comparison abims_xcms_xcmsSet.xml @ 6:0888f7ef739a draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6

5:588b0a7ae4b0

<tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.0.7">
    
    <description>Filtration and Peak Identification using xcmsSet function from xcms R package to preprocess LC/MS data for relative quantification and statistical analysis </description>
    
    <requirements>
        <requirement type="package" version="3.1.2">R</requirement>
        <requirement type="binary">Rscript</requirement>
        <requirement type="package" version="1.44.0">xcms</requirement>
        <requirement type="package" version="2.2.0">xcms_w4m_script</requirement>
    </requirements>
    
    <stdio>
        <exit_code range="1:" level="fatal" />
    </stdio>
    
    <command><![CDATA[
        xcms.r
        #if $inputs.input == "lib":
            library $__app__.config.user_library_import_dir/$__user_email__/$inputs.library
        #elif $inputs.input == "zip_file":
            zipfile $inputs.zip_file
        #end if

        ## profmethod $profmethod 
        nSlaves \${GALAXY_SLOTS:-1} method $methods.method 
        #if $methods.method == "centWave":
            ppm $methods.ppm
            peakwidth "c($methods.peakwidth)"
        #if $methods.options_scanrange.option == "show":
                scanrange "c($methods.options_scanrange.scanrange)"
        #end if 
        #if $methods.options_c.option == "show":
            mzdiff $methods.options_c.mzdiff
            snthresh $methods.options_c.snthresh
            integrate $methods.options_c.integrate
            noise $methods.options_c.noise
            prefilter "c($methods.options_c.prefilter)"
        #end if
        #elif $methods.method == "matchedFilter":
            step $methods.step
            fwhm $methods.fwhm
            #if $methods.options_m.option == "show":
                ## sigma "$methods.options_m.sigma"

            winSize.noise $methods.winSize_noise
            amp.Th $methods.amp_Th
            scales "c($methods.scales)"
            SNR.method "$methods.SNR_method"
        #end if
        ;
        return=\$?;
        mv log.txt $log;
        cat $log;
        sh -c "exit \$return"
    ]]></command>
    
    <inputs>

        <conditional name="inputs">

        <data name="log" format="txt" label="xset.log.txt" />
    </outputs>
    
    <tests>
        <test>
            <param name="inputs.input" value="zip_file" />
            <param name="inputs.zip_file" value="sacuri.zip" />
            <param name="methods.method" value="matchedFilter" />
            <param name="methods.step" value="0.01" />
            <param name="methods.fwhm" value="4" />
            <param name="methods.options_m.option" value="show" />
            <param name="methods.options_m.max" value="50" />
            <param name="methods.options_m.snthresh" value="1" />
            <param name="methods.options_m.steps" value="2" />
            <!--<output name="xsetRData" file="xset.RData" />-->
            <!--<output name="sampleMetadata" file="sampleMetadata.tsv" />-->
            <!--<output name="ticsRawPdf" file="xset.TICs_raw.pdf" />-->
            <!--<output name="bpcsRawPdf" file="xset.BPCs_raw.pdf" />-->
            <output name="log">
                <assert_contents>
                    <has_text text="object with 9 samples" />
                    <has_text text="Time range: 0.7-1140 seconds (0-19 minutes)" />
                    <has_text text="Mass range: 50.0019-999.9863 m/z" />
                    <has_text text="Peaks: 135846 (about 15094 per sample)" />
                    <has_text text="Peak Groups: 0" />
                    <has_text text="Sample classes: bio, blank" />
                </assert_contents>
            </output>
        </test>
    </tests>
    
    <help><![CDATA[

.. class:: infomark

**Authors**  Colin A. Smith [e-mail], Ralf Tautenhahn [e-mail], Steffen Neumann [e-mail], Paul Benton [e-mail] and Christopher Conley [e-mail] 

.. class:: infomark

**Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton [e-mail] - part of Workflow4Metabolomics.org [W4M]

 | Contact [e-mail] for any questions or concerns about the Galaxy implementation of this tool.

---------------------------------------------------

============
Xcms.xcmsSet
============

---------------------------------------------------

Changelog/News
--------------


**Version 2.0.7 - 10/02/2016**

- BUGFIX: better management of errors. Datasets remained green although the process failed

- BUGFIX/IMPROVEMENT: New step to check and delete bad characters in the XML: accented characters in the storage path of the mass spectrometer

- UPDATE: refactoring of internal management of inputs/outputs

- UPDATE: refactoring to feed the new report tool


**Version 2.0.2 - 18/01/2016

- BUGFIX: Some zip files were tag as "corrupt" by R. We have changed the extraction mode to deal with thoses cases.

- IMPROVEMENT: parameter labels have changed to facilitate their reading.

