist" type="integer" min="0" value="0" label="Hamming distance for query kmers"/>
182 <param argument="editdistance" type="integer" value="0" min="0" label="Maximum edit distance from ref kmers (subs and indels)"/> 182 <param argument="editdistance" type="integer" min="0" value="0" label="Maximum edit distance from ref kmers (subs and indels)"/>
183 <param argument="forbidn" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Do not match kmers comntaining N?"/> 183 <param argument="forbidn" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Do not match kmers comntaining N?"/>
184 <param argument="trimfailures" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Trim failed reads to 1bp instead of discarding them?"/> 184 <param argument="trimfailures" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Trim failed reads to 1bp instead of discarding them?"/>
185 <param argument="findbestmatch" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Associate read with sequence sharing most kmers if multiple matches?"/> 185 <param argument="findbestmatch" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Associate read with sequence sharing most kmers if multiple matches?"/>
186 <param argument="skipr1" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Don't do kmer-based operations on read 1?"/> 186 <param argument="skipr1" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Don't do kmer-based operations on read 1?"/>
187 <param argument="skipr2" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Don't do kmer-based operations on read 2?"/> 187 <param argument="skipr2" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Don't do kmer-based operations on read 2?"/>
188 </section> 188 </section>
189 <param name="outputs_select" type="select" multiple="true" optional="false" label="Specify outputs"> 189 <param name="outputs_select" type="select" optional="false" label="Specify outputs" multiple="true">
190 <option value="outu">Unmatched</option> 190 <option value="outu">Unmatched</option>
191 <option value="outm">Matched</option> 191 <option value="outm">Matched</option>
192 <option value="outs">Single</option> 192 <option value="outs">Single</option>
193 </param> 193 </param>
194 <conditional name="output_stats_cond"> 194 <conditional name="output_stats_cond">
195 <param name="output_stats" type="select" label="Output statistics?"> 195 <param name="output_stats" type="select" label="Output statistics?">
196 <option value="no" selected="true">No</option> 196 <option value="no" selected="true">No</option>
197 <option value="yes">Yes</option> 197 <option value="yes">Yes</option>
198 </param> 198 </param>
199 <when value="no"/> 199 <when value="no"/>
200 <when value="yes"> 200 <when value="yes">
201 <param name="output_stats_select" type="select" multiple="true" optional="false" label="Specify statistics outputs"> 201 <param name="output_stats_select" type="select" optional="false" label="Specify statistics outputs" multiple="true">
202 <option value="stats">Statistics about which contamininants were detected</option> 202 <option value="stats">Statistics about which contamininants were detected</option>
203 <option value="ref">Statistics on a per-reference-file basis</option> 203 <option value="ref">Statistics on a per-reference-file basis</option>
204 <option value="rpkm">RPKM for each reference sequence (for RNA-seq)</option> 204 <option value="rpkm">RPKM for each reference sequence (for RNA-seq)</option>
205 <option value="dump">kmer tables in fasta format</option> 205 <option value="dump">kmer tables in fasta format</option>
206 </param> 206 </param>
207 </when> 207 </when>
208 </conditional> 208 </conditional>
209 <conditional name="output_hists_cond"> 209 <conditional name="output_hists_cond">
210 <param name="output_hists" type="select" label="Output histograms?"> 210 <param name="output_hists" type="select" label="Output histograms?">
211 <option value="no" selected="true">No</option> 211 <option value="no" selected="true">No</option>
212 <option value="yes">Yes</option> 212 <option value="yes">Yes</option>
213 </param> 213 </param>
214 <when value="no"/> 214 <when value="no"/>
215 <when value="yes"> 215 <when value="yes">
216 <param name="output_hists_select" type="select" multiple="true" optional="false" label="Specify statistics outputs"> 216 <param name="output_hists_select" type="select" optional="false" label="Specify statistics outputs" multiple="true">
217 <option value="bhist">Base composition histogram by position</option> 217 <option value="bhist">Base composition histogram by position</option>
218 <option value="quhist">Quality histogram by position</option> 218 <option value="quhist">Quality histogram by position</option>
219 <option value="quchist">Count of bases with each quality value</option> 219 <option value="quchist">Count of bases with each quality value</option>
220 <option value="aqhist">Histogram of average read quality</option> 220 <option value="aqhist">Histogram of average read quality</option>
221 <option value="bqhist">Quality histogram designed for box plots</option> 221 <option value="bqhist">Quality histogram designed for box plots</option>
227 </when> 227 </when>
228 </conditional> 228 </conditional>
229 </inputs> 229 </inputs>
230 <outputs> 230 <outputs>
231 <data name="outputu" format="fastqsanger" label="${tool.name} on ${on_string} (Forward Unmatched)"> 231 <data name="outputu" format="fastqsanger" label="${tool.name} on ${on_string} (Forward Unmatched)">
232 <filter>str(outputs_select).find('outu') >= 0</filter> 232 <filter>str(outputs_select).find('outu') &gt;= 0</filter>
233 <filter>'outu' in outputs_select</filter> 233 <filter>'outu' in outputs_select</filter>
234 </data> 234 </data>
235 <data name="outputu2" format="fastqsanger" label="${tool.name} on ${on_string} (Reverse Unmatched)"> 235 <data name="outputu2" format="fastqsanger" label="${tool.name} on ${on_string} (Reverse Unmatched)">
236 <filter>'outu' in outputs_select and input_type_cond['input_type'] != 'single'</filter> 236 <filter>'outu' in outputs_select and input_type_cond['input_type'] != 'single'</filter>
237 </data> 237 </data>
348 * **Matched** - Reads failing any filter criteria (such as matching a reference kmer). By default, if either read in a pair fails, both will be included in *Matched*. 348 * **Matched** - Reads failing any filter criteria (such as matching a reference kmer). By default, if either read in a pair fails, both will be included in *Matched*.
349 * **Single** - Singleton reads whose mate was trimmed shorter than the value of **Minimum read length**. 349 * **Single** - Singleton reads whose mate was trimmed shorter than the value of **Minimum read length**.
350 </help> 350 </help>
351 <expand macro="citations"/> 351 <expand macro="citations"/>
352 </tool> 352 </tool>
353