view macros.xml @ 1:79fdd9fc8eba draft default tip

planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 42331bc61ea07d75f88007e5a2c65eaf9e811f06

<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="1.2.0">dimspy</requirement>
        </requirements>
    </xml>
    
    <token name="@HDF5_PM_TO_TXT@">
        dimspy hdf5-pm-to-txt
        --input '$hdf5_file_out'
        --output '$matrix_file_out'
        --delimiter $delimiter
        --attribute_name $hdf5_to_txt.matrix_attr
        --representation-samples $hdf5_to_txt.representation_samples
    </token>

    <token name="@HDF5_PM_TO_TXT_COMPREHENSIVE@">
        dimspy hdf5-pm-to-txt
        --input '$hdf5_file_out'
        --output '$matrix_comprehensive_file_out'
        --delimiter $delimiter
        --comprehensive
        --attribute_name $hdf5_to_txt.matrix_attr
        --representation-samples $hdf5_to_txt.representation_samples
    </token>

    <xml name="hdf5_pm_to_txt">
        <section name="hdf5_to_txt" title="Show options for addtional output (*.tsv files)" expanded="False">
            <param name="standard" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Standard output?" help="Set to &quot;yes&quot; to produce a &quot;standard&quot; Peak Matrix (i.e. m/z and intensity)."/>
            <param name="comprehensive" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Comprehensive output?" help="Set to &quot;yes&quot; to produce a Peak Matrix with additional information (e.g. m/z and intensity, rsd, missing values)."/>
            <param name="representation_samples" type="select" label="Should the rows or columns represent the samples?">
                <option value="rows" selected="true">Rows</option>
                <option value="columns">Columns</option>
            </param>
            <param name="matrix_attr" type="select" label="The Peak Matrix should contain ... values">
                <option value="intensity" selected="true">Intensity</option>
                <option value="mz">m/z</option>
                <option value="snr">Signal-to-noise ratio (SNR)</option>
            </param>
        </section>
    </xml>

    <xml name="outputs_peak_intensity_matrix">
        <data name="hdf5_file_out" format="h5" label="${tool.name} on ${on_string}: Peak Intensity Matrix (HDF5 file)"/>
        <data name="matrix_file_out" format="tsv" label="${tool.name} on ${on_string}: Peak Intensity Matrix">
            <filter>hdf5_to_txt["standard"] is True</filter>
        </data>
        <data name="matrix_comprehensive_file_out" format="tsv" label="${tool.name} on ${on_string}: Peak Intensity Matrix (comprehensive)" >
            <filter>hdf5_to_txt["comprehensive"] is True</filter>
        </data>
    </xml>
    
    <xml name="citations">
        <citations>
            <citation type="doi">10.1038/nprot.2016.156</citation>
            <citation type="doi">10.1038/sdata.2014.12</citation>
            <citation type="doi">10.1021/ac062446p</citation>
            <citation type="doi">10.1021/ac2001803</citation>
            <yield />
        </citations>
    </xml>
    
    <token name="@example_filelist@">
  <![CDATA[

        +-----------------+-----------+-------+------------+----------------+
        | filename        | replicate | batch | classLabel | injectionOrder |
        +-----------------+-----------+-------+------------+----------------+
        | sample_rep1.raw | 1         | 1     | sample     | 1              |
        +-----------------+-----------+-------+------------+----------------+
        | sample_rep2.raw | 2         | 1     | sample     | 2              |
        +-----------------+-----------+-------+------------+----------------+
        | sample_rep3.raw | 3         | 1     | sample     | 3              |
        +-----------------+-----------+-------+------------+----------------+
        | sample_rep4.raw | 4         | 1     | sample     | 4              |
        +-----------------+-----------+-------+------------+----------------+
        | blank_rep1.raw  | 1         | 1     | blank      | 5              |
        +-----------------+-----------+-------+------------+----------------+
        | blank_rep2.raw  | 2         | 1     | blank      | 6              |
        +-----------------+-----------+-------+------------+----------------+
        | blank_rep3.raw  | 3         | 1     | blank      | 7              |
        +-----------------+-----------+-------+------------+----------------+
        | blank_rep4.raw  | 4         | 1     | blank      | 8              |
        +-----------------+-----------+-------+------------+----------------+
        | ...             | ...       | ...   | ...        | ...            |
        +-----------------+-----------+-------+------------+----------------+

  ]]>
    </token>


    <token name="@help_options_addtional_output@">
| 
| **Show options for additonal output(s)** (OPTIONAL)
| 

**\A. Standard output** (default = &quot;No&quot;)

Boolean toggle where selection of: 

- &quot;Yes&quot; will generate a .txt formatted Peak Matrix (i.e. m/z and intensity).	
- &quot;No&quot; will prevent the creation of a .txt formatted Peak Matrix.

**\B. Comprehensive output** (default = &quot;No&quot;)

Boolean toggle where selection of:

- &quot;Yes&quot; generates a Peak Matrix containing the m/z, intensity, missing values and other metrics associated with the aligned peaks.
- &quot;No&quot; will prevent the creation of a .txt formatted comprehensive Peak Matrix..

**\C. Should rows or columns represent the samples?** (default = &quot;rows&quot;)

Binary toggle (default = &quot;rows&quot;) where selection of:

- &quot;rows&quot; puts sample information in to the rows and m/z values (for aligned mass spectral peaks) in to columns of any output Peak Matrix.			
- &quot;columns&quot; puts sample information in the columns and m/z values (for aligned mass spectral peaks) in to the rows of any output Peak Matrix.

**\D. The Peak Matrix should contain ... values**

Use this option to define which metric is inserted in to the cells of the output Peak Matrix.

- &quot;Intensity&quot; writes the absolute peak intensity to the Peak Matrix.
- &quot;m/z&quot; writes the m/z value to the Peak Matrix.
- &quot;Signal-to-noise ratio (SNR)&quot; writes the signal-to-noise ratio to the Peak Matrix. 

Output file(s)
--------------

| A HDF5 file containing a Peak Matrix
| 
| **OPTIONAL**
| A (standard and/or comprehenstive) Peak Matrix comprising samples on one axis and m/z values on the perpendicular axis
| 

- Tab-delimited text file containing a numeric data matrix, with . as decimal, and NA for missing values.
- File only created if user toggles &quot;Standard output&quot; and/or &quot;Comprehensive output&quot; to &quot;Yes&quot;
- By default, samples are in rows and peaks are in columns. Altering the &quot;Should rows or columns represent samples&quot; toggle will transpose this matrix.

    </token>

    <token name="@github_developers_contributors@"> 
Github respository (source code)
--------------------------------

https://github.com/computational-metabolomics/dimspy-galaxy/

Developers and contributors
---------------------------

- **Ralf Weber ([e-mail]) - University of Birmingham (UK)**
- **Martin R. Jones ([e-mail]) - University of Birmingham (UK)**
- **Thomas Lawson ([e-mail]) - University of Birmingham (UK)**

| 
    </token>

</macros>