view mzml2isa.xml @ 2:26b1c61f7b4c draft

planemo upload for repository https://github.com/ISA-tools/mzml2isa commit d9868158b4c63574b9d0d72461b9aa4443e612ba-dirty

<tool id="mzml2isa" name="mzml2isa" version="1.1.1+galaxy0">
    <description>Parser to get meta information from mzML files and create an ISA-Tab structure</description>
    
    <requirements>
        <requirement type="package" version="1.1.1">mzml2isa</requirement>
    </requirements>

    <stdio>
        <exit_code range="1:" />
    </stdio>
    
    <command detect_errors="exit_code">
    <![CDATA[


    #if $input.format == "data_collection"
        mkdir "temp"
        &&
        cd "temp"
        &&
        #for $fn in $input.source
            #if str( $fn ).endswith(".dat")
                ln -s '$fn' '$fn.name'
                &&
            #end if
        #end for
        cd ..
        &&
    #end if

    #if $metadata
        ln -s '$metadata' 'metadata.json' &&
    #end if

    mzml2isa -s $name_of_study -o . -i

    #if $input.format == "zip_file"
         "zip://$input.source"
    #else if $input.format == "tar_file"
         "tar://$input.source"
    #else if $input.format == "data_collection"
         "temp"
    #end if

     #if $metadata
        -m "metadata.json"
     #end if

	 && zip isa.zip i_* a_* s_* && mv isa.zip "$ISA_zip";
    ]]>
    </command>

    <inputs>
        <param name="name_of_study" type="text" label="Name study" help="This should not contain any spaces as the name will be used a prefix for ISA-tab file names" />
        <conditional name="input">
            <param name="format" type="select" label="Choose the source for the dataset (zip, tar or data collection)" >
                <option value="zip_file" selected="true">Zip file from your History containing a folder of *.mzML files</option>
                <option value="tar_file">TAR file from your history containing a folder of *.mzML files</option>
                <option value="data_collection">Data collection (*.mzML files)</option>
            </param>
            <when value="zip_file">
                <param name="source" type="data" format="zip" label="Zip file from your History containing *.mzml files">
                </param>
            </when>
            <when value="tar_file">
		<param name="source" type="data" format="tar" label="TAR file from your History containing *.mzml files"/>
	    </when>
            <when value="data_collection">
                <param name="source" type="data_collection" format="mzml" label="Data collection of *.mzml" >
                </param>
            </when>
        </conditional>

        <param optional="true" format="json" name="metadata" type="data" label="Additional user Metadata in json"  help="A user can add additional metadata directory through a json file"/>

    </inputs>
    <outputs>

    <data name="ISA_zip" format="zip" label="ISA Zip file"/>
    <collection type="list" label="Assay files" name="a_files">
        <discover_datasets pattern="(?P&lt;designation&gt;a_.+)\.txt" directory="."  format="tabular"/>
	</collection>
	<collection type="list" label="Study files" name="s_files">
		<discover_datasets pattern="(?P&lt;designation&gt;s_.+)\.txt" directory="." format="tabular"/>
	</collection>
	<data name="i_file" format="tabular" label="Investigation file" from_work_dir="i_Investigation.txt"/>
    </outputs>

    <tests>
        <test>
            <param name="name_of_study" value="test" />
            <param name="input|format" value="zip_file" />
            <param name="input|source" value="metabolomics_study.zip" ftype="zip" />
            <output name="i_file" value="i_Investigation.txt" />
            <output_collection name="a_files" type="list" count="1">
                <element name="a_test_metabolite_profiling_mass_spectrometry">
                    <assert_contents>
                        <has_n_columns n="80" />
                    </assert_contents>
                </element>
            </output_collection>
            <output_collection name="s_files" type="list" count="1">
                <element name="s_test">
                    <assert_contents>
                        <has_n_columns n="12" />
                    </assert_contents>
                </element>
            </output_collection>
        </test>
        <test>
            <param name="name_of_study" value="test" />
            <param name="input|format" value="data_collection" />
            <param name="input|source" >
                <collection type="list">
                    <element name="1_samp" value="1_samp.mzML" />
                    <element name="2_samp" value="2_samp.mzML" />
                    <element name="3_samp" value="3_samp.mzML" />
                    <element name="4_samp" value="4_samp.mzML" />
                    <element name="5_samp" value="5_samp.mzML" />
                    <element name="6_samp" value="6_samp.mzML" />
                </collection>
            </param >
            <output name="i_file" value="i_Investigation.txt" />
            <output_collection name="a_files" type="list" count="1">
                <element name="a_test_metabolite_profiling_mass_spectrometry">
                    <assert_contents>
                        <has_n_columns n="80" />
                    </assert_contents>
                </element>
            </output_collection>
            <output_collection name="s_files" type="list" count="1">
                <element name="s_test">
                    <assert_contents>
                        <has_n_columns n="12" />
                    </assert_contents>
                </element>
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
**Overview**
 A program to automatically generate ISA-Tab metadata files from metabolomics raw XML (mzML and imzML) data files.

 Additional meta-information not found within the mzML file can be added through a JSON file.
 However, it is recommended that the mzML2ISA tool is used to create a semi-completed ISA-Tab file structure
 that is further annotated using ISAcreator https://github.com/ISA-tools/ISAcreator or via the ISA-API.

.. image::mzml2isa.png
    ]]></help>
    <citations>
        <citation type="doi">10.1002/0471250953.bi1413s53</citation>
        <citation type="doi">10.1007/s11306-015-0879-3</citation>
        <citation type="doi">10.1038/ng.1054</citation>
    </citations>
</tool>