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comparison metaphlan2.xml @ 6:9603321a8519 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 12:37:13 -0400
parents 167876cbcdd5
children 4e4002bfc9b3
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5:167876cbcdd5 6:9603321a8519
15 <![CDATA[ 15 <![CDATA[
16 python \${METAPHLAN2_DIR}/metaphlan.py -v 16 python \${METAPHLAN2_DIR}/metaphlan.py -v
17 ]]> 17 ]]>
18 </version_command> 18 </version_command>
19 19
20 <command><![CDATA[ 20 <command>
21 <![CDATA[
21 python \${METAPHLAN2_DIR}/metaphlan.py 22 python \${METAPHLAN2_DIR}/metaphlan.py
22 $input_file 23 $input_file
23 -o $output_file 24 -o $output_file
24 25
25 --input_type ${input_reads.datatype.file_ext} 26 --input_type ${input_reads.datatype.file_ext}
33 34
34 -t $analysis_type 35 -t $analysis_type
35 36
36 #if $analysis_type.analysis_type_select == "rel_ab" 37 #if $analysis_type.analysis_type_select == "rel_ab"
37 --tax_lev $analysis_type.taxonomic_level 38 --tax_lev $analysis_type.taxonomic_level
38 #else 39 #else if $analysis_type.analysis_type_select == "marker_ab_table"
39 #if $analysis_type.analysis_type_select == "marker_ab_table" 40 --nreads $analysis_type.nreads
40 --nreads $analysis_type.nreads 41 #else if $analysis_type.analysis_type_select == "marker_pres_table"
41 #else 42 --pres_th $analysis_type.pres_th
42 #if $analysis_type.analysis_type_select == "marker_pres_table"
43 --pres_th $analysis_type.pres_th
44 #end if
45 #end if
46 #end if 43 #end if
47 44
48 --min_cu_len $min_cu_len 45 --min_cu_len $min_cu_len
49 --min_alignment_len $min_alignment_len 46 --min_alignment_len $min_alignment_len
50 47
55 52
56 --stat_q $stat_q 53 --stat_q $stat_q
57 54
58 #if $sam_output 55 #if $sam_output
59 -s $sam_output_file 56 -s $sam_output_file
60 #endif 57 #end if
61 58
62 #if $biom_output 59 #if $biom_output
63 -biom $biom_output_file 60 -biom $biom_output_file
64 #endif 61 #end if
65 62 ]]>
66 ]]></command> 63 </command>
67 64
68 <inputs> 65 <inputs>
69 <param name="input_file" type="data" format="fastq,fasta,sam,bowtie2out" label="Input file" help=""/> 66 <param name="input_file" type="data" format="fastq,fasta,sam,bowtie2out" label="Input file" help=""/>
70 67
71 <conditional name="analysis_type"> 68 <conditional name="analysis_type">
165 162
166 **Parameters** 163 **Parameters**
167 164
168 Several parameters can modulate the MetaPhlAn execution 165 Several parameters can modulate the MetaPhlAn execution
169 166
170 * Mapping arguments 167 * Mapping arguments
171 168
172 * Test to avoid saving the output of BowTie2 169 * Test to avoid saving the output of BowTie2
173 170
174 * Post-mapping arguments 171 * Post-mapping arguments
175 172
176 * Taxonomic level for the relative abundance output 173 * Taxonomic level for the relative abundance output
177 * Minimum total nucleotide length for the markers in a clade for estimating the abundance without considering sub-clade abundances 174 * Minimum total nucleotide length for the markers in a clade for estimating the abundance without considering sub-clade abundances
178 * Sam records for aligned reads with the longest subalignment length smaller than this threshold will be discarded 175 * Sam records for aligned reads with the longest subalignment length smaller than this threshold will be discarded
179 * Tests to avoid profiling of virus, eukaryotes, bacteria and/or archea 176 * Tests to avoid profiling of virus, eukaryotes, bacteria and/or archea
180 * Quantile value 177 * Quantile value
181 178
182 * Additional analysis types and arguments 179 * Additional analysis types and arguments
183 180
184 * Type of analyse to perform and some parameters for specific analysis type 181 * Type of analyse to perform and some parameters for specific analysis type
185 182
186 ----- 183 -----
187 184
188 **Outputs** 185 **Outputs**
189 186
190 The main output file is a tab-separated output file of the predicted taxon 187 The main output file is a tab-separated output file of the predicted taxon
191 relative abundances. 188 relative abundances.
192 189
193 Given the choosen parameters, other output files can be: 190 Given the choosen parameters, other output files can be:
194 191
195 * a sam output file 192 * a sam output file
196 * a biom output fime 193 * a biom output fime
197 * a BowTie2 output file 194 * a BowTie2 output file
198 195
199 ]]></help> 196 ]]></help>
200 197
201 <citations> 198 <citations>
202 <citation type="doi">10.1038/nmeth.3589</citation> 199 <citation type="doi">10.1038/nmeth.3589</citation>