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comparison metaphlan2.xml @ 1:11bb77fab91f draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 3f43a4146305ef11621ab786ab20b3ab46aca139-dirty
author bebatut
date Wed, 28 Oct 2015 11:37:45 -0400
parents 35d3ad2fb7a4
children 9f341c9cfa6a
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0:35d3ad2fb7a4 1:11bb77fab91f
90 <option value="g">Genera only</option> 90 <option value="g">Genera only</option>
91 <option value="s">Species only</option> 91 <option value="s">Species only</option>
92 </param> 92 </param>
93 </when> 93 </when>
94 <when value="marker_ab_table"> 94 <when value="marker_ab_table">
95 <param name="nreads" type="integer" label="Total number of reads in the original metagenome" help="It is used for normalizing the length-normalized counts with the metagenome size as well. No normalization applied if the value is not specified"/> 95 <param name="nreads" type="integer" value="0" label="Total number of reads in the original metagenome" help="It is used for normalizing the length-normalized counts with the metagenome size as well. No normalization applied if the value is not specified"/>
96 </when> 96 </when>
97 <when value="marker_pres_table"> 97 <when value="marker_pres_table">
98 <param name="pres_th" type="integer" label=" Threshold for calling a marker present" help=""/> 98 <param name="pres_th" type="integer" value="0" label=" Threshold for calling a marker present" help=""/>
99 </when> 99 </when>
100 </conditional> 100 </conditional>
101 101
102 <param name="min_cu_len" type="integer" value="2000" label="Minimum total nucleotide length for the markers in a clade for estimating the abundance without considering sub-clade abundances" help=""/> 102 <param name="min_cu_len" type="integer" value="2000" label="Minimum total nucleotide length for the markers in a clade for estimating the abundance without considering sub-clade abundances" help=""/>
103 103
104 <param name="min_alignment_len" type="integer" label="The sam records for aligned reads with the longest subalignment length smaller than this threshold will be discarded." help=""/> 104 <param name="min_alignment_len" type="integer" value="0" label="The sam records for aligned reads with the longest subalignment length smaller than this threshold will be discarded." help=""/>
105 105
106 <param name="ignore_viruses" type='boolean' checked="true" truevalue='' falsevalue='--ignore_viruses' label="Profile viral organisms?" help="" /> 106 <param name="ignore_viruses" type='boolean' checked="true" truevalue='' falsevalue='--ignore_viruses' label="Profile viral organisms?" help="" />
107 <param name="ignore_eukaryotes" type='boolean' checked="true" truevalue='' falsevalue='--ignore_eukaryotes' label="Profile eukaryotic organisms?" help="" /> 107 <param name="ignore_eukaryotes" type='boolean' checked="true" truevalue='' falsevalue='--ignore_eukaryotes' label="Profile eukaryotic organisms?" help="" />
108 <param name="ignore_bacteria" type='boolean' checked="true" truevalue='' falsevalue='--ignore_bacteria' label="Profile bacteria organisms?" help="" /> 108 <param name="ignore_bacteria" type='boolean' checked="true" truevalue='' falsevalue='--ignore_bacteria' label="Profile bacteria organisms?" help="" />
109 <param name="ignore_archaea" type='boolean' checked="true" truevalue='' falsevalue='--ignore_archaea' label="Profile archea organisms?" help="" /> 109 <param name="ignore_archaea" type='boolean' checked="true" truevalue='' falsevalue='--ignore_archaea' label="Profile archea organisms?" help="" />
157 157
158 ----- 158 -----
159 159
160 **Input** 160 **Input**
161 161
162 Metaphlan2 takes as input a sequence file in fasta, fastq, a BowTie2 produced
163 SAM file or an intermediary mapping file of the metagenome generated by a
164 previous MetaPhlAn
165
162 ----- 166 -----
163 167
164 **Parameters** 168 **Parameters**
165 169
170 Several parameters can modulate the MetaPhlAn execution
171
172 - Mapping arguments
173 - Test to avoid saving the output of BowTie2
174 - Post-mapping arguments
175 - 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
177 - 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
179 - Quantile value
180 - Additional analysis types and arguments
181 - Type of analyse to perform and some parameters for specific analysis type
182
166 ----- 183 -----
167 184
168 **Outputs** 185 **Outputs**
186
187 The main output file is a tab-separated output file of the predicted taxon
188 relative abundances.
189
190 Given the choosen parameters, other output files can be:
191
192 - a sam output file
193 - a biom output fime
194 - a BowTie2 output file
169 195
170 ]]></help> 196 ]]></help>
171 197
172 <citations> 198 <citations>
173 <citation type="doi">10.1038/nmeth.3589</citation> 199 <citation type="doi">10.1038/nmeth.3589</citation>