galaxy

<tool id="metabolights_downloader" name="Download MetaboLights Study" version="0.1.0">
    <command detect_errors="exit_code"><![CDATA[
#if $aspera_download.use_aspera == 'true'
    #if $aspera_download.aspera_password
        export ASPERA_SCP_PASS="$aspera_download.aspera_password";
    #else
        export ASPERA_SCP_PASS="Xz68YfDe";
    #end if

    #set $ascp_path='which ascp || which ~/.aspera/cli/bin/ascp || echo "false"'
    
    #if $ascp_path == "false"
        wget http://download.asperasoft.com/download/sw/cli/3.7.2/aspera-cli-3.7.2.354.010c3b8-linux-64-release.sh &&
        bash aspera-cli-3.7.2.354.010c3b8-linux-64-release.sh &&
        rm -r aspera-cli-3.7.2.354.010c3b8-linux-64-release.sh &&
        PATH ~/.aspera/cli/bin:$PATH
    #end if

    #if $download_rawfiles
        ascp -QT -l 1g -P 33001 fasp-ml@fasp.ebi.ac.uk:/studies/public/'$study_id' .;
    #else
        ascp -QT -l 1g -P 33001 -N "?_*.t*"  -E "*.*" fasp-ml@fasp.ebi.ac.uk:/studies/public/'$study_id' .;
    #end if
    mv '$study_id'/* .;
    rm -r '$study_id'
#else
    #if $download_rawfiles
        wget ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/'$study_id'/*
    #else
        wget ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/'$study_id'/i_*.txt ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/'$study_id'/s_*.txt ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/'$study_id'/a_*.txt ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/'$study_id'/m_*.t*
    #end if
#end if

]]></command>
    <inputs>
            <param name="study_id" value="MTBLS1" type="text" label="Public Study Identifier at MetaboLights" help="This should be obtained from the MetaboLights website. For public studies, Ex. MTBLS253">
                    <validator type="empty_field" />
            </param>
            <param type="boolean" name="download_rawfiles" label="Download raw files" help="Please note downloading raw files may take a while due to large file size(s)">
                    <option value="true">YES</option>
                    <option value="false" selected="true">FALSE</option>
            </param>
            <conditional name="aspera_download">
                <param name="use_aspera" type="boolean" label="Use ASPERA Download (optional)" help="High speed files download using aspera fasp protocol">
                    <option value="true" selected="true">Yes</option>
                    <option value="false">No</option>
                </param>
                <when value="true">
                    <param name="aspera_password" type="text" format="" label="ASPERA Password" />
                </when>
            </conditional>
    </inputs>
    <outputs>
        <collection type="list" label="Assay File(s)" name="a_files">
                <discover_datasets pattern="(?P&lt;designation&gt;a_.+)\.txt" format="tabular"/>
          </collection>
        <collection type="list" label="Sample File(s)" name="s_files">
                <discover_datasets pattern="(?P&lt;designation&gt;s_.+)\.txt" format="tabular"/>
        </collection>
        <collection type="list" label="Metabolite Annotation File(s)" name="maf_files">
                <discover_datasets pattern="(?P&lt;designation&gt;m_.+)\.tsv" format="tabular"/>
        </collection>
        <collection type="list" label="Raw File(s)" name="raw_files">
                <discover_datasets pattern="(?P&lt;designation&gt;[^(m_|a_|s_|i_)].+)\.+" format="tabular"/>
        </collection>
        <data name="i_file" format="tabular" label="Investigation File" from_work_dir="i_Investigation.txt" />
    </outputs>
    <tests>
        <test>
            <param name="study_id" value="MTBLS1"/>
            <param name="download_rawfiles" value="true"/>
            <output name="i_file" file="i_Investigation.txt" ftype="tabular" />
            <output_collection name="a_files" type="list">
                <discovered_dataset designation="a_mtbls1_metabolite_profiling_NMR_spectroscopy.txt" ftype="tabular">
                </discovered_dataset>
            </output_collection>
            <output_collection name="raw_files" type="list">
                <discovered_dataset designation="ADG10003u_007.nmrML" ftype="nmrML">
                </discovered_dataset>
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
**Overview**
 A program to download MetaboLights study. 
]]></help>
    <citations>
        <citation type="doi">10.1002/0471250953.bi1413s53</citation>
    </citations>
</tool>