Mercurial > repos > iuc > qiime_filter_otus_from_otu_table
comparison 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 |
---|---|
date | Sat, 05 Aug 2017 07:31:22 -0400 |
parents | 8824c27efae2 |
children | 9db0d2cf4451 |
comparison
equal
deleted
inserted
replaced
4:caeec9478937 | 5:e84a31935a8b |
---|---|
1 <tool id="qiime_filter_otus_from_otu_table" name="Filter otus from otu table" version="@WRAPPER_VERSION@.0"> | 1 <tool id="qiime_filter_otus_from_otu_table" name="Filter OTUs from an OTU table" version="@WRAPPER_VERSION@.0"> |
2 <description>Filter OTUs from an OTU table based on their observation counts or identifier</description> | 2 <description> based on their observation counts or identifier (filter_otus_from_otu_table)</description> |
3 <macros> | 3 <macros> |
4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro="requirements"/> | 6 <expand macro="requirements"/> |
7 <version_command>filter_otus_from_otu_table.py --version</version_command> | 7 <version_command>filter_otus_from_otu_table.py --version</version_command> |
8 <command detect_errors="aggressive"><![CDATA[ | 8 <command detect_errors="aggressive"><![CDATA[ |
9 filter_otus_from_otu_table.py | 9 filter_otus_from_otu_table.py |
10 --input_fp '$input_fp' | 10 --input_fp '$input_fp' |
11 --output_fp '$output_fp' | 11 --output_fp '$output_fp' |
12 #if $min_count != '': | 12 #if $min_count != '': |
13 --min_count '$min_count' | 13 --min_count '$min_count' |
14 #end if | 14 #end if |
15 #if $min_count_fraction != '': | 15 #if $min_count_fraction != '': |
16 --min_count_fraction '$min_count_fraction' | 16 --min_count_fraction '$min_count_fraction' |
17 #end if | 17 #end if |
18 #if $max_count != '': | 18 #if $max_count != '': |
19 --max_count '$max_count' | 19 --max_count '$max_count' |
20 #end if | 20 #end if |
21 #if $min_samples != '': | 21 #if $min_samples != '': |
22 --min_samples '$min_samples' | 22 --min_samples '$min_samples' |
23 #end if | 23 #end if |
24 #if $max_samples != '': | 24 #if $max_samples != '': |
25 --max_samples '$max_samples' | 25 --max_samples '$max_samples' |
26 #end if | 26 #end if |
27 #if $id_filtering_condition.id_filtering_switch == 'yes': | 27 #if $id_filtering_condition.id_filtering_switch == 'yes': |
28 --otu_ids_to_exclude_fp '$id_filtering_condition.otu_ids_to_exclude_fp' | 28 --otu_ids_to_exclude_fp '$id_filtering_condition.otu_ids_to_exclude_fp' |
29 $id_filtering_condition.negate_ids_to_exclude | 29 $id_filtering_condition.negate_ids_to_exclude |
30 #end if | 30 #end if |
31 ]]></command> | 31 ]]></command> |
32 <inputs> | 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" /> | 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" /> | 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" /> | 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" /> | 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" /> | 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" /> | 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"> | 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 ?" > | 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> | 41 <option value="no" selected="true">No</option> |
42 <option value="yes">Yes</option> | 42 <option value="yes">Yes</option> |
43 </param> | 43 </param> |
44 <when value="no"/> | 44 <when value="no"/> |
45 <when value="yes"> | 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)" /> | 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)" /> |
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" /> | 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" /> |
48 </when> | 48 </when> |
49 </conditional> | 49 </conditional> |
50 </inputs> | 50 </inputs> |
51 <outputs> | 51 <outputs> |
52 <data name="output_fp" format="biom1" label="${tool.name} on ${on_string}: Filtered OTU table (biom format)"/> | 52 <data name="output_fp" format="biom1" label="${tool.name} on ${on_string}: Filtered OTU table (biom format)"/> |