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author bebatut
date Wed, 20 Apr 2016 07:52:22 -0400
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aa68d226892e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty
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1 <tool id="format_metaphlan2_output" name="Format MetaPhlAn2" version="0.1.0">
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2 <description>output to extract abundance at different taxonomic levels</description>
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4 <requirements>
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5 </requirements>
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7 <stdio>
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8 </stdio>
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10 <version_command></version_command>
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12 <command><![CDATA[
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13 python $__tool_directory__/format_metaphlan2_output.py
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14 --metaphlan2_output $input_file
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15 --all_taxo_level_abundance_file $all_taxo_level_abundance_file
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16 --kingdom_abundance_file $kingdom_abundance_file
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17 --phylum_abundance_file $phylum_abundance_file
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18 --class_abundance_file $class_abundance_file
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19 --order_abundance_file $order_abundance_file
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20 --family_abundance_file $family_abundance_file
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21 --genus_abundance_file $genus_abundance_file
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22 --species_abundance_file $species_abundance_file
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23 --strains_abundance_file $strains_abundance_file
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24 ]]></command>
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25
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26 <inputs>
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27 <param name="input_file" type="data" format="tabular,tsv,csv" label="Input file" help="Output file of MetaPhlAN with all taxonomic levels (from kingdom to strains, --metaphlan2_output)"/>
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28 </inputs>
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29
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30 <outputs>
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31 <data name="all_taxo_level_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Abundances for all taxonomic levels" />
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32 <data name="kingdom_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Kingdom abundances" />
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33 <data name="phylum_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Phylum abundances" />
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34 <data name="class_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Class abundances" />
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35 <data name="order_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Order abundances" />
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36 <data name="family_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Family abundances" />
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37 <data name="genus_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Genus abundances" />
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38 <data name="species_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Species abundances" />
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39 <data name="strains_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Stain abundances" />
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40 </outputs>
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41
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42 <tests>
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43 <test>
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44 <param name="input_file" value="metaphlan2_output.txt"/>
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45 <output name="all_taxo_level_abundance_file" file="all_taxo_level_abundance.txt"/>
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46 <output name="kingdom_abundance_file" file="kingdom_abundance.txt"/>
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47 <output name="phylum_abundance_file" file="phylum_abundance.txt"/>
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48 <output name="class_abundance_file" file="class_abundance.txt"/>
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49 <output name="order_abundance_file" file="order_abundance.txt"/>
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50 <output name="family_abundance_file" file="family_abundance.txt"/>
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51 <output name="genus_abundance_file" file="genus_abundance.txt"/>
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52 <output name="species_abundance_file" file="species_abundance.txt"/>
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53 <output name="strains_abundance_file" file="strains_abundance.txt"/>
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54 </test>
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55 </tests>
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56
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57 <help><![CDATA[
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58 **What it does**
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59
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60 This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains).
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61
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62 9 files are generated: one file per taxonomic levels with abundance for corresponding clades and one file combining all taxonomic levels and corresponding abundances.
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63 ]]></help>
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64
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65 <citations>
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66 </citations>
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67 </tool>