annotate rawtools.xml @ 0:51e4aa55ea04 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e

<tool id="rawtools" name="Raw Tools" version="@RAWTOOLS_VERSION@.@TOOL_SUBVERSION@" profile="16.04">
    <description>
        Perform scan data parsing, quantification and quality control analysis of Thermo Orbitrap raw mass spectrometer files.
    </description>
    <macros>
       <token name="@RAWTOOLS_VERSION@">1.4.2</token>
       <token name="@TOOL_SUBVERSION@">0</token>
       <xml name="input_fasta">
         <param format="fasta" name="input_database" type="data" label="Protein Database"
             help="Select FASTA database from history"/>
       </xml>
    </macros>
    <requirements>
        <requirement type="package" version="@RAWTOOLS_VERSION@">rawtools</requirement>
    </requirements>
    <command detect_errors="exit_code">
<![CDATA[
        #from datetime import datetime
        #import json
        #import os
        #import re
        #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
        #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
        #set $temp_stderr = "rawtools_stderr"
        #set $bin_dir = "bin"

        mkdir output &&
        cwd=`pwd` &&
        ## TODO: To remove this patch when dropping support for Galaxy 17_09, adding profile="18.01" to the tool.
        export HOME=\$cwd  &&

        mkdir raws_folder &&
        #for $input_raw in $input_raws:
            #set $input_name = re.sub('[^\w\-\.]', '_',$input_raw.element_identifier.split('/')[-1].replace(".raw", "") + ".raw")
            ln -s -f '${input_raw}' './raws_folder/${input_name}' &&
        #end for

        #####################
        ## Raw Tools ##
        #####################
        (rawtools.sh

            ## PARSING AND QUANTIFICATION OPTIONS

            ## If any processing option is enabled in parsing & quantification, "parse" command is mandatory
            #if $pq_options.pq_conditional.matrix_select  == "yes" or $pq_options.chromatogram_conditional.chromatogram_select == "yes" or $pq_options.mgf_conditional.mgf_select  == "yes" or  $pq_options.metrics_boolean  == "yes":
                parse
            #end if
            --directory ./raws_folder

            ## Generates Matrix file
            #if $pq_options.pq_conditional.matrix_select == "yes":
                --parse
            #end if

            ## Generates quantification information
            #if $pq_options.pq_conditional.matrix_select == "yes" and $pq_options.pq_conditional.q_conditional.q_select == "yes" :
                --quant
                --labelingreagent ${pq_options.pq_conditional.q_conditional.q_labeling_reagent}
            #end if

            ## Unlabeled quant
            #if $pq_options.pq_conditional.matrix_select == "yes" and $pq_options.pq_conditional.unlabeledquant_boolean  == "yes":
                --unlabeledquant
            #end if

            ## Generates Mgf file
            #if $pq_options.mgf_conditional.mgf_select == "yes":
                --writemgf
                --masscutoff ${pq_options.mgf_conditional.mgf_masscutoff}
            ## DEPRECATED    --intensitycutoff ${pq_options.mgf_conditional.mgf_intensitycutoff}
                #if $pq_options.mgf_conditional.mgf_refinement == "yes":
                    -R
                #end if
            #end if

            ## Generates chromatogram file
            #if $pq_options.chromatogram_conditional.chromatogram_select == "yes":
                --chro ${pq_options.chromatogram_conditional.chromatogram_type}${pq_options.chromatogram_conditional.chromatogram_order}
            #end if

            ## Generates metrics file
            #if $pq_options.metrics_boolean  == "yes":
                --metrics
            #end if

