comparison filter_otus_from_otu_table.xml @ 7:9db0d2cf4451 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c845cb240f57663cf1e2240c5c506ea0b294872c"

6:8b42de6ad28a

<tool id="qiime_filter_otus_from_otu_table" name="Filter OTUs from an OTU table" version="@WRAPPER_VERSION@.0">
    <description> based on their observation counts or identifier (filter_otus_from_otu_table)</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'

            <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**

7:9db0d2cf4451

<tool id="qiime_filter_otus_from_otu_table" name="Filter OTUs from an OTU table" version="@WRAPPER_VERSION@.0" profile="@PROFILE@">
    <description> based on their observation counts or identifier (filter_otus_from_otu_table)</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[
@MPLBACKEND@
filter_otus_from_otu_table.py
    --input_fp '$input_fp'
    --output_fp '$output_fp'
    #if $min_count != '':
        --min_count '$min_count'

            <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="200" />
        </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="200" />
        </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="200" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**