view hdf5_to_txt.xml @ 1:6585fa639f7f draft default tip

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

<tool id="dimspy_hdf5_to_txt" name="Convert DIMSpy-based HDF5 to tsv" version="1.0.0">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code">
    <![CDATA[
        #if $input.object_type == "peak_lists"
            dimspy hdf5-pls-to-txt
            --input '$input.hdf5_file_in'
            --output .
            --delimiter $delimiter
        #elif $input.object_type == "peak_matrix"
            #if $input.matrix_format == "standard" or $input.matrix_format == "standard_comprehensive"
                dimspy hdf5-pm-to-txt
                --input '$input.hdf5_file_in'
                --output '$matrix_file_out'
                --delimiter $delimiter
                --attribute_name $input.matrix_attr
                --representation-samples $input.representation_samples
            #end if
            #if $input.matrix_format == "standard_comprehensive"
                &&
            #end if
            #if $input.matrix_format == "comprehensive" or $input.matrix_format == "standard_comprehensive"
                dimspy hdf5-pm-to-txt
                --input '$input.hdf5_file_in'
                --output '$matrix_comprehensive_file_out'
                --delimiter $delimiter
                --comprehensive
                --attribute_name '$input.matrix_attr'
                --representation-samples $input.representation_samples
            #end if
        #end if
    ]]>
    </command>
    <inputs>
        <param name="delimiter" type="hidden" value="tab" argument="--delimiter"/>
        <conditional name="input">
            <param name="object_type" type="select" label="Content HDF5 file" help="" argument="">
                <option value="peak_matrix" selected="true">Peak Intensity Matrix</option>
                <option value="peak_lists">Peak list(s)</option>
            </param>
            <when value="peak_lists">
                <param name="hdf5_file_in" type="data" format="h5" label="Peaklist(s) (HDF5 file)" help="" argument="--input"/>
            </when>
            <when value="peak_matrix">
                <param name="hdf5_file_in" type="data" format="h5" label="Peak intensity matrix (HDF5 file)" help="" argument="--input"/>
                <param name="matrix_format" type="select" label="Select format(s) tsv formatted peak instensity matrix" >
                    <option value="standard" selected="true">Standard Peak Matrix (i.e. m/z and intensity).</option>
                    <option value="comprehensive">Comprehensive Peak Matrix (e.g. m/z and intensity, rsd, missing values).</option>
                    <option value="standard_comprehensive">Standard and comprehensive</option>
                </param>
                <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>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <collection name="peaklists_txt" type="list" label="${tool.name} on ${on_string}: Peaklists">
            <filter>input["object_type"] == "peak_lists"</filter>
            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tsv" directory="." visible="false" />
        </collection>
        <data name="matrix_file_out" format="tsv" label="${tool.name} on ${on_string}: Peak Matrix">
            <filter>input["object_type"] == "peak_matrix" and (input["matrix_format"] == "standard" or input["matrix_format"] == "standard_comprehensive")</filter>
        </data>
        <data name="matrix_comprehensive_file_out" format="tsv" label="${tool.name} on ${on_string}: Peak Matrix (comprehensive)" >
            <filter>input["object_type"] == "peak_matrix" and (input["matrix_format"] == "comprehensive" or input["matrix_format"] == "standard_comprehensive")</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input|object_type" value="peak_lists"/>
            <param name="input|hdf5_file_in" value="pls.h5" ftype="h5"/>
            <output_collection name="peaklists_txt" type="list">
                <element name="batch04_QC17_rep01_262" file="batch04_QC17_rep01_262.txt" ftype="tsv"/>
                <element name="batch04_QC17_rep02_263" file="batch04_QC17_rep02_263.txt" ftype="tsv"/>
                <element name="batch04_QC17_rep03_264" file="batch04_QC17_rep03_264.txt" ftype="tsv"/>
            </output_collection>
        </test>
        <test>
            <param name="input|object_type" value="peak_matrix"/>
            <param name="input|hdf5_file_in" value="pm_as_bf_sf.h5" ftype="h5"/>
            <param name="input|matrix_format" value="comprehensive"/>
            <param name="input|representation_samples" value="columns"/>
            <param name="input|matrix_attr" value="intensity"/>
            <output name="matrix_comprehensive_file_out" file="peak_matrix_hdf5_to_txt_intensity.txt" ftype="tsv" compare="sim_size"/>
        </test>
        <test>
            <param name="input|object_type" value="peak_matrix"/>
            <param name="input|hdf5_file_in" value="pm_as_bf_sf.h5" ftype="h5"/>
            <param name="input|matrix_format" value="standard"/>
            <param name="input|representation_samples" value="rows"/>
            <param name="input|matrix_attr" value="mz"/>
            <output name="matrix_file_out" file="peak_matrix_hdf5_to_txt_mz.txt" ftype="tsv" compare="sim_size"/>
        </test>
        <test>
            <param name="input|object_type" value="peak_matrix"/>
            <param name="input|hdf5_file_in" value="pm_as_bf_sf.h5" ftype="h5"/>
            <param name="input|matrix_format" value="standard_comprehensive"/>
            <param name="input|representation_samples" value="rows"/>
            <param name="input|matrix_attr" value="snr"/>
            <output name="matrix_file_out" file="peak_matrix_hdf5_to_txt_snr.txt" ftype="tsv" compare="sim_size"/>
            <output name="matrix_comprehensive_file_out" file="peak_matrix_hdf5_to_txt_comprehensive_snr.txt" ftype="tsv" compare="sim_size"/>
        </test>
    </tests>
    <help>
--------------------------------
Convert DIMSpy-based HDF5 to tsv
--------------------------------

Description
-----------

| Use this tool to convert Peak Intensity Matrix or Peaklist(s) to user-friendly .tsv file(s).

Parameters
----------

**\1. Select the content of the specified hdf5 file** (default = 'Peak Intensity Matrix')

**\2. Peak Intensity Matrix or Peak Lists (HDF5 file)** (REQUIRED)

Selection menu in which user can select the Peak Intensity Matrix or Peaklists requiring conversion to .tsv format.

**\3. output type** (default = &quot;Standard&quot; - Peak Intensity Matrix specific)

 - **Comprehensive output** - a Peak Intensity Matrix containing the m/z, intensity, missing values and other metrics associated with the aligned peaks. 
 - **Standard ouptut** - a .txt formatted Peak Intensity Matrix (i.e. m/z and intensity).    
 - **Standard and Comprehensive**


**\4) Should rows or columns represent the samples?** (default = &quot;rows&quot;  - Peak Intensity Matrix specific)

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.

**\5) **The Peak Intensity Matrix should contain ... values** (Peak Intensity Matrix specific)

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 (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.

| **OPTIONAL**
| A Data Collection containing Peaklists, in .tsv format
| 

- Tab-delimited text file containing a numeric data matrix, with . as decimal, and NA for missing values.
- Includes additional information, such as the signal-to-noise ratio, relative-standard deviation (rsd) and 'purity' for each peak.

@github_developers_contributors@
    
    </help>
    <expand macro="citations" />
</tool>