Mercurial > repos > iuc > qiime_filter_otus_from_otu_table
annotate filter_otus_from_otu_table.xml @ 5:e84a31935a8b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
author | iuc |
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date | Sat, 05 Aug 2017 07:31:22 -0400 |
parents | 8824c27efae2 |
children | 9db0d2cf4451 |
rev | line source |
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5
e84a31935a8b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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1 <tool id="qiime_filter_otus_from_otu_table" name="Filter OTUs from an OTU table" version="@WRAPPER_VERSION@.0"> |
e84a31935a8b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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2 <description> based on their observation counts or identifier (filter_otus_from_otu_table)</description> |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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3 <macros> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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4 <import>macros.xml</import> |
8824c27efae2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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5 </macros> |
8824c27efae2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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6 <expand macro="requirements"/> |
8824c27efae2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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7 <version_command>filter_otus_from_otu_table.py --version</version_command> |
8824c27efae2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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8 <command detect_errors="aggressive"><![CDATA[ |
5
e84a31935a8b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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9 filter_otus_from_otu_table.py |
e84a31935a8b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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10 --input_fp '$input_fp' |
e84a31935a8b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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11 --output_fp '$output_fp' |
e84a31935a8b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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12 #if $min_count != '': |
e84a31935a8b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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13 --min_count '$min_count' |
e84a31935a8b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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14 #end if |
e84a31935a8b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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15 #if $min_count_fraction != '': |
e84a31935a8b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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16 --min_count_fraction '$min_count_fraction' |
e84a31935a8b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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17 #end if |
e84a31935a8b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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18 #if $max_count != '': |
e84a31935a8b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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19 --max_count '$max_count' |
e84a31935a8b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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20 #end if |
e84a31935a8b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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21 #if $min_samples != '': |
e84a31935a8b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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22 --min_samples '$min_samples' |
e84a31935a8b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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23 #end if |
e84a31935a8b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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24 #if $max_samples != '': |
e84a31935a8b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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25 --max_samples '$max_samples' |
e84a31935a8b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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26 #end if |
e84a31935a8b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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27 #if $id_filtering_condition.id_filtering_switch == 'yes': |
e84a31935a8b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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28 --otu_ids_to_exclude_fp '$id_filtering_condition.otu_ids_to_exclude_fp' |
e84a31935a8b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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29 $id_filtering_condition.negate_ids_to_exclude |
e84a31935a8b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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30 #end if |
0
8824c27efae2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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31 ]]></command> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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32 <inputs> |
5
e84a31935a8b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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33 <param argument="--input_fp" type="data" format="biom1" optional="false" label="Input OTU table" help="The input otu table filepath in biom format" /> |
e84a31935a8b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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34 <param argument="--min_count" type="integer" value="0" optional="true" label="Minimum total observation count of an otu for that otu to be retained" /> |
e84a31935a8b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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35 <param argument="--min_count_fraction" type="float" value="0.0" optional="true" label="Fraction of the total observation (sequence) count to apply as the minimum total observation count of an otu for that otu to be retained" help="This is a fraction (float), not a percentage, so if you want to filter to 1%, you need to use 0.01 as value here" /> |
e84a31935a8b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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36 <param argument="--max_count" type="integer" value="" optional="true" label="Maximum total observation count of an otu for that otu to be retained" /> |
e84a31935a8b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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37 <param argument="--min_samples" type="integer" value="0" optional="true" label="Minimum number of samples an OTU must be observed in for that otu to be retained" /> |
e84a31935a8b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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38 <param argument="--max_samples" type="integer" value="" optional="true" label="Maximum number of samples an OTU must be observed in for that otu to be retained" /> |
0
8824c27efae2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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39 <conditional name="id_filtering_condition"> |
5
e84a31935a8b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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40 <param name="id_filtering_switch" type="select" label="Do you want to exclude a predefined list of OTUs from the OTU table?" > |
0
8824c27efae2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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41 <option value="no" selected="true">No</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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42 <option value="yes">Yes</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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43 </param> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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44 <when value="no"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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45 <when value="yes"> |
5
e84a31935a8b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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46 <param argument="--otu_ids_to_exclude_fp" type="data" format="fasta,txt" label="Filtering by ID / Chimera filtering - Input text/Fasta file containing a list of OTU ids to exclude" help="The selected file can be a text file with one id per line, a text file where id is the first value in a tab-separated line, or can be a fasta file (extension must be .fna or .fasta)" /> |