            --out \$cwd/output

        2>> $temp_stderr) &&

        cat $temp_stderr 2>&1;
]]>
    </command>
    <inputs>
        <param format="thermo.raw" name="input_raws" type="data" label="Raw file" multiple="true"
            help="Select the raw file from history"/>
        <param name="license_agreement" type="boolean" label="Do you agree to the vendor licenses?" help="This tool uses a proprietary vendor library; to run it you must agree to the vendor license. Read it at https://github.com/kevinkovalchik/RawTools/blob/master/RawFileReaderLicense">
            <validator type="expression" message="You must agree to the vendor license to run RawTools.">True == value</validator>
        </param>
        <section name="pq_options" expanded="true" title="Parsing and Quantification">
            <conditional name="pq_conditional">
                <param name="matrix_select" type="select"
                    label="Create Matrix file"
                    help="Parses raw file meta and scan data and creates a tab-delimited text file.">
                    <option value="yes" selected="True">Yes</option>
                    <option value="no" >No</option>
                </param>
                <when value="yes">
                    <conditional name="q_conditional">
                        <param name="q_select" type="select"
                          label="Quantification"
                          help="Also quantifies reporter ions and write results to output matrix.">
                            <option value="yes" >Yes</option>
                            <option value="no" selected="True">No</option>
                        </param>
                        <when value="yes">
                            <param name="q_labeling_reagent" label="Labeling reagent" type="select"
                              help="Reagents used to label peptides.">
                                <option value="TMT0" selected="True">TMT0</option>
                                <option value="TMT2" >TMT2</option>
                                <option value="TMT6" >TMT6</option>
                                <option value="TMT10" >TMT10</option>
                                <option value="TMT11" >TMT11</option>
                                <option value="iTRAQ4" >iTRAQ4</option>
                                <option value="iTRAQ8" >iTRAQ8</option>
                            </param>
                        </when>
                        <when value="no" />
                    </conditional>
                    <param name="unlabeledquant_boolean" label="Unlabeled quant" type="boolean" truevalue="yes" falsevalue="no"
                      help="Calculate areas of precursor peaks and writes them to the matrix file as ParentPeakArea column."/>
                </when>
                <when value="no" />
            </conditional>

            <conditional name="mgf_conditional">
                <param name="mgf_select" type="select" label="Creates a mgf file"
                  help="Creates a standard MGF file.">
                    <option value="yes" >Yes</option>
                    <option value="no" selected="True">No</option>
                </param>
                <when value="yes">
                    <param name="mgf_masscutoff" label="Mass cutoff" value="0" type="float"
                      help="Specify a mass cutoff to be applied when generating MGF files. May be of use if removal of reporter ions is desired prior to searching of MS2 spectra."/>
                    <!--<param name="mgf_intensitycutoff" label="Intensity cutoff" value="0" type="float"
                      help="Relative intensity cutoff for ions included in a MGF file. The value is relative to the highest intensity ion found in a given scan."/>
                    -->
                    <param name="mgf_refinement" label="Precursor mass and charge refinement" type="boolean" truevalue="yes" falsevalue="no" checked="false"
                      help="Refine precursor charge and monoisotopic mass assignments. Highly recommended if monoisotopic precursor selection was turned off in the instrument method (or peptide match on a QE instrument)."/>

                </when>
                <when value="no" />
            </conditional>
            <conditional name="chromatogram_conditional">
                <param name="chromatogram_select" type="select"
                    label="Create chromatogram"
                    help="Creates a text file of chromatographic data for investigation or plotting.">
                    <option value="yes" >Yes</option>
                    <option value="no" selected="True">No</option>
                </param>
                <when value="yes">
                    <param name="chromatogram_type" label="Chromatogram type" type="select" help="MS Level">
                        <option value="1" selected="True">MS1</option>
                        <option value="2" >MS2</option>
                        <option value="3" >MS3</option>
                    </param>
                    <param name="chromatogram_order" label="Chromatogram order" type="select" help="MS Order">
                        <option value="T" >TIC</option>
                        <option value="B" >Base peak</option>
                        <option value="TB" selected="True">TIC and base peak</option>
                    </param>
                </when>
                <when value="no" />
            </conditional>
            <param name="metrics_boolean" label="Create metrics" type="boolean" truevalue="yes" falsevalue="no"
              help="Creates a text file containing general metrics about the Ms run." />

