Mercurial > repos > iuc > picrust_compare_biom
annotate compare_biom.xml @ 3:9168545e09df draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
author | iuc |
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date | Sat, 18 Dec 2021 16:08:32 +0000 |
parents | 43244ad9e7ef |
children | 8e2ac1b8f70a |
rev | line source |
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3
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
parents:
0
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changeset
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1 <tool id="picrust_compare_biom" name="Compare BIOM tables" version="@TOOL_VERSION@.1"> |
0
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
diff
changeset
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2 <description>Compare the accuracy of biom files (expected and observed) either by observations (default) or by samples.</description> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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3 <macros> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
diff
changeset
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4 <import>macros.xml</import> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
diff
changeset
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5 </macros> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
diff
changeset
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6 <expand macro="requirements"/> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
diff
changeset
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7 <expand macro="version_command"/> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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8 <command detect_errors="exit_code"><![CDATA[ |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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9 compare_biom.py |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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changeset
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10 -e '$expected' |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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11 -o '$outfile' |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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changeset
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12 $not_relative_abundance_scores |
3
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
parents:
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13 $advanced.compare_observations |
0
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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14 $advanced.normalize |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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15 $advanced.limit_to_observed_observations |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
diff
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16 $advanced.limit_to_expected_observations |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
diff
changeset
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17 $advanced.shuffle_samples |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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changeset
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18 '$observed' |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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19 ]]></command> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
diff
changeset
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20 <inputs> |
3
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
parents:
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changeset
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21 <param argument="-o" name="observed" type="data" format="biom1" label="Observed table" help="The observed table of either relative abundance or real counts"/> |
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
parents:
0
diff
changeset
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22 <param argument="-e" name="expected" type="data" format="biom1" label="Expected table" help="The expected table of either relative abundance or real counts"/> |
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
parents:
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23 <param argument="--not_relative_abundance_scores" type="boolean" truevalue="--not_relative_abundance_scores" falsevalue="" checked="false" label="Real counts instead of relative abundances?" |
0
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
diff
changeset
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24 help="Round numbers (instead of taking ceil() which is used for RA) before calculating TP,FP,FN,TN"/> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
diff
changeset
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25 <section name="advanced" title="Advanced parameters" expanded="false"> |
3
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
parents:
0
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changeset
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26 <param argument="--compare_observations" type="boolean" truevalue="--compare_observations" falsevalue="" checked="false" label="Compare observations" |
0
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
diff
changeset
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27 help="Calculate accuracy values by comparing between observations (instead of between samples)."/> |
3
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
parents:
0
diff
changeset
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28 <param argument="--normalize" type="boolean" truevalue="--normalize" falsevalue="" checked="false" label="Normalize?" |
0
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
diff
changeset
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29 help="Convert both expected and observed tables to relative abundances (instead of observations)."/> |
3
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
parents:
0
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30 <param argument="--limit_to_observed_observations" type="boolean" truevalue="--limit_to_observed_observations" falsevalue="" checked="false" label="Limit to observed observations?" |
0
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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31 help="Ignore observations that are not in the observed table."/> |
3
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
parents:
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32 <param argument="--limit_to_expected_observations" type="boolean" truevalue="--limit_to_expected_observations" falsevalue="" checked="false" label="Limit to expected observations?" |
0
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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33 help="Ignore observations that are not in the expected table."/> |
3
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
parents:
0
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34 <param argument="--shuffle_samples" type="boolean" truevalue="--shuffle_samples" falsevalue="" checked="false" label="Shuffle samples?" |
0
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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35 help="Shuffle samples ids randomly before measuring accuracy."/> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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36 </section> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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37 </inputs> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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38 <outputs> |
3
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
parents:
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39 <data format="tabular" name="outfile" label="${tool.name} on ${on_string}"/> |
0
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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changeset
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40 </outputs> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
diff
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41 <tests> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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42 <test><!-- relative abundance test --> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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43 <param name="observed" value="observed_ra.biom" ftype="biom1"/> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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44 <param name="expected" value="expected_ra.biom" ftype="biom1"/> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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45 <output name="outfile" ftype="tabular"> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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46 <assert_contents> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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47 <has_text_matching expression="file\tlabel\taccuracy"/> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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48 <has_text text="sample1"/> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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49 <has_text text="sample3"/> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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50 <has_text text="sample2"/> |
3
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
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51 <has_n_lines n="4"/> |
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
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52 <has_n_columns n="16"/> |
0
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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53 </assert_contents> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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54 </output> |
3
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
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55 <assert_command> |
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
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56 <not_has_text text="--not_relative_abundance_scores"/> |
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
parents:
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57 <not_has_text text="--compare_observations"/> |
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
parents:
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58 <not_has_text text="--normalize"/> |
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
parents:
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59 <not_has_text text="--limit_to_observed_observations"/> |
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
parents:
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60 <not_has_text text="--limit_to_expected_observations"/> |
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
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61 <not_has_text text="--shuffle_samples"/> |
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
parents:
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62 </assert_command> |
0
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
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63 </test> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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64 <test><!-- real counts test --> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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65 <param name="observed" value="observed.biom" ftype="biom1"/> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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66 <param name="expected" value="expected.biom" ftype="biom1"/> |
3
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
parents:
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67 <param name="not_relative_abundance_scores" value="true"/> |
0
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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68 <output name="outfile" ftype="tabular"> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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69 <assert_contents> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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70 <has_text_matching expression="file\tlabel\taccuracy"/> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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71 <has_text text="sample1"/> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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72 <has_text text="sample3"/> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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73 <has_text text="sample2"/> |