e84a31935a8b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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47 <param argument="--negate_ids_to_exclude" type="boolean" truevalue="--negate_ids_to_exclude" falsevalue="" checked="false" label="Do you want to reverse the filtering by ID / Chimera filtering ?" help="When this parameter is set to yes, then only the OTUs listed in the file passed to the --otu_ids_to_exclude_fp parameters will be kept in the output biom file" /> |
0
8824c27efae2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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48 </when> |
8824c27efae2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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49 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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50 </inputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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51 <outputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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52 <data name="output_fp" format="biom1" label="${tool.name} on ${on_string}: Filtered OTU table (biom format)"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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53 </outputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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54 <tests> |
8824c27efae2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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55 <!-- Qiime filter_otus_from_otu_table.py generates a binary file (filtered biom file) that can't be directly compared to the sample biom file using diff --> |
8824c27efae2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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56 <!-- In addition, the files generated by 2 sucessive executions of filter_otus_from_otu_table with the same input files/data are slightly different --> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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57 <!-- As a consequence, md5 checksums/SHA hash are not a valid comparison option either --> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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58 <!-- The following tests on output biom files are then based on a comparison of file sizes with a maximum delta of 0 bytes instead of the classic diff-based comparison --> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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59 <test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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60 <param name="input_fp" value="filter_otus_from_otu_table/otu_table.biom" /> |
8824c27efae2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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61 <param name="min_count" value="2" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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62 <param name="max_count" value="1000" /> |
8824c27efae2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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63 <param name="min_samples" value="5" /> |
8824c27efae2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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64 <param name="max_samples" value="350" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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65 <conditional name="id_filtering_condition"> |
8824c27efae2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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66 <param name="id_filtering_switch" value="no"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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67 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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68 <output name="output_fp" file="filter_otus_from_otu_table/filtered_otu_table.biom" ftype="biom1" compare="sim_size" delta="0" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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69 </test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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70 <test> |
8824c27efae2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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71 <param name="input_fp" value="filter_otus_from_otu_table/otu_table.biom" /> |
8824c27efae2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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72 <conditional name="id_filtering_condition"> |
8824c27efae2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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73 <param name="id_filtering_switch" value="yes"/> |
8824c27efae2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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74 <param name="otu_ids_to_exclude_fp" value="filter_otus_from_otu_table/chimeric_otus.txt"/> |
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75 <param name="negate_ids_to_exclude" value="False"/> |
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76 </conditional> |
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77 <output name="output_fp" file="filter_otus_from_otu_table/chimera_filtered_otu_table.biom" ftype="biom1" compare="sim_size" delta="0" /> |
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78 </test> |
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79 <test> |
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80 <param name="input_fp" value="filter_otus_from_otu_table/otu_table.biom" /> |
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81 <conditional name="id_filtering_condition"> |
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82 <param name="id_filtering_switch" value="yes"/> |
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83 <param name="otu_ids_to_exclude_fp" value="filter_otus_from_otu_table/chimeric_otus.txt"/> |
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84 <param name="negate_ids_to_exclude" value="True"/> |
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85 </conditional> |
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86 <output name="output_fp" file="filter_otus_from_otu_table/chimera_picked_otu_table.biom" ftype="biom1" compare="sim_size" delta="0" /> |
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87 </test> |
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88 </tests> |
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89 <help><![CDATA[ |
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90 **What it does** |
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91 |
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92 The Qiime script `filter_otus_from_otu_table.py <http://qiime.org/scripts/filter_otus_from_otu_table.html>`_ filter OTUs from an OTU table based on their observation counts or identifier. |
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93 |
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94 The output of `filter_otus_from_otu_table.py <http://qiime.org/scripts/filter_otus_from_otu_table.html>`_ is a `biom file <http://biom-format.org/>`_. |
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95 |
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96 Different kind of filtering can be applied on the input biom file depending on the selected parameters: |
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97 - Singleton filtering (minimum number of occurence) by using the -n/--min_count parameters |
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98 - Abundance filtering (maximum number of occurence) by using the -x/--max_count parameters |
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99 - Chimera filtering by using the -e/--otu_ids_to_exclude_fp parameters |
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100 |
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101 More information about this tool is available on |
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102 `QIIME documentation <http://qiime.org/scripts/filter_otus_from_otu_table.html>`_. |
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103 ]]></help> |
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104 <citations> |
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105 <expand macro="citations"/> |
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106 </citations> |
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107 </tool> |