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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit d28e31b1b4dbcc3c406a4e8a5a41ac4576bf4f43-dirty
author bebatut
date Tue, 02 Feb 2016 03:13:51 -0500
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1479a794253d planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit d28e31b1b4dbcc3c406a4e8a5a41ac4576bf4f43-dirty
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1 <tool id="metaphlan2krona" name="Format MetaPhlAn2" version="0.1.0">
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3 <description>output for Krona</description>
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5 <requirements>
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6 <requirement type="package" version="2.2.5">bowtie2</requirement>
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7 <requirement type="package" version="2.0">metaphlan2</requirement>
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8 </requirements>
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10 <stdio>
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11 <exit_code range="1:" level="fatal" description="" />
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12 <regex match="ERROR"
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13 source="stderr"
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14 level="fatal"
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15 description="" />
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16 <regex match="WARNING"
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17 source="stderr"
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18 level="warning"
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19 description="" />
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20 </stdio>
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22 <version_command>
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23 <![CDATA[
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24 python \${METAPHLAN2_DIR}/utils/metaphlan2krona.py -v
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25 ]]>
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26 </version_command>
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28 <command>
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29 <![CDATA[
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30 python \${METAPHLAN2_DIR}/utils/metaphlan2krona.py
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31 -p $input_file
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32 -k $krona
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33 ]]>
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34 </command>
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36 <inputs>
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37 <param name="input_file" type="data" format="tabular,txt" label="Input
1479a794253d planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit d28e31b1b4dbcc3c406a4e8a5a41ac4576bf4f43-dirty
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38 file (MetaPhlAN2 output)" help="(--profile)"/>
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39 </inputs>
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41 <outputs>
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42 <data format="tabular" name="krona"
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43 label="${tool.name} on ${on_string}: Krona file" />
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44 </outputs>
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45
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46 <tests>
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47 </tests>
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49 <help><![CDATA[
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50
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51 **What it does**
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52
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53 MetaPhlAn is a computational tool for profiling the composition of microbial
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54 communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun
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55 sequencing data with species level resolution. For more information, check the
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56 `user manual <https://bitbucket.org/biobakery/metaphlan2/>`_.
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57
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58 This tool format MetaPhlAn2 output for Krona.
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59
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60 ]]></help>
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61
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62 <citations>
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63 <citation type="doi">10.1038/nmeth.3589</citation>
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64 </citations>
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65 </tool>