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view filter_otus_from_otu_table.xml @ 2:18590df9277d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit e5d24fc90f811c8994ec8b72371ab4100d2c294c
author | iuc |
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date | Fri, 19 May 2017 04:08:21 -0400 |
parents | 8824c27efae2 |
children | e84a31935a8b |
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<tool id="qiime_filter_otus_from_otu_table" name="Filter otus from otu table" version="@WRAPPER_VERSION@.0"> <description>Filter OTUs from an OTU table based on their observation counts or identifier</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <version_command>filter_otus_from_otu_table.py --version</version_command> <command detect_errors="aggressive"><![CDATA[ filter_otus_from_otu_table.py --input_fp '$input_fp' --output_fp '$output_fp' #if $min_count != '': --min_count '$min_count' #end if #if $min_count_fraction != '': --min_count_fraction '$min_count_fraction' #end if #if $max_count != '': --max_count '$max_count' #end if #if $min_samples != '': --min_samples '$min_samples' #end if #if $max_samples != '': --max_samples '$max_samples' #end if #if $id_filtering_condition.id_filtering_switch == 'yes': --otu_ids_to_exclude_fp '$id_filtering_condition.otu_ids_to_exclude_fp' $id_filtering_condition.negate_ids_to_exclude #end if ]]></command> <inputs> <param argument="--input_fp" type="data" format="biom1" optional="False" label="Input OTU table" help="The input otu table filepath in biom format" /> <param argument="--min_count" type="integer" value="0" optional="True" label="Minimum total observation count of an otu for that otu to be retained" /> <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" /> <param argument="--max_count" type="integer" value="" optional="True" label="Maximum total observation count of an otu for that otu to be retained" /> <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" /> <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" /> <conditional name="id_filtering_condition"> <param name="id_filtering_switch" type="select" label="Do you want to exclude a predefined list of OTUs from the OTU table ?" > <option value="no" selected="true">No</option> <option value="yes">Yes</option> </param> <when value="no"/> <when value="yes"> <param argument="--otu_ids_to_exclude_fp" type="data" format="fasta,txt" optional="False" 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)" /> <param argument="--negate_ids_to_exclude" type="boolean" label="Do you want to reverse the filtering by ID / Chimera filtering ?" truevalue="--negate_ids_to_exclude" falsevalue="" checked="False" 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" /> </when> </conditional> </inputs> <outputs> <data name="output_fp" format="biom1" label="${tool.name} on ${on_string}: Filtered OTU table (biom format)"/> </outputs> <tests> <!-- 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 --> <!-- In addition, the files generated by 2 sucessive executions of filter_otus_from_otu_table with the same input files/data are slightly different --> <!-- As a consequence, md5 checksums/SHA hash are not a valid comparison option either --> <!-- 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 --> <test> <param name="input_fp" value="filter_otus_from_otu_table/otu_table.biom" /> <param name="min_count" value="2" /> <param name="max_count" value="1000" /> <param name="min_samples" value="5" /> <param name="max_samples" value="350" /> <conditional name="id_filtering_condition"> <param name="id_filtering_switch" value="no"/> </conditional> <output name="output_fp" file="filter_otus_from_otu_table/filtered_otu_table.biom" ftype="biom1" compare="sim_size" delta="0" /> </test> <test> <param name="input_fp" value="filter_otus_from_otu_table/otu_table.biom" /> <conditional name="id_filtering_condition"> <param name="id_filtering_switch" value="yes"/> <param name="otu_ids_to_exclude_fp" value="filter_otus_from_otu_table/chimeric_otus.txt"/> <param name="negate_ids_to_exclude" value="False"/> </conditional> <output name="output_fp" file="filter_otus_from_otu_table/chimera_filtered_otu_table.biom" ftype="biom1" compare="sim_size" delta="0" /> </test> <test> <param name="input_fp" value="filter_otus_from_otu_table/otu_table.biom" /> <conditional name="id_filtering_condition"> <param name="id_filtering_switch" value="yes"/> <param name="otu_ids_to_exclude_fp" value="filter_otus_from_otu_table/chimeric_otus.txt"/> <param name="negate_ids_to_exclude" value="True"/> </conditional> <output name="output_fp" file="filter_otus_from_otu_table/chimera_picked_otu_table.biom" ftype="biom1" compare="sim_size" delta="0" /> </test> </tests> <help><![CDATA[ **What it does** 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. 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/>`_. Different kind of filtering can be applied on the input biom file depending on the selected parameters: - Singleton filtering (minimum number of occurence) by using the -n/--min_count parameters - Abundance filtering (maximum number of occurence) by using the -x/--max_count parameters - Chimera filtering by using the -e/--otu_ids_to_exclude_fp parameters More information about this tool is available on `QIIME documentation <http://qiime.org/scripts/filter_otus_from_otu_table.html>`_. ]]></help> <citations> <expand macro="citations"/> </citations> </tool>