view kmd_hmdb_data_plot.xml @ 0:59c8bad5f6bc draft default tip

planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/ commit 7fa454b6a4268b89fe18043e8dd10f30a7b4c7ca

<tool id="kmd_hmdb_data_plot" name="KMD HMDB Data Plot" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
    <description>
        retrieves data from KMD HMDB API and produce plot and tsv file
    </description>
    <macros>
        <import>macro.xml</import>
        <token name="@TOOL_VERSION@">1.0.0</token>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <edam_topics>
        <edam_topic>topic_0091</edam_topic>
    </edam_topics>
    <edam_operations>
        <edam_operation>operation_3803</edam_operation>
    </edam_operations>
    <requirements>
        <requirement type="package" version="3.10">python</requirement>
        <requirement type="package" version="2.0.3">pandas</requirement>
        <requirement type="package" version="5.15.0">plotly</requirement>
        <requirement type="package" version="1.0.1">kmd_hmdb_api_client</requirement>
    </requirements>
    <command detect_errors="exit_code">
<![CDATA[
#if "get_data" in str($what.to_do)
    python3 '$__tool_directory__/kmd_hmdb_interrogator.py' compound
        --mz-ratio '$what.mz_ratio'
        --database '$what.database'
        --mass-tolerance '$what.mass_tolerance'
        #for adduct in $what.adducts
            --adducts '$adduct'
        #end for
        --output-path '$output_path'
#end if

#if $what.to_do == "get_data_and_produce_plot"
    &&
#end if

#if "produce_plot" in str($what.to_do)
    python3 '$__tool_directory__/kmd_hmdb_plot_generator.py' plot

    #if "get_data" in str($what.to_do)
        --input '$output_path'
    #else
        --input '$what.tsv_input'
    #end if

    #if $what.x_columns
        #for x in $what.x_columns
          --x-column '$x'
        #end for
    #end if

    #if $what.y_columns
        #for y in $what.y_columns
          --y-column '$y'
        #end for
    #end if

    #if $what.annotation_columns
        #for annotation_column in $what.annotation_columns
            --annotation-column '$annotation_column'
        #end for
    #end if

      --output 'out.html'

    && cat 'out.html' > '$output'
#end if
]]>
    </command>

    <inputs>
        <conditional name="what">
            <param name="to_do" type="select"
                label="What to do"
            >
                <option value="get_data">Only get data</option>
                <option value="produce_plot">Only produce plot</option>
                <option value="get_data_and_produce_plot" selected="true">
                    Get data from database + Produce Plot
                </option>
            </param>
            <when value="produce_plot">
                <expand macro="produce_plot_inputs" />
                <expand macro="not_get_data" />
            </when>
            <when value="get_data">
                <expand macro="get_data_inputs" />
                <expand macro="not_produce_plot" />
            </when>
            <when value="get_data_and_produce_plot">
                <expand macro="get_data_inputs" />
                <expand macro="not_produce_plot" />
            </when>
        </conditional>
    </inputs>

    <outputs>
        <expand macro="get_data_outputs" />
        <expand macro="produce_plot_outputs" />
    </outputs>

    <tests>
        <test>
            <!-- #1 get_data with tolerance = 0.01 -->
            <param name="to_do" value="get_data" />
            <param name="mass_tolerance" value="0.01" />
            <param name="mz_ratio" value="303.05" />
            <param name="database" value="hmdb" />
            <param name="adducts" value="M+H" />
            <output name="output_path" file="get_data_tol_0.01.tsv" />
        </test>
    </tests>

    <help><![CDATA[

This tool includes two utilities.
One that retrieves data from the KMD HMDB API formated as a tsv file,
and the other plots those data in a plotly graph.

The default behavior of the plot is to produce a plot of the kmd in
in function of the nominal mass of the compound.

Compounds are retrieved using a query with default parameters:
 - mz default to @DEFAULT_MZ@
 - mz tolerance defaults to @DEFAULT_TOLERENCE@
 - adduct list defaults to "@DEFAULT_ADDUCT@"
 - database default to "@DEFAULT_DATABASE@", and possible values are one of:

   - KMD Metabolites
   - HMDB

Those two utilities are usable independently, or sequentially in galaxy.

Multiple X / Y values in the X/Y column selection can be
selected to produce a lot of graphs at once.

For example, imagine you have 5 columns in you tsv file,
and those columns are named: A, B, C, D and F.

If you choose X = [A, C] and Y = [B],
then you will get two graphs (in one single HTML file) with:

 - f(A) = B
 - f(C) = B

But if you choose multiple values for both X and Y, you get
all combinations of columns X and Y. For example, if you
select X = [A, B] and Y = [C, D, E], then you will get six
graphs on the same plot:

 - f(A) = C
 - f(A) = D
 - f(A) = E
 - f(B) = C
 - f(B) = D
 - f(B) = E

All those graph's traces will be tooglable in the HTML page.
So don't hesitate to select a lot of parameters for X and Y!

]]>
    </help>
    <citations></citations>
    <creator>
        <person
            honorificPrefix="Mx."
            givenName="Lain"
            familyName="Pavot"
            email="[e-mail]"
            identifier="https://orcid.org/0009-0007-1841-4358"
        />
    </creator>

</tool>