view Testtest/GCMS-test.xml @ 0:40de28c7d3fb draft

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<tool id="GCMSt" name="GCMS-test" version="17.11">
	<description>Test parameters for GC-MS data preprocessing using metaMS package</description>
    
    <requirements>
        <requirement type="package" version="1.8.0">bioconductor-metams</requirement>
        <requirement type="package" version="1.46.0">bioconductor-xcms</requirement>
        <requirement type="package" version="1.1_4">r-batch</requirement>
    </requirements>
    
    <stdio>
        <exit_code range="1:" level="fatal" />
    </stdio>

	<command>
		Rscript $__tool_directory__/GCMS-test.R
		
		<!-- Inputs -->
		
		<!-- nb_cores \${GALAXY_SLOTS:-1} -->
		nb_cores \${GALAXY_SLOTS}
		
		zip_file $zip_file
		
		step_min $step.step_min
		step_max $step.step_max
		step_step $step.step_step
		
		steps_min $steps.steps_min
		steps_max $steps.steps_max
		steps_step $steps.steps_step
		
		mzdiff_min $mzdiff.mzdiff_min
		mzdiff_max $mzdiff.mzdiff_max
		mzdiff_step $mzdiff.mzdiff_step
		
		fwhm_min $fwhm.fwhm_min
		fwhm_max $fwhm.fwhm_max
		fwhm_step $fwhm.fwhm_step
		
		simthresh_min $simthresh.simthresh_min
		simthresh_max $simthresh.simthresh_max
		simthresh_step $simthresh.simthresh_step
		
		snthresh_min $snthresh.snthresh_min
		snthresh_max $snthresh.snthresh_max
		snthresh_step $snthresh.snthresh_step
		
		max_min $max.max_min
		max_max $max.max_max
		max_step $max.max_step
		
		minclassfraction_min $minclassfraction.minclassfraction_min
		minclassfraction_max $minclassfraction.minclassfraction_max
		minclassfraction_step $minclassfraction.minclassfraction_step
		
		minclasssize_min $minclasssize.minclasssize_min
		minclasssize_max $minclasssize.minclasssize_max
		minclasssize_step $minclasssize.minclasssize_step
		
		rtdiff_min $rtdiff.rtdiff_min
		rtdiff_max $rtdiff.rtdiff_max
		rtdiff_step $rtdiff.rtdiff_step
		
		<!--minfeat_min $minfeat.minfeat_min
		minfeat_max $minfeat.minfeat_max
		minfeat_step $minfeat.minfeat_step-->
		
		count_duplicates $outputs_options.count_duplicates.count_duplicates_bool
		#if $outputs_options.count_duplicates.count_duplicates_bool:
			duplicates_delta_rt $outputs_options.count_duplicates.duplicates_delta_rt
			duplicates_delta_mz $outputs_options.count_duplicates.duplicates_delta_mz
		#end if
		
		check_ions $outputs_options.check_ions.check_ions_bool
		#if $outputs_options.check_ions.check_ions_bool:
			ions_delta_rt $outputs_options.check_ions.ions_delta_rt
			ions_delta_mz $outputs_options.check_ions.ions_delta_mz
			
			#for $i, $s in enumerate($outputs_options.check_ions.ions_to_check)
				ions_name_${i+1} $s.name
				ions_rt_${i+1} $s.rt
				ions_mzs_${i+1} $s.mzs
			#end for
		#end if
		
		<!-- Outputs -->
		
		summary_out $summary_out
		peakspectra_out $peakspectra_out
		intensity_graph_out $intensity_graph_out
		
		#if $outputs_options.count_duplicates.count_duplicates_bool:
			duplicates_out $duplicates_out
		#end if
		
		compare_graph_out $compare_graph_out
	</command>
  
	<inputs>
		<param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" help="Zip file containing the chromatograms to analyse" />
		
		<section name="fwhm" title="FWHM (default: 6)" help="The full width at half maximum of the peaks" >
			<param name="fwhm_min" value="6" type="float" label="From" />
			<param name="fwhm_max" value="6" type="float" label="To" />
			<param name="fwhm_step" value="1" type="float" label="Step" />
		</section>
		
		<section name="max" title="Max (default: 500)" help="Maximum number of peaks per extracted ion chromatogram" >
			<param name="max_min" value="500" type="integer" label="From" />
			<param name="max_max" value="500" type="integer" label="To" />
			<param name="max_step" value="1" type="integer" label="Step" />
		</section>
		
		<section name="minclassfraction" title="Minimum class fraction (default: 0.5)" help="The fraction of samples in which a pseudospectrum is present before it is regarded as an unknown" >
			<param name="minclassfraction_min" value="0.5" type="float" label="From" />
			<param name="minclassfraction_max" value="0.5" type="float" label="To" />
			<param name="minclassfraction_step" value="0.5" type="float" label="Step" />
		</section>
		
		<section name="minclasssize" title="Minimum class size (default: 5)" help="The absolute number of samples in which a pseudospectrum is present before it is regarded as an unknown" >
			<param name="minclasssize_min" value="5" type="integer" label="From" />
			<param name="minclasssize_max" value="5" type="integer" label="To" />
			<param name="minclasssize_step" value="1" type="integer" label="Step" />
		</section>
		
		<!-- <section name="minfeat" title="minfeat (default: 0.05)" help="The minimum number of ion in a mass spectra to consider it a molecule" >
			<param name="minfeat_min" value="0.05" type="float" label="From" />
			<param name="minfeat_max" value="0.05" type="float" label="To" />
			<param name="minfeat_step" value="0.01" type="float" label="Step" />
		</section> -->
		