        </section>

        <!-- TODO: QUALITY CONTROL
        <section name="quality_control_options" expanded="false" title="Quality control">

        </section>
        -->

    </inputs>
    <outputs>
        <!-- Matrix -->

        <collection name="output_matrix" type="list" label="${tool.name} - ${on_string}: Matrix">
            <filter>pq_options['pq_conditional']['matrix_select'] == "yes"</filter>
            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.raw_Matrix.txt" ext="txt" directory="output"/>
        </collection>

        <!-- MGF file -->

        <collection name="output_mgf" type="list" label="${tool.name} - ${on_string}: MGF">
            <filter>pq_options['mgf_conditional']['mgf_select'] == "yes"</filter>
            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.mgf" ext="mgf" directory="output"/>
        </collection>

        <!-- Chromatogram file -->

        <collection name="output_chromatogram" type="list" label="${tool.name} - ${on_string}: Chromatogram" >
            <filter>pq_options['chromatogram_conditional']['chromatogram_select'] == "yes"</filter>
            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.raw_Ms_BP_chromatogram.txt" ext="txt" directory="output"/>
        </collection>

        <!-- Metrics file -->

        <collection name="output_metrics" type="list" label="${tool.name} - ${on_string}: Metrics" >
            <filter>pq_options['metrics_boolean'] is True</filter>
            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.raw_Metrics.txt" ext="txt" directory="output"/>
        </collection>
    </outputs>
    <tests>

        <!-- Test Matrix -->
        <test>
            <param name="input_raws" value="really_small.raw" ftype="thermo.raw"/>
            <param name="license_agreement" value="true" />
            <param name="pq_conditional|matrix_select" value="yes"/>
            <output_collection name="output_matrix" type="list">
                <element name="really_small" file="really_small.raw_Matrix.txt" ftype="txt" compare="sim_size" delta="3000"/>
            </output_collection>
        </test>

        <!-- Test mgf conversion -->
        <test>
            <param name="input_raws" value="really_small.raw" ftype="thermo.raw"/>
            <param name="license_agreement" value="true" />
            <param name="pq_conditional|matrix_select" value="no"/>
            <param name="mgf_conditional|mgf_select" value="yes"/>
            <param name="mgf_conditional|mgf_refinement" value="yes"/>
            <output_collection name="output_mgf" type="list">
                <element name="really_small.raw" ftype="mgf">
                    <assert_contents>
                        <has_text text="PEPMASS=675.248779296875"/>
                        <has_text text="RTINSECONDS=73.863181104"/>
                        <has_text text="SCANS=36"/>
                        <has_text text="121.31165 920.2368"/>
                    </assert_contents>
                </element>
            </output_collection>
        </test>
        <!-- Test chromatogram -->
        <test>
            <param name="input_raws" value="really_small.raw" ftype="thermo.raw"/>
            <param name="license_agreement" value="true" />
            <param name="pq_conditional|matrix_select" value="no"/>
            <param name="chromatogram_conditional|chromatogram_select" value="yes"/>
            <output_collection name="output_chromatogram" type="list" >
                <element name="really_small" file="really_small.raw_Ms_BP_chromatogram.txt" ftype="txt" compare="sim_size" delta="3000"/>
            </output_collection>
        </test>


    </tests>
    <help>
**What it does**

RawTools is an open-source and freely available package designed to perform scan data parsing and quantification, and quality control analysis (to be developed in further versions) of Thermo Orbitrap raw mass spectrometer files.

RawTools is written in C# and uses the Thermo RawFileReader library. RawTools is the replacement for RawQuant Python package.

https://github.com/kevinkovalchik/RawTools

**License**

Raw Tools is a free open-source project, following an Apache License 2.0.

RawFileReader reading tool. Copyright © 2016 by Thermo Fisher Scientific, Inc. All rights reserved.
Using this software implies the acceptance of RawFileReader license terms.

    </help>
    <citations>
        <citation type="doi">doi:10.1021/acs.jproteome.8b00721</citation>
    </citations>
</tool>