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comparison metaphlan2.xml @ 5:167876cbcdd5 draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 259ec654231c792a102f99ab7bfd63cbabd4874a-dirty
author bebatut
date Wed, 28 Oct 2015 12:34:12 -0400
parents 575f1f4420ee
children 9603321a8519
comparison
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4:575f1f4420ee 5:167876cbcdd5
33 33
34 -t $analysis_type 34 -t $analysis_type
35 35
36 #if $analysis_type.analysis_type_select == "rel_ab" 36 #if $analysis_type.analysis_type_select == "rel_ab"
37 --tax_lev $analysis_type.taxonomic_level 37 --tax_lev $analysis_type.taxonomic_level
38 #else if $analysis_type.analysis_type_select == "marker_ab_table" 38 #else
39 --nreads $analysis_type.nreads 39 #if $analysis_type.analysis_type_select == "marker_ab_table"
40 #else if $analysis_type.analysis_type_select == "marker_pres_table" 40 --nreads $analysis_type.nreads
41 --pres_th $analysis_type.pres_th 41 #else
42 #if $analysis_type.analysis_type_select == "marker_pres_table"
43 --pres_th $analysis_type.pres_th
44 #end if
45 #end if
42 #end if 46 #end if
43 47
44 --min_cu_len $min_cu_len 48 --min_cu_len $min_cu_len
45 --min_alignment_len $min_alignment_len 49 --min_alignment_len $min_alignment_len
46 50
161 165
162 **Parameters** 166 **Parameters**
163 167
164 Several parameters can modulate the MetaPhlAn execution 168 Several parameters can modulate the MetaPhlAn execution
165 169
166 - Mapping arguments 170 * Mapping arguments
167 - Test to avoid saving the output of BowTie2 171
168 - Post-mapping arguments 172 * Test to avoid saving the output of BowTie2
169 - Taxonomic level for the relative abundance output 173
170 - Minimum total nucleotide length for the markers in a clade for estimating the abundance without considering sub-clade abundances 174 * Post-mapping arguments
171 - Sam records for aligned reads with the longest subalignment length smaller than this threshold will be discarded 175
172 - Tests to avoid profiling of virus, eukaryotes, bacteria and/or archea 176 * Taxonomic level for the relative abundance output
173 - Quantile value 177 * Minimum total nucleotide length for the markers in a clade for estimating the abundance without considering sub-clade abundances
174 - Additional analysis types and arguments 178 * Sam records for aligned reads with the longest subalignment length smaller than this threshold will be discarded
175 - Type of analyse to perform and some parameters for specific analysis type 179 * Tests to avoid profiling of virus, eukaryotes, bacteria and/or archea
180 * Quantile value
181
182 * Additional analysis types and arguments
183
184 * Type of analyse to perform and some parameters for specific analysis type
176 185
177 ----- 186 -----
178 187
179 **Outputs** 188 **Outputs**
180 189
181 The main output file is a tab-separated output file of the predicted taxon 190 The main output file is a tab-separated output file of the predicted taxon
182 relative abundances. 191 relative abundances.
183 192
184 Given the choosen parameters, other output files can be: 193 Given the choosen parameters, other output files can be:
185 194
186 - a sam output file 195 * a sam output file
187 - a biom output fime 196 * a biom output fime
188 - a BowTie2 output file 197 * a BowTie2 output file
189 198
190 ]]></help> 199 ]]></help>
191 200
192 <citations> 201 <citations>
193 <citation type="doi">10.1038/nmeth.3589</citation> 202 <citation type="doi">10.1038/nmeth.3589</citation>