Mercurial > repos > iuc > qiime_filter_otus_from_otu_table
comparison 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 |
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date | Thu, 18 May 2017 09:29:01 -0400 |
parents | |
children | e84a31935a8b |
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1 <tool id="qiime_filter_otus_from_otu_table" name="Filter otus from otu table" version="@WRAPPER_VERSION@.0"> | |
2 <description>Filter OTUs from an OTU table based on their observation counts or identifier</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements"/> | |
7 <version_command>filter_otus_from_otu_table.py --version</version_command> | |
8 <command detect_errors="aggressive"><![CDATA[ | |
9 filter_otus_from_otu_table.py | |
10 --input_fp '$input_fp' | |
11 --output_fp '$output_fp' | |
12 #if $min_count != '': | |
13 --min_count '$min_count' | |
14 #end if | |
15 #if $min_count_fraction != '': | |
16 --min_count_fraction '$min_count_fraction' | |
17 #end if | |
18 #if $max_count != '': | |
19 --max_count '$max_count' | |
20 #end if | |
21 #if $min_samples != '': | |
22 --min_samples '$min_samples' | |
23 #end if | |
24 #if $max_samples != '': | |
25 --max_samples '$max_samples' | |
26 #end if | |
27 #if $id_filtering_condition.id_filtering_switch == 'yes': | |
28 --otu_ids_to_exclude_fp '$id_filtering_condition.otu_ids_to_exclude_fp' | |
29 $id_filtering_condition.negate_ids_to_exclude | |
30 #end if | |
31 ]]></command> | |
32 <inputs> | |
33 <param argument="--input_fp" type="data" format="biom1" optional="False" label="Input OTU table" help="The input otu table filepath in biom format" /> | |
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" /> | |
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" /> | |
36 <param argument="--max_count" type="integer" value="" optional="True" label="Maximum total observation count of an otu for that otu to be retained" /> | |
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" /> | |
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" /> | |
39 <conditional name="id_filtering_condition"> | |
40 <param name="id_filtering_switch" type="select" label="Do you want to exclude a predefined list of OTUs from the OTU table ?" > | |
41 <option value="no" selected="true">No</option> | |
42 <option value="yes">Yes</option> | |
43 </param> | |
44 <when value="no"/> | |
45 <when value="yes"> | |
46 <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)" /> | |
47 <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" /> | |
48 </when> | |
49 </conditional> | |
50 </inputs> | |
51 <outputs> | |
52 <data name="output_fp" format="biom1" label="${tool.name} on ${on_string}: Filtered OTU table (biom format)"/> | |
53 </outputs> | |
54 <tests> | |
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 --> | |
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 --> | |
57 <!-- As a consequence, md5 checksums/SHA hash are not a valid comparison option either --> | |
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 --> | |
59 <test> | |
60 <param name="input_fp" value="filter_otus_from_otu_table/otu_table.biom" /> | |
61 <param name="min_count" value="2" /> | |
62 <param name="max_count" value="1000" /> | |
63 <param name="min_samples" value="5" /> | |
64 <param name="max_samples" value="350" /> | |
65 <conditional name="id_filtering_condition"> | |
66 <param name="id_filtering_switch" value="no"/> | |
67 </conditional> | |
68 <output name="output_fp" file="filter_otus_from_otu_table/filtered_otu_table.biom" ftype="biom1" compare="sim_size" delta="0" /> | |
69 </test> | |
70 <test> | |
71 <param name="input_fp" value="filter_otus_from_otu_table/otu_table.biom" /> | |
72 <conditional name="id_filtering_condition"> | |
73 <param name="id_filtering_switch" value="yes"/> | |
74 <param name="otu_ids_to_exclude_fp" value="filter_otus_from_otu_table/chimeric_otus.txt"/> | |
75 <param name="negate_ids_to_exclude" value="False"/> | |
76 </conditional> | |
77 <output name="output_fp" file="filter_otus_from_otu_table/chimera_filtered_otu_table.biom" ftype="biom1" compare="sim_size" delta="0" /> | |
78 </test> | |
79 <test> | |
80 <param name="input_fp" value="filter_otus_from_otu_table/otu_table.biom" /> | |
81 <conditional name="id_filtering_condition"> | |
82 <param name="id_filtering_switch" value="yes"/> | |
83 <param name="otu_ids_to_exclude_fp" value="filter_otus_from_otu_table/chimeric_otus.txt"/> | |
84 <param name="negate_ids_to_exclude" value="True"/> | |
85 </conditional> | |
86 <output name="output_fp" file="filter_otus_from_otu_table/chimera_picked_otu_table.biom" ftype="biom1" compare="sim_size" delta="0" /> | |
87 </test> | |
88 </tests> | |
89 <help><![CDATA[ | |
90 **What it does** | |
91 | |
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. | |
93 | |
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/>`_. | |
95 | |
96 Different kind of filtering can be applied on the input biom file depending on the selected parameters: | |
97 - Singleton filtering (minimum number of occurence) by using the -n/--min_count parameters | |
98 - Abundance filtering (maximum number of occurence) by using the -x/--max_count parameters | |
99 - Chimera filtering by using the -e/--otu_ids_to_exclude_fp parameters | |
100 | |
101 More information about this tool is available on | |
102 `QIIME documentation <http://qiime.org/scripts/filter_otus_from_otu_table.html>`_. | |
103 ]]></help> | |
104 <citations> | |
105 <expand macro="citations"/> | |
106 </citations> | |
107 </tool> |