    ]]></help>


    <citations>
        <citation type="doi">10.1021/ac051437y</citation>
        <citation type="doi">10.1093/bioinformatics/btu813</citation>
    </citations>

</tool>

6:0888f7ef739a

<tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.0.8">
    
    <description>Filtration and Peak Identification using xcmsSet function from xcms R package to preprocess LC/MS data for relative quantification and statistical analysis </description>
    
    <macros>
        <import>macros.xml</import>
    </macros>

    <expand macro="requirements"/>
    <expand macro="stdio"/>
    
    <command><![CDATA[
        @COMMAND_XCMS_SCRIPT@
        #if $inputs.input == "lib":
            library $__app__.config.user_library_import_dir/$__user_email__/$inputs.library
        #elif $inputs.input == "zip_file":
            zipfile $inputs.zip_file
        #end if

        ## profmethod $profmethod 
        nSlaves \${GALAXY_SLOTS:-1} method $methods.method 
        #if $methods.method == "centWave":
            ppm $methods.ppm
            peakwidth "c($methods.peakwidth)"
            #if $methods.options_scanrange.option == "show":
                scanrange "c($methods.options_scanrange.scanrange)"
            #end if 
            #if $methods.options_c.option == "show":
                mzdiff $methods.options_c.mzdiff
                snthresh $methods.options_c.snthresh
                integrate $methods.options_c.integrate
                noise $methods.options_c.noise
                prefilter "c($methods.options_c.prefilter)"
            #end if
        #elif $methods.method == "matchedFilter":
            step $methods.step
            fwhm $methods.fwhm
            #if $methods.options_m.option == "show":
                ## sigma "$methods.options_m.sigma"

            winSize.noise $methods.winSize_noise
            amp.Th $methods.amp_Th
            scales "c($methods.scales)"
            SNR.method "$methods.SNR_method"
        #end if
        @COMMAND_LOG_EXIT@
    ]]></command>
    
    <inputs>

        <conditional name="inputs">

        <data name="log" format="txt" label="xset.log.txt" />
    </outputs>
    
    <tests>
        <test>
            <param name="inputs|input" value="zip_file" />
            <param name="inputs|zip_file" value="sacuri_dir_root.zip"  ftype="zip" />
            <param name="methods|method" value="matchedFilter" />
            <param name="methods|step" value="0.01" />
            <param name="methods|fwhm" value="4" />
            <param name="methods|options_m|option" value="show" />
            <param name="methods|options_m|max" value="50" />
            <param name="methods|options_m|snthresh" value="1" />
            <param name="methods|options_m|steps" value="2" />
            <output name="log">
                <assert_contents>
                    <has_text text="object with 4 samples" />
                    <has_text text="Time range: 0.7-1139.7 seconds (0-19 minutes)" />
                    <has_text text="Mass range: 50.0021-999.9863 m/z" />
                    <has_text text="Peaks: 59359 (about 14840 per sample)" />
                    <has_text text="Peak Groups: 0" />
                    <has_text text="Sample classes: bio, blank" />
                </assert_contents>
            </output>
        </test> 
        <test>
            <param name="inputs|input" value="zip_file" />
            <param name="inputs|zip_file" value="sacuri_current_root.zip"  ftype="zip" />
            <param name="methods|method" value="centWave" />
            <param name="methods|ppm" value="25" />
            <param name="methods|peakwidth" value="20,50" />
            <output name="log">
                <assert_contents>
                    <has_text text="object with 4 samples" />
                    <has_text text="Time range: 3.5-1139.2 seconds (0.1-19 minutes)" />
                    <has_text text="Mass range: 57.9756-593.4086 m/z" />
                    <has_text text="Peaks: 1535 (about 384 per sample)" />
                    <has_text text="Peak Groups: 0" />
                    <has_text text="Sample classes: bio, blank" />
                </assert_contents>
            </output>
        </test>
    </tests>
    
    <help><![CDATA[

@HELP_AUTHORS@

============
Xcms.xcmsSet
============

---------------------------------------------------

Changelog/News
--------------

**Version 2.0.8 - 06/04/2016**

- TEST: refactoring to pass planemo test using conda dependencies


**Version 2.0.7 - 10/02/2016**

- BUGFIX: better management of errors. Datasets remained green although the process failed

- BUGFIX/IMPROVEMENT: New step to check and delete bad characters in the XML: accented characters in the storage path of the mass spectrometer

- UPDATE: refactoring of internal management of inputs/outputs

- TEST: refactoring to feed the new report tool


**Version 2.0.2 - 18/01/2016

- BUGFIX: Some zip files were tag as "corrupt" by R. We have changed the extraction mode to deal with thoses cases.

- IMPROVEMENT: parameter labels have changed to facilitate their reading.

    ]]></help>

    <expand macro="citation" />
</tool>