		<section name="mzdiff" title="m/z diff (default: 0.05)" help="Minimum difference in m/z for peaks with overlapping retention times" >
			<param name="mzdiff_min" value="0.05" type="float" label="From" />
			<param name="mzdiff_max" value="0.05" type="float" label="To" />
			<param name="mzdiff_step" value="0.01" type="float" label="Step" />
		</section>
		
		<section name="rtdiff" title="RT diff (default: 0.05)" help="The allowed RT shift between same molecules in different samples" >
			<param name="rtdiff_min" value="0.05" type="float" label="From" />
			<param name="rtdiff_max" value="0.05" type="float" label="To" />
			<param name="rtdiff_step" value="0.01" type="float" label="Step" />
		</section>
		
		<section name="simthresh" title="Similarity threshold (default: 0.7)" help="The minimum similarity allowed between peaks' mass spectra to be considered as equal" >
			<param name="simthresh_min" value="0.7" type="float" label="From" />
			<param name="simthresh_max" value="0.7" type="float" label="To" />
			<param name="simthresh_step" value="0.1" type="float" label="Step" />
		</section>
		
		<section name="snthresh" title="s/n threshold (default: 2)" help="Signal to noise ratio cutoff" >
			<param name="snthresh_min" value="2" type="integer" label="From" />
			<param name="snthresh_max" value="2" type="integer" label="To" />
			<param name="snthresh_step" value="1" type="integer" label="Step" />
		</section>
		
		<section name="step" title="Step (default: 0.05)" help="Step size to use for profile generation" >
			<param name="step_min" value="0.05" type="float" label="From" />
			<param name="step_max" value="0.05" type="float" label="To" />
			<param name="step_step" value="0.01" type="float" label="Step" />
		</section>
		
		<section name="steps" title="Steps (default: 2)" help="Number of steps to merge prior to filtration" >
			<param name="steps_min" value="2" type="integer" label="From" />
			<param name="steps_max" value="2" type="integer" label="To" />
			<param name="steps_step" value="1" type="integer" label="Step" />
		</section>
		
		<section name="outputs_options" title="Output options" expanded="True" >
			<conditional name="count_duplicates" >
				<param name="count_duplicates_bool" type="boolean" checked="false" label="Count the duplicates?" help="Counting the number of duplicates for each test slows the process down" />
				<when value="true" >
					<param name="duplicates_delta_rt" value="0.1" type="float" label="Delta rt" help="Maximum difference in two ions' m/z to consider them as equal" />
					<param name="duplicates_delta_mz" value="0.1" type="float" label="Delta m/z" help="Maximum difference in two ions' rt to consider them as equal" />
				</when>
				<when value="false" />
			</conditional>
			
			<conditional name="check_ions" >
				<param name="check_ions_bool" type="boolean" checked="false" label="Check the presence of ions?" help="Checking the presence of ions for each test slows the process down" />
				<when value="true" >
					<param name="ions_delta_rt" value="0.1" type="float" label="Delta rt" help="Maximum difference in two ions' m/z to consider them as equal" />
					<param name="ions_delta_mz" value="0.5" type="float" label="Delta m/z" help="Maximum difference in two ions' rt to consider them as equal" />
					<repeat name="ions_to_check" title="Check ion" min="1" help="Add as many ions as necessary" >
						<param name="name" value="Valine" type="text" label="Name" help="Name to be displayed. Ex: Valine" />
						<param name="rt" value="9.67" type="float" label="Retention time" help="The ion's retention time. Ex: 9.67" />
						<param name="mzs" value="218.1105,219.1146" type="text" label="Mass-to-charge ratio for each isotope" help="List of the isotopes' m/zs separated by commas, without spaces. Ex: 218.1105,219.1146"/>
					</repeat>
				</when>
				<when value="false" />
			</conditional>
		</section>
	</inputs>
  
	<outputs>
		<data name="summary_out" label="summary.tsv" format="tabular" />
		<data name="peakspectra_out" label="peakspectra.zip" format="zip" />
		<data name="intensity_graph_out" label="intensity_graph.pdf" format="pdf" />
		<data name="duplicates_out" label="duplicates.zip" format="zip" >
			<filter>outputs_options['count_duplicates']['count_duplicates_bool']</filter>
		</data>
		<data name="compare_graph_out" label="compare_graph.pdf" format="pdf" />
    </outputs>
	
	<help>

**Author** Pauline Ribeyre

=========
GCMS-test
=========

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

This tool allows the user to run the method metaMS.runGC() with several sets of parameters and to compare the results of each run.

-----------------
Workflow position
-----------------

**Upstream tools**

You must start from here.

**Downstream tools**

+---------------------------+---------------------------------------+--------+
| Name                      | Output file                           | Format |
+===========================+=======================================+========+
|                           |                                       |        |
+---------------------------+---------------------------------------+--------+

----------
Parameters
----------

The **zip file** contains the data (the chromatograms to analyse with metaMS.runGC).

Each section allows the user to vary one parameter by choosing a start value, a stop value and a step for this parameter.

The last section allows the user to set output preferences.

-------
Outputs
-------

The output file **summary.tsv** is a tabular file. It contains the summary of the tests.

The output file **peakspectra.zip** is a zip file. It contains the .msp and .tsv peakspectra files for each test.

The output file **intensity_graph.zip** is a pdf file. It contains the "number of ions vs intensity range" graph for each test.

The output file **duplicates.zip** is a zip file. It contains the .tsv duplicates file for each test.

---------
Changelog
---------

**Version 1.0 - 21/07/2017**

	</help>
</tool>