Mercurial > repos > bebatut > metaphlan2
annotate metaphlan2krona.xml @ 1:8991e05c44e4 draft default tip
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit c641bf32192cd4281a14f504fc97f1dc6edd6f7a-dirty
| author | bebatut |
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| date | Thu, 16 Jun 2016 06:08:11 -0400 |
| parents | d2448d2bf1f8 |
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| rev | line source |
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d2448d2bf1f8
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
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1 <tool id="metaphlan2krona" name="Format MetaPhlAn2" version="2.5.0"> |
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d2448d2bf1f8
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
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d2448d2bf1f8
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
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3 <description>output for Krona</description> |
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d2448d2bf1f8
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
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d2448d2bf1f8
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
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5 <macros> |
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d2448d2bf1f8
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
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6 <import>metaphlan2_macros.xml</import> |
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d2448d2bf1f8
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
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7 </macros> |
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d2448d2bf1f8
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
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d2448d2bf1f8
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
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9 <expand macro="requirements"/> |
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8991e05c44e4
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit c641bf32192cd4281a14f504fc97f1dc6edd6f7a-dirty
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10 <expand macro="stdio"/> |
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d2448d2bf1f8
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
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11 |
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d2448d2bf1f8
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
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12 <version_command> |
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d2448d2bf1f8
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
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13 <![CDATA[ |
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d2448d2bf1f8
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
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14 metaphlan2krona.py -v |
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d2448d2bf1f8
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
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15 ]]> |
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d2448d2bf1f8
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
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16 </version_command> |
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d2448d2bf1f8
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
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d2448d2bf1f8
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
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18 <command> |
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8991e05c44e4
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit c641bf32192cd4281a14f504fc97f1dc6edd6f7a-dirty
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19 <![CDATA[ |
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d2448d2bf1f8
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
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20 metaphlan2krona.py |
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d2448d2bf1f8
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
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21 -p $input_file |
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d2448d2bf1f8
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
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22 -k $krona |
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d2448d2bf1f8
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
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23 ]]> |
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d2448d2bf1f8
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
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24 </command> |
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d2448d2bf1f8
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
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25 |
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d2448d2bf1f8
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
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26 <inputs> |
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d2448d2bf1f8
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
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27 <param name="input_file" type="data" format="tabular,txt" label="Input file (MetaPhlAN2 output)" help="(--profile)"/> |
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d2448d2bf1f8
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
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28 </inputs> |
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d2448d2bf1f8
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
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d2448d2bf1f8
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
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30 <outputs> |
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8991e05c44e4
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit c641bf32192cd4281a14f504fc97f1dc6edd6f7a-dirty
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31 <data format="tabular" name="krona" label="${tool.name} on ${on_string}: Formatted file for Krona" /> |
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d2448d2bf1f8
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
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32 </outputs> |
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d2448d2bf1f8
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
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33 |
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d2448d2bf1f8
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
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34 <tests> |
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d2448d2bf1f8
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
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35 <test> |
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d2448d2bf1f8
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
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36 <param name="input_file" value="community_profile.tabular"/> |
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d2448d2bf1f8
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
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37 <output name="krona" file="formatted_to_krona.tabular"/> |
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8991e05c44e4
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit c641bf32192cd4281a14f504fc97f1dc6edd6f7a-dirty
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38 </test> |
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d2448d2bf1f8
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
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39 </tests> |
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d2448d2bf1f8
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
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40 |
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d2448d2bf1f8
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
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41 <help><![CDATA[ |
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d2448d2bf1f8
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
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42 |
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d2448d2bf1f8
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
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43 **What it does** |
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d2448d2bf1f8
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
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44 |
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8991e05c44e4
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit c641bf32192cd4281a14f504fc97f1dc6edd6f7a-dirty
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45 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/>`_. |
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d2448d2bf1f8
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
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46 |
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8991e05c44e4
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit c641bf32192cd4281a14f504fc97f1dc6edd6f7a-dirty
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47 This tool formats MetaPhlAn2 output to be ready for Krona. |
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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
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48 |
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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
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49 ]]></help> |
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d2448d2bf1f8
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
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50 |
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d2448d2bf1f8
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
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51 <citations> |
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d2448d2bf1f8
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
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52 <citation type="doi">10.1038/nmeth.3589</citation> |
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d2448d2bf1f8
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
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53 </citations> |
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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit c641bf32192cd4281a14f504fc97f1dc6edd6f7a-dirty
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54 </tool> |