Mercurial > repos > iuc > biom_summarize_table
annotate biom_summarize_table.xml @ 7:d44a91ba162b draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 5fc41e15cb372b3ae635c550c387ccd41af166f7
| author | iuc |
|---|---|
| date | Sat, 21 Jan 2023 11:15:46 +0000 |
| parents | 08263138e233 |
| children |
| rev | line source |
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08263138e233
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 4ca0a67fd4126f8b2a135b6cb7894042e980b39a"
iuc
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1 <tool id="biom_summarize_table" name="Summarize sample or observation data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
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b0d014ba42c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
iuc
parents:
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2 <description>in a BIOM table</description> |
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b0d014ba42c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
iuc
parents:
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3 <macros> |
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b0d014ba42c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
iuc
parents:
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4 <import>macros.xml</import> |
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b0d014ba42c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
iuc
parents:
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5 </macros> |
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b0d014ba42c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
iuc
parents:
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6 <expand macro="requirements" /> |
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b0d014ba42c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
iuc
parents:
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7 <expand macro="version_command" /> |
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b0d014ba42c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
iuc
parents:
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8 <command detect_errors="exit_code"> |
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b0d014ba42c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
iuc
parents:
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9 <![CDATA[ |
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b0d014ba42c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
iuc
parents:
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10 biom summarize-table |
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b0d014ba42c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
iuc
parents:
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changeset
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11 --input-fp '$input_fp' |
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b0d014ba42c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
iuc
parents:
diff
changeset
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12 --output-fp '$output_fp' |
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b0d014ba42c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
iuc
parents:
diff
changeset
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13 $qualitative |
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b0d014ba42c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
iuc
parents:
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14 $observations |
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b0d014ba42c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
iuc
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15 ]]> |
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b0d014ba42c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
iuc
parents:
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changeset
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16 </command> |
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b0d014ba42c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
iuc
parents:
diff
changeset
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17 <inputs> |
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b0d014ba42c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
iuc
parents:
diff
changeset
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18 <param name="input_fp" argument="--input-fp" type="data" format="biom1" label="Input BIOM table" /> |
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b0d014ba42c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
iuc
parents:
diff
changeset
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19 <param argument="--qualitative" type="boolean" checked="True" truevalue="--qualitative" falsevalue="" label="Present counts as number of unique observation ids per sample, rather than counts of observations per sample" /> |
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b0d014ba42c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
iuc
parents:
diff
changeset
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20 <param argument="--observations" type="boolean" checked="True" truevalue="--observations" falsevalue="" label="Summarize over observations" /> |
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b0d014ba42c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
iuc
parents:
diff
changeset
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21 </inputs> |
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b0d014ba42c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
iuc
parents:
diff
changeset
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22 <outputs> |
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b0d014ba42c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
iuc
parents:
diff
changeset
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23 <data format="text" name="output_fp"/> |
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b0d014ba42c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
iuc
parents:
diff
changeset
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24 </outputs> |
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b0d014ba42c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
iuc
parents:
diff
changeset
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25 <tests> |
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b0d014ba42c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
iuc
parents:
diff
changeset
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26 <test> |
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b0d014ba42c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
iuc
parents:
diff
changeset
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27 <param name="input_fp" value="input_abundance_1.biom1" /> |
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b0d014ba42c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
iuc
parents:
diff
changeset
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28 <param name="qualitative" value="" /> |
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b0d014ba42c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
iuc
parents:
diff
changeset
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29 <param name="observations" value="" /> |
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b0d014ba42c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
iuc
parents:
diff
changeset
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30 <output name="output_fp" value="summarize" compare="sim_size"/> |
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b0d014ba42c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
iuc
parents:
diff
changeset
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31 </test> |
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b0d014ba42c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
iuc
parents:
diff
changeset
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32 <test> |
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b0d014ba42c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
iuc
parents:
diff
changeset
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33 <param name="input_fp" value="input_abundance_1.biom1" /> |
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b0d014ba42c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
iuc
parents:
diff
changeset
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34 <param name="qualitative" value="--qualitative" /> |
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b0d014ba42c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
iuc
parents:
diff
changeset
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35 <param name="observations" value="--observations" /> |
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b0d014ba42c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
iuc
parents:
diff
changeset
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36 <output name="output_fp" value="summarize_qualitative_observations" compare="sim_size"/> |
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b0d014ba42c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
iuc
parents:
diff
changeset
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37 </test> |
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b0d014ba42c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
iuc
parents:
diff
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38 </tests> |
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b0d014ba42c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
iuc
parents:
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39 <help><![CDATA[ |
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b0d014ba42c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
iuc
parents:
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40 Provides details on the observation counts per sample, including summary statistics, as well as metadata categories associated with samples and observations. |
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b0d014ba42c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
iuc
parents:
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41 ]]></help> |
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b0d014ba42c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
iuc
parents:
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42 <expand macro="citations" /> |
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b0d014ba42c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
iuc
parents:
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43 </tool> |