3
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
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74 <has_n_lines n="4"/> |
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
parents:
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75 <has_n_columns n="16"/> |
0
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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76 </assert_contents> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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77 </output> |
3
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
parents:
0
diff
changeset
|
78 <assert_command> |
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
parents:
0
diff
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|
79 <has_text text="--not_relative_abundance_scores"/> |
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
parents:
0
diff
changeset
|
80 <not_has_text text="--compare_observations"/> |
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
parents:
0
diff
changeset
|
81 <not_has_text text="--normalize"/> |
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
parents:
0
diff
changeset
|
82 <not_has_text text="--limit_to_observed_observations"/> |
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
parents:
0
diff
changeset
|
83 <not_has_text text="--limit_to_expected_observations"/> |
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
parents:
0
diff
changeset
|
84 <not_has_text text="--shuffle_samples"/> |
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
parents:
0
diff
changeset
|
85 </assert_command> |
0
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
diff
changeset
|
86 </test> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
diff
changeset
|
87 <test><!-- all other switches test --> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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88 <param name="observed" value="observed.biom" ftype="biom1"/> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
diff
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89 <param name="expected" value="expected.biom" ftype="biom1"/> |
3
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
parents:
0
diff
changeset
|
90 <param name="not_relative_abundance_scores" value="true"/> |
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
parents:
0
diff
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|
91 <section name="advanced"> |
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
parents:
0
diff
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|
92 <param name="compare_observations" value="true"/> |
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
parents:
0
diff
changeset
|
93 <param name="normalize" value="true"/> |
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
parents:
0
diff
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|
94 <param name="limit_to_observed_observations" value="true"/> |
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
parents:
0
diff
changeset
|
95 <param name="limit_to_expected_observations" value="true"/> |
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
parents:
0
diff
changeset
|
96 <param name="shuffle_samples" value="true"/> |
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
parents:
0
diff
changeset
|
97 </section> |
0
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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98 <output name="outfile" ftype="tabular"> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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99 <assert_contents> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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100 <has_text_matching expression="file\tlabel\taccuracy"/> |
3
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
parents:
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101 <has_text text="K00005"/> |
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
parents:
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102 <has_text text="K00004"/> |
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
parents:
0
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changeset
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103 <has_text text="K00003"/> |
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
parents:
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104 <has_n_lines n="6"/> |
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
parents:
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105 <has_n_columns n="16"/> |
0
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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106 </assert_contents> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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107 </output> |
3
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
parents:
0
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|
108 <assert_command> |
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
parents:
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109 <has_text text="--not_relative_abundance_scores"/> |
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
parents:
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110 <has_text text="--compare_observations"/> |
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
parents:
0
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|
111 <has_text text="--normalize"/> |
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
parents:
0
diff
changeset
|
112 <has_text text="--limit_to_observed_observations"/> |
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
parents:
0
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|
113 <has_text text="--limit_to_expected_observations"/> |
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
parents:
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114 <has_text text="--shuffle_samples"/> |
9168545e09df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
iuc
parents:
0
diff
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|
115 </assert_command> |
0
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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116 </test> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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|
117 </tests> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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118 <help> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
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119 <![CDATA[ |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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120 @PICRUST_OVERVIEW@ |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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121 |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
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122 **Command Documentation** |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
diff
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|
123 |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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124 Compare an observed table to an expected table using either relative abundance or real counts. |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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125 |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
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126 **Input files:** |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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127 |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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128 **Observed table:** A table of observed relative abundances or real counts in .biom format. |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
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129 |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
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130 **Expected table:** The expected table of relative abundances or real counts in .biom format. |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
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parents:
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131 |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
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132 **Output file:** Tab delimited file with various accuracy metrics. |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
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|
133 |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
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134 **Optional Parameters:** |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
diff
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|
135 |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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|
136 *compare observations* |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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|
137 |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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|
138 Calculate accuracy values by comparing between observations (instead of between samples) [default: False] |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
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parents:
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|
139 |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
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140 *normalize* |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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|
141 |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
diff
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|
142 Convert both expected and observed tables to relative abundances (instead of observations) [default: False] |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
diff
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|
143 |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
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parents:
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|
144 *limit to expected observations* |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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|
145 |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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|
146 Ignore observations that are not in the expected table[default: False] |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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|
147 |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
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148 *limit to observed observations* |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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|
149 |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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|
150 Ignore observations that are not in the observed table[default: False] |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
diff
changeset
|
151 |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
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parents:
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|
152 *shuffle samples* |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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|
153 |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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|
154 Shuffle samples ids randomly before measuring accuracy[default: False] |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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|
155 |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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|
156 *not relative abundance scores* |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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|
157 |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
diff
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|
158 Round numbers (instead of taking ceil() which is used for RA) before calculating TP,FP,FN,TN [default: False] |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
parents:
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|
159 |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
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|
160 ]]> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
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161 </help> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
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162 <expand macro="citations"/> |
43244ad9e7ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
iuc
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163 </tool> |