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comparison metaphlan2.xml @ 3:9f341c9cfa6a 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 12:24:00 -0400
parents 11bb77fab91f
children 575f1f4420ee
comparison
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2:8ce82a6b20d7 3:9f341c9cfa6a
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 #elif $analysis_type.analysis_type_select == "marker_ab_table" 38 #else if $analysis_type.analysis_type_select == "marker_ab_table"
39 #if $analysis_type.nreads != '' 39 --nreads $analysis_type.nreads
40 --nreads $analysis_type.nreads 40 #else if $analysis_type.analysis_type_select == "marker_pres_table"
41 #end if 41 --pres_th $analysis_type.pres_th
42 #elif $analysis_type.analysis_type_select == "marker_pres_table"
43 #if $analysis_type.pres_th != ''
44 --pres_th $analysis_type.pres_th
45 #end if
46 #end if 42 #end if
47 43
48 --min_cu_len $min_cu_len 44 --min_cu_len $min_cu_len
49 45 --min_alignment_len $min_alignment_len
50 #if $min_alignment_len != ''
51 --min_alignment_len $min_alignment_len
52 #end if
53 46
54 $ignore_viruses 47 $ignore_viruses
55 $ignore_eukaryotes 48 $ignore_eukaryotes
56 $ignore_bacteria 49 $ignore_bacteria
57 $ignore_archaea 50 $ignore_archaea
58 51
59 --stat_q $stat_q 52 --stat_q $stat_q
60 53
61 #if $sam_output: 54 #if $sam_output
62 -s $sam_output_file 55 -s $sam_output_file
63 #endif 56 #endif
64 #if $biom_output: 57
58 #if $biom_output
65 -biom $biom_output_file 59 -biom $biom_output_file
66 #endif 60 #endif
67 61
68 ]]></command> 62 ]]></command>
69 63
167 161
168 **Parameters** 162 **Parameters**
169 163
170 Several parameters can modulate the MetaPhlAn execution 164 Several parameters can modulate the MetaPhlAn execution
171 165
172 - Mapping arguments 166 - Mapping arguments
173 - Test to avoid saving the output of BowTie2 167 - Test to avoid saving the output of BowTie2
174 - Post-mapping arguments 168 - Post-mapping arguments
175 - Taxonomic level for the relative abundance output 169 - Taxonomic level for the relative abundance output
176 - Minimum total nucleotide length for the markers in a clade for estimating the abundance without considering sub-clade abundances 170 - Minimum total nucleotide length for the markers in a clade for estimating the abundance without considering sub-clade abundances
177 - Sam records for aligned reads with the longest subalignment length smaller than this threshold will be discarded 171 - Sam records for aligned reads with the longest subalignment length smaller than this threshold will be discarded
178 - Tests to avoid profiling of virus, eukaryotes, bacteria and/or archea 172 - Tests to avoid profiling of virus, eukaryotes, bacteria and/or archea
179 - Quantile value 173 - Quantile value
180 - Additional analysis types and arguments 174 - Additional analysis types and arguments
181 - Type of analyse to perform and some parameters for specific analysis type 175 - Type of analyse to perform and some parameters for specific analysis type
182 176
183 ----- 177 -----
184 178
185 **Outputs** 179 **Outputs**
186 180
187 The main output file is a tab-separated output file of the predicted taxon 181 The main output file is a tab-separated output file of the predicted taxon
188 relative abundances. 182 relative abundances.
189 183
190 Given the choosen parameters, other output files can be: 184 Given the choosen parameters, other output files can be:
191 185
192 - a sam output file 186 - a sam output file
193 - a biom output fime 187 - a biom output fime
194 - a BowTie2 output file 188 - a BowTie2 output file
195 189
196 ]]></help> 190 ]]></help>
197 191
198 <citations> 192 <citations>
199 <citation type="doi">10.1038/nmeth.3589</citation> 193 <citation type="doi">10.1038/nmeth.3589</citation>