Mercurial > repos > iuc > qiime_filter_otus_from_otu_table
diff filter_otus_from_otu_table.xml @ 0:8824c27efae2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
| author | iuc |
|---|---|
| date | Thu, 18 May 2017 09:29:01 -0400 |
| parents | |
| children | e84a31935a8b |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/filter_otus_from_otu_table.xml Thu May 18 09:29:01 2017 -0400 @@ -0,0 +1,107 @@ +<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>