Mercurial > repos > iuc > qiime_make_otu_table
annotate make_otu_table.xml @ 0:e00b6983b175 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
author | iuc |
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date | Mon, 10 Jul 2017 16:39:15 -0400 |
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e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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1 <tool id="qiime_make_otu_table" name="Make OTU table" version="@WRAPPER_VERSION@.0"> |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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2 <description>Make an OTU table from an OTU map and a taxonomy assignment file</description> |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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3 <macros> |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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4 <import>macros.xml</import> |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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5 </macros> |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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6 <expand macro="requirements"/> |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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7 <version_command>make_otu_table.py --version</version_command> |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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8 <command detect_errors="aggressive"><![CDATA[ |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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9 make_otu_table.py |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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10 --otu_map_fp '$otu_map_fp' |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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11 --output_biom_fp '$output_biom_fp' |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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12 #if $taxonomy |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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13 --taxonomy '$taxonomy' |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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14 #end if |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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15 #if $exclude_otus_fp |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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16 --exclude_otus_fp '$exclude_otus_fp' |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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17 #end if |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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18 #if $mapping_fp |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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19 --mapping_fp '$mapping_fp' |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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20 #end if |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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21 ]]></command> |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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22 <inputs> |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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23 <param argument="--otu_map_fp" type="data" format="tabular,txt,biom" label="OTU map" help="An OTU map file generated by the pick_otus.py script" /> |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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24 <param argument="--taxonomy" type="data" format="txt" optional="True" label="Taxonomy assignment" help="Text file generated by the assign_taxonomy.py script and contains the assignments of taxons to sequences" /> |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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25 <param argument="--exclude_otus_fp" type="data" format="tabular,fasta,txt" optional="True" label="List of OTU identifiers to reject" help="A text file listing OTU identifiers that should not be included in the OTU table (generated by the identify_chimeric_seqs.py script) or a failure file in fasta format (generated by the align_seqs.py script)" /> |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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26 <param argument="--mapping_fp" type="data" format="tabular,txt" optional="True" label="Validated mapping file" help="A mapping file in tabular format verified by the validate_mapping_file.py script" /> |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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27 </inputs> |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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28 <outputs> |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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29 <data name="output_biom_fp" format="biom1" label="${tool.name} on ${on_string}: OTU table (biom format)"/> |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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30 </outputs> |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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31 <tests> |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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32 <!-- Qiime make_otu_table.py generates a binary file that can't be compared directly with diff --> |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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33 <!-- In addition, the files generated by 2 different executions of make_otu_table with the same input data are different --> |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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34 <!-- As a consequence, standard comparisons based on "diff" or md5 checksums/SHA hash are impossible --> |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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35 <!-- The following tests are then based on a comparison of file sizes with a maximum delta of 0 bytes --> |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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36 <test> |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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37 <param name="otu_map_fp" value="make_otu_table/otu_map.txt" /> |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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38 <param name="taxonomy" value="make_otu_table/tax_assignments.txt" /> |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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39 <param name="exclude_otus_fp" value="make_otu_table/chimeric_seqs.txt" /> |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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40 <param name="mapping_fp" value="make_otu_table/mapping_file.txt" /> |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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41 <output name="output_biom_fp" file="make_otu_table/OTU_table_chimeric.biom" compare="sim_size" /> |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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42 </test> |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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43 <test> |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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44 <param name="otu_map_fp" value="make_otu_table/otu_map.txt" /> |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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45 <param name="taxonomy" value="make_otu_table/tax_assignments.txt" /> |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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46 <param name="exclude_otus_fp" value="make_otu_table/pynast_failures.fna" /> |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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47 <param name="mapping_fp" value="make_otu_table/mapping_file.txt" /> |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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48 <output name="output_biom_fp" file="make_otu_table/OTU_table_pynast.biom" compare="sim_size" /> |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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49 </test> |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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50 </tests> |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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51 <help><![CDATA[ |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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52 **What it does** |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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53 |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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54 The script `make_otu_table.py <http://qiime.org/scripts/make_otu_table.html>`_ tabulates the number of times an OTU is found in each |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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55 sample, and adds the taxonomic predictions for each OTU in the last column if a taxonomy file is supplied. |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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56 |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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57 The output of `make_otu_table.py <http://qiime.org/scripts/make_otu_table.html>`_ is a `biom file <http://biom-format.org/>`_, where the columns correspond to |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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58 Samples and rows correspond to OTUs and the number of times a sample appears in a particular OTU. |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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59 |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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60 More information about this tool is available on |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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61 `QIIME documentation <http://qiime.org/scripts/make_otu_table.html>`_. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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62 ]]></help> |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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63 <citations> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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64 <expand macro="citations"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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65 </citations> |
e00b6983b175
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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66 </tool> |