view visualize_pore_diameter_aqp.xml @ 14:1f08a90393be draft default tip

"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 83670d9ceed855c9f58e0fa63a682edcaace5354-dirty"

<tool id="visualize_pore_diameter_aqp" name="visualize pore diameter of AQP" version="1.0.0" python_template_version="3.5" profile="@GALAXY_VERSION@">
    <macros>
        <token name="@GALAXY_VERSION@">21.05</token>
    </macros>
    <requirements>
        <requirement type="package" version="1.20.3">r-getopt</requirement>
        <requirement type="package" version="3.3.6">r-ggplot2</requirement>
        <requirement type="package" version="1.3.1">r-tidyverse</requirement>
        <requirement type="package" version="0.4.0">r-ggpubr</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        ln -s '$input_file' '$input_file.element_identifier' &&
        Rscript '$__tool_directory__/visualize_pore_diameter_aqp.R'
            -i '$input_file.element_identifier'
            #if 'aqp' in $select_graph:
                -a TRUE
            #else:
                -a FALSE
            #end if
            #if 'protomer' in $select_graph:
                -p TRUE
            #else:
                -p FALSE
            #end if
            #if 'all' in $select_graph :
                -d TRUE
            #else:
                -d FALSE
            #end if
            #if $pdf == 'yes' :
                -f TRUE
            #else:
                -f FALSE
            #end if
    ]]></command>
    <inputs>
        <param name="input_file" type="data" format="tabular" label="Aquaporin pore diameter table" help="Put your table containing the means and standard deviations of aquaporins pore diameter"/>
        <param name="select_graph" type="select" multiple="true" display="checkboxes" label="Choose which graphics you want to get">
            <option value="aqp" selected="true">Distance distribution by aquaporin</option>
            <option value="protomer" selected="true">Distance distribution by protomer</option>
            <option value="all" selected="true">Distance distribution by aquaporin and by protomer</option>
        </param>
        <param name="pdf" type="select" label="Do you want a pdf file that contains all the selected graphics?">
            <option value="yes" selected="true">Yes</option>
            <option value="no">No</option>
        </param>
    </inputs>
    <outputs>
        <data name="out_file" format="png" from_work_dir="./Distance_distribution_by_aquaporin.png" label="Distance_distribution_by_aquaporin.png">
            <filter>"aqp" in select_graph</filter>
        </data>
        <data name="out_file2" format="png" from_work_dir="./Distance_distribution_by_protomer.png" label="Distance_distribution_by_protomer.png">
            <filter>"protomer" in select_graph</filter>
        </data>
        <data name="out_file3" format="png" from_work_dir="./Distance_distribution_on_all_protomers.png" label="Distance_distribution_on_all_protomers.png">
            <filter>"all" in select_graph</filter>
        </data>
        <data name="out_file4" format="pdf" from_work_dir="./*.pdf" label="Distance distribution (PDF)">
            <filter>pdf == "yes"</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input_file" value="table_sort_pore_diameter_aqp.tabular" ftype="tabular"/>
            <param name="select_graph" value="aqp,protomer,all"/>
            <param name="pdf" value="yes"/>
            <output name="out_file" file="Distance_distribution_by_aquaporin.png"/>
            <output name="out_file2" file="Distance_distribution_by_protomer.png"/>
            <output name="out_file3" file="Distance_distribution_on_all_protomers.png"/>
            <output name="out_file4" file="all_graphics_distribution.pdf"/>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

**What it does**

This tool allows to visualize the pore diameter of an aquaporin over time.

_____

.. class:: infomark

**Inputs**

    - Aquaporin pore diameter table : table containing the average distance and standard deviation of each subpath for a complete trajectory
    - Choose which graphics you want to get :
        - Distance distribution by aquaporin : for each aquaporin, a ribbon graph is created showing the distance distribution over time
        - Distance distribution by protomer : for each protomer, a ribbon graph is created showing the distance distribution over time
        - Distance distribution by aquaporin and by protomer : for each protomer of each aquaporin, a ribbon graph is created showing the distribution of the distance over time
    - Do you want a pdf file that contains all the selected graphics? :
        - Yes : a PDF file containing all the selected graphics will be created in addition to the PNG files of the graphics
        - No : only PNG files of the graphics will be created

_____

.. class:: infomark

**Outputs**

    - PNG file for each selected graphic type
    - PDF file containing all selected graphics

    ]]></help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btz107</citation>
    </citations>
</tool>