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comparison metaphlan2.xml @ 1:8991e05c44e4 draft default tip

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit c641bf32192cd4281a14f504fc97f1dc6edd6f7a-dirty
author bebatut
date Thu, 16 Jun 2016 06:08:11 -0400
parents d2448d2bf1f8
children
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0:d2448d2bf1f8 1:8991e05c44e4
144 <param name="stat_q" type="float" value="0.1" label="Quantile value for the robust average" help=""/> 144 <param name="stat_q" type="float" value="0.1" label="Quantile value for the robust average" help=""/>
145 </inputs> 145 </inputs>
146 146
147 <outputs> 147 <outputs>
148 <data format="tabular" name="output_file" label="${tool.name} on ${on_string}: Community profile" /> 148 <data format="tabular" name="output_file" label="${tool.name} on ${on_string}: Community profile" />
149 <data format="sam" name="sam_output_file" label="${tool.name} on ${on_string}: Sam file" /> 149 <data format="sam" name="sam_output_file" label="${tool.name} on ${on_string}: SAM file" />
150 </outputs> 150 </outputs>
151 151
152 <tests> 152 <tests>
153 <test> 153 <test>
154 <param name="input_file" value="input_sequences.fasta"/> 154 <param name="input_file" value="input_sequences.fasta"/>
169 </tests> 169 </tests>
170 170
171 <help><![CDATA[ 171 <help><![CDATA[
172 **What it does** 172 **What it does**
173 173
174 MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution. For more information, check the `user manual <https://bitbucket.org/biobakery/metaphlan2/>`_. 174 MetaPhlAn is a computational tool to profile the structure and the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution. For more information, check the `user manual <https://bitbucket.org/biobakery/metaphlan2/>`_.
175 175
176 **Inputs** 176 **Inputs**
177 177
178 Metaphlan2 takes as input a sequence file in fasta, fastq, a BowTie2 produced SAM file. 178 Metaphlan2 takes as input a sequence file in fasta, fastq, a BowTie2 produced SAM file.
179 179
197 } 197 }
198 ... 198 ...
199 } 199 }
200 } 200 }
201 201
202 The marker names correspond to sequence name in corresponding fasta file with marker gene sequences. 202 The marker name correspond to the corresponding sequence name in the FastA file containing marker gene sequences.
203 203
204 **Outputs** 204 **Outputs**
205 205
206 The main output file is a tab-separated output file of the predicted taxon relative abundances. 206 The main output file is a tab-separated file with the predicted taxon relative abundances.
207 207
208 ]]></help> 208 ]]></help>
209 209
210 <citations> 210 <citations>
211 <citation type="doi">10.1038/nmeth.3589</citation> 211 <citation type="doi">10.1038/nmeth.3589</citation>