Mercurial > repos > iuc > biom_subset_table
annotate biom_subset_table.xml @ 1:b45ef5bb4241 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f1b3e36f79747fca391321389276ac196d3f7cd0"
| author | iuc |
|---|---|
| date | Fri, 24 Jan 2020 16:40:01 -0500 |
| parents | 806ff6f90364 |
| children | 9d84e99a4253 |
| rev | line source |
|---|---|
|
0
806ff6f90364
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
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changeset
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1 <tool id="biom_subset_table" name="Subset" version="@VERSION@.1"> |
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806ff6f90364
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
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2 <description>a BIOM table</description> |
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806ff6f90364
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
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3 <macros> |
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806ff6f90364
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff
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4 <import>macros.xml</import> |
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806ff6f90364
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff
changeset
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5 </macros> |
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806ff6f90364
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
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changeset
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6 <expand macro="requirements" /> |
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806ff6f90364
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff
changeset
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7 <expand macro="version_command" /> |
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806ff6f90364
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff
changeset
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8 <command detect_errors="exit_code"> |
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806ff6f90364
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff
changeset
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9 <![CDATA[ |
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806ff6f90364
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff
changeset
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10 biom subset-table |
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806ff6f90364
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff
changeset
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11 --input-json-fp '$input_json_fp' |
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806ff6f90364
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff
changeset
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12 --output-fp '$output_fp' |
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806ff6f90364
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff
changeset
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13 --axis '$axis' |
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806ff6f90364
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff
changeset
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14 --ids '$ids' |
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806ff6f90364
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff
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15 ]]> |
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806ff6f90364
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff
changeset
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16 </command> |
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806ff6f90364
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff
changeset
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17 <inputs> |
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806ff6f90364
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff
changeset
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18 <param name="input_json_fp" argument="--input-json-fp" type="data" format="biom1" label="BIOM table to subset" /> |
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806ff6f90364
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff
changeset
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19 <param argument="--axis" type="select" label="The axis to subset over"> |
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806ff6f90364
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff
changeset
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20 <option value="sample" selected="True">Sample</option> |
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806ff6f90364
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff
changeset
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21 <option value="observation">Observation</option> |
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806ff6f90364
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff
changeset
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22 </param> |
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806ff6f90364
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff
changeset
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23 <param argument="--ids" type="data" format="text,tabular" label="file containing a single column of IDs to retain" /> |
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806ff6f90364
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff
changeset
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24 </inputs> |
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806ff6f90364
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff
changeset
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25 <outputs> |
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806ff6f90364
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff
changeset
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26 <data format="biom1" name="output_fp"/> |
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806ff6f90364
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff
changeset
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27 </outputs> |
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806ff6f90364
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff
changeset
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28 <tests> |
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806ff6f90364
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff
changeset
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29 <test> |
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806ff6f90364
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff
changeset
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30 <param name="input_json_fp" value="input_abundance_1.biom1" /> |
|
806ff6f90364
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff
changeset
|
31 <param name="axis" value="sample" /> |
|
806ff6f90364
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff
changeset
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32 <param name="ids" value="sample_subsetting" /> |
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806ff6f90364
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff
changeset
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33 <output name="output_fp" file="subset_samples.biom" ftype="biom1" compare="sim_size"/> |
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806ff6f90364
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff
changeset
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34 </test> |
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806ff6f90364
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff
changeset
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35 <test> |
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806ff6f90364
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff
changeset
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36 <param name="input_json_fp" value="input_abundance_1.biom1" /> |
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806ff6f90364
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff
changeset
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37 <param name="axis" value="observation" /> |
|
806ff6f90364
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff
changeset
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38 <param name="ids" value="observation_subsetting" /> |
|
806ff6f90364
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff
changeset
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39 <output name="output_fp" file="subset_observations.biom" ftype="biom1" compare="sim_size"/> |
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806ff6f90364
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff
changeset
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40 </test> |
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806ff6f90364
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff
changeset
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41 </tests> |
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806ff6f90364
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
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changeset
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42 <help><![CDATA[ |
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806ff6f90364
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff
changeset
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43 Subset a BIOM table, over either observations or samples, without fully parsing it. This command is intended to assist in working with very large tables when tight on memory, or as a lightweight way to subset a full table. Currently, it is possible to produce tables with rows or columns (observations or samples) that are fully zeroed. |
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806ff6f90364
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
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44 ]]></help> |
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806ff6f90364
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
diff
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45 <expand macro="citations" /> |
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806ff6f90364
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents:
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46 </tool> |