Mercurial > repos > iuc > megan_blast2rma

comparison blast2rma.xml @ 1:2f8d3924bb3b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
author iuc
date Fri, 03 Dec 2021 23:09:53 +0000
parents fa3c3a64c993
children 5be253dd3e08
comparison
equal deleted inserted replaced
0:fa3c3a64c993 1:2f8d3924bb3b
112 --minPercentReferenceCover $advanced_options.minPercentReferenceCover 112 --minPercentReferenceCover $advanced_options.minPercentReferenceCover
113 --minReadLength $advanced_options.minReadLength 113 --minReadLength $advanced_options.minReadLength
114 --lcaAlgorithm '$advanced_options.lcaAlgorithm' 114 --lcaAlgorithm '$advanced_options.lcaAlgorithm'
115 --lcaCoveragePercent $advanced_options.lcaCoveragePercent 115 --lcaCoveragePercent $advanced_options.lcaCoveragePercent
116 --readAssignmentMode '$advanced_options.readAssignmentMode' 116 --readAssignmentMode '$advanced_options.readAssignmentMode'
117 #if str($advanced_options.con_file_cond.conFile) == 'yes': 117 #if $advanced_options.conFile:
118 --conFile '$advanced_options.con_file_cond.conFile' 118 --conFile '$advanced_options.conFile'
119 #end if 119 #end if
120 #if str($input_type_cond.input_type) == 'paired': 120 #if str($input_type_cond.input_type) == 'paired':
121 && mv './tmp.rma6' '$rma6_output' 121 && mv './tmp.rma6' '$rma6_output'
122 #end if 122 #end if
123 ]]></command> 123 ]]></command>
125 <expand macro="input_type_cond"/> 125 <expand macro="input_type_cond"/>
126 <param argument="--blastMode" type="select" label="Blast mode"> 126 <param argument="--blastMode" type="select" label="Blast mode">
127 <expand macro="blast_mode_options"/> 127 <expand macro="blast_mode_options"/>
128 </param> 128 </param>
129 <section name="advanced_options" title="Advanced options" expanded="false"> 129 <section name="advanced_options" title="Advanced options" expanded="false">
130 <param argument="--longReads" type="boolean" truevalue="--longReads" falsevalue="" checked="false" label="Parse and analyse input reads as long reads?"/> 130 <expand macro="long_reads_param"/>
131 <param argument="--maxMatchesPerRead" type="integer" value="100" label="Maximum matches per read"/> 131 <param argument="--maxMatchesPerRead" type="integer" value="100" label="Maximum matches per read"/>
132 <param argument="--classify" type="boolean" truevalue="--classify" falsevalue="" checked="true" label="Run classification algorithm?"/> 132 <expand macro="classify_param"/>
133 <expand macro="common_blast_params"/> 133 <expand macro="blast_params"/>
134 <param argument="--minSupportPercent" type="float" value="0.05" min="0.0" max="100.0" label="Minimum support as percent of assigned reads" help="0 value ignores"/> 134 <expand macro="min_max_params"/>
135 <param argument="--minSupport" type="integer" value="0" label="Minimum support" help="0 value ignores"/> 135 <expand macro="lca_params"/>
136 <param argument="--minPercentReadCover" type="float" value="0.0" min="0.0" max="100.0" label="Minimum percent of read length to be covered by alignments"/> 136 <expand macro="read_assignment_mode_param"/>
137 <param argument="--minPercentReferenceCover" type="float" value="0.0" min="0.0" max="100.0" label="Minimum percent of reference length to be covered by alignments"/> 137 <expand macro="con_file_param"/>
138 <param argument="--minReadLength" type="integer" value="0" label="Minimum read length"/>
139 <param argument="--lcaAlgorithm" type="select" label="Select the LCA algorithm to use for taxonomic assignment">
140 <option value="naive" selected="true">naive</option>
141 <option value="weighted">weighted</option>
142 <option value="longReads">longReads</option>
143 </param>
144 <param argument="--lcaCoveragePercent" type="float" value="100.0" min="0.0" max="100.0" label="Percent for the LCA to cover"/>
145 <param argument="--readAssignmentMode" type="select" label="Select the read assignment mode">
146 <option value="alignedBases" selected="true">alignedBases</option>
147 <option value="readCount">readCount</option>
148 </param>
149 <conditional name="con_file_cond">
150 <param argument="--conFile" type="select" label="Process a file of contaminant taxa" help="One id or name per line">
151 <option value="no" selected="true">No</option>
152 <option value="yes">Yes</option>
153 </param>
154 <when value="no"/>
155 <when value="yes">
156 <param argument="conFile" type="data" format="txt" label="File of contaminant taxa"/>
157 </when>
158 </conditional>
159 </section> 138 </section>
160 </inputs> 139 </inputs>
161 <outputs> 140 <outputs>
162 <data name="rma6_output" format="rma6"/> 141 <data name="rma6_output" format="rma6"/>
163 </outputs> 142 </outputs>
176 <!-- Single dataset input, contaminants file --> 155 <!-- Single dataset input, contaminants file -->
177 <test expect_num_outputs="1"> 156 <test expect_num_outputs="1">
178 <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz"/> 157 <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz"/>
179 <param name="blast1" value="blast_R1.txt" ftype="txt"/> 158 <param name="blast1" value="blast_R1.txt" ftype="txt"/>
180 <param name="blastMode" value="BlastN"/> 159 <param name="blastMode" value="BlastN"/>
181 <param name="conFile" value="yes"/>
182 <param name="conFile" value="contaminants.txt" ftype="txt"/> 160 <param name="conFile" value="contaminants.txt" ftype="txt"/>
183 <output name="rma6_output" ftype="rma6"> 161 <output name="rma6_output" ftype="rma6">
184 <assert_contents> 162 <assert_contents>
185 <has_size value="19596"/> 163 <has_size value="19596"/>
186 </assert_contents> 164 </assert_contents>
237 * **Text** - plain text format 215 * **Text** - plain text format
238 216
239 This tool outputs a RealMedia Audio (RMA) file. MEGAN uses an update of the original RMA file format known as RMA6. This update 217 This tool outputs a RealMedia Audio (RMA) file. MEGAN uses an update of the original RMA file format known as RMA6. This update
240 requires less disk space for files. 218 requires less disk space for files.
241 </help> 219 </help>
242 <citations> 220 <expand macro="citations"/>
243 <citation type="doi">https://doi.org/10.1101/050559</citation>
244 </citations>
245 </tool> 221 </tool>
246 222