comparison diann.xml @ 1:c9228a392c74 draft

planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71

0:9aa386e5f239

<tool id="diann" name="DIA-NN" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>is a software for DIA/SWATH data processing</description>
    <macros>
        <token name="@TOOL_VERSION@">1.8.1</token>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <requirements>
        <container type="docker">biocontainers/diann:v@TOOL_VERSION@_cv1</container>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[

                ln -s '$infile' './input_data/$infile.element_identifier' &&
                #set $infiles_str += '--f ./input_data/' + str($infile.element_identifier)
            #end if
        #end for

        diann
            #if len($input.f) > 0
            '$infiles_str'
            #end if
            --dir ./
            #if $input.spectral_lib_options.lib
            --lib '$input.spectral_lib_options.lib'
            #else
            --lib
            #end if
            --out ./report.tsv
            #if $input.spectral_lib_options.gen_spec_lib
            --out-lib ./report-lib.tsv
            #end if
            --threads \${GALAXY_SLOTS:-1}
            --temp ./tmp

            #if $input.spectral_lib_options.ref
            --ref '$input.spectral_lib_options.ref'
            #end if

            ## FASTA database options
            --fasta '$input.fasta_db_options.fasta'
            #if $input.fasta_db_options.fasta_filter
            --fasta-filter '$input.fasta_db_options.fasta_filter'
            #end if
            $input.fasta_db_options.fasta_search

            && cp ./report.tsv '$output_report'
            #end if

            #if $input.spectral_lib_options.gen_spec_lib
            && cp ./report-lib.tsv '$output_report_lib'
            #end if
    ]]></command>
    <inputs>
        <!-- not used: cfg, convert, dir, ext, no_quant_files, out, out_lib, out_lib_copy, prefix, temp, threads, use-quant -->
        <section name="input" expanded="true" title="Input files">

                <param name="reannotate" type="boolean" truevalue="--reannotate" falsevalue="" checked="false" label="Reannotate the spectral library with protein information from the FASTA database" help="Reannotate the spectral library with protein information from the FASTA database, using the specified digest specificity"/>
                <param name="ref" type="text" optional="true" label="Reference run" help="(Experimental) Specify a special (small) spectral library which will be used exclusively for calibration - this function can speed up calibration in library-free searches"/>
            </section>
            <section name="fasta_db_options" title="FASTA database">
                <!-- ToDo fasta: use multiple fasta commands to specify multiple databases -->
                <param name="fasta" type="data" format="fasta" label="Sequence database" help="Specify a sequence database in FASTA format"/>
                <param name="fasta_filter" type="data" format="txt" optional="true" label="Fasta filter" help="Only consider peptides matching the stripped sequences specified in the text file provided, when processing a sequence database"/>
                <param name="fasta_search" type="boolean" truevalue="--fasta-search" falsevalue="" checked="false" label="Perform in silico digest of the sequence database" help="Instructs DIA-NN to perform an in silico digest of the sequence database"/>
            </section>
        </section>
        <section name="algo_options" title="Algorithm">

            <param name="verbose" type="integer" min="0" max="4" value="1" label="Verbose level" help="Sets the level of detail of the log"/>
        </section>
    </inputs>
    <outputs>
        <data format="tabular" name="output_report" label="${tool.name} on ${on_string}: report.tsv">
            <filter>len(input['f']) > 0</filter>
        </data>
        <data format="tabular" name="output_report_lib" label="${tool.name} on ${on_string}: report-lib.tsv">
            <filter>input['spectral_lib_options']['gen_spec_lib'] == True</filter>
        </data>
    </outputs>
    <tests>
        <!-- test for default run -->
        <test expect_num_outputs="2">
            <section name="input">
                <param name="f" value="small-peakpicking-cwt-allMS.mzML" />
                <section name="spectral_lib_options">
                    <param name="gen_spec_lib" value="True"/>
                    <param name="predictor" value="True"/>

                </assert_contents>
            </output>
            <output name="output_report_lib" file="report-lib.tsv">
                <assert_contents>
                    <has_text text="PrecursorMz"/>
                </assert_contents>
            </output>
        </test>
        <!-- test for Bruker data -->
<!--        <test expect_num_outputs="2">-->

1:c9228a392c74

<tool id="diann" name="DIA-NN" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>is a software for DIA/SWATH data processing</description>
    <macros>
        <token name="@TOOL_VERSION@">1.8.1</token>
        <token name="@VERSION_SUFFIX@">1</token>
    </macros>
    <requirements>
        <container type="docker">biocontainers/diann:v@TOOL_VERSION@_cv1</container>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[

                ln -s '$infile' './input_data/$infile.element_identifier' &&
                #set $infiles_str += '--f ./input_data/' + str($infile.element_identifier)
            #end if
        #end for

        #set $fasta_file_str = ''
        #for $fasta_file in $input.fasta_db_options.fasta
            #set $fasta_file_str += '--fasta ' + str($fasta_file) + ' '
        #end for

        diann
            #if $input.f != 'None'
            '$infiles_str'
            #end if
            --dir ./
            #if $input.spectral_lib_options.lib
            --lib '$input.spectral_lib_options.lib'
            #else
            --lib
            #end if
            #if $input.f != 'None'
            --out ./report.tsv
            #end if
            #if $input.spectral_lib_options.gen_spec_lib
            --out-lib ./report-lib.tsv
            #end if
            --threads \${GALAXY_SLOTS:-1}
            --temp ./tmp

            #if $input.spectral_lib_options.ref
            --ref '$input.spectral_lib_options.ref'
            #end if

            ## FASTA database options
            #if $fasta_file_str != 'None'
            '$fasta_file_str'
            #end if
            #if $input.fasta_db_options.fasta_filter
            --fasta-filter '$input.fasta_db_options.fasta_filter'
            #end if
            $input.fasta_db_options.fasta_search

            && cp ./report.tsv '$output_report'
            #end if

            #if $input.spectral_lib_options.gen_spec_lib
            && cp ./report-lib.tsv '$output_report_lib'
            && cp ./report-lib.tsv.speclib '$output_report_speclib'
            && cp ./report-lib.predicted.speclib '$output_report_pred_speclib'
            #end if
    ]]></command>
    <inputs>
        <!-- not used: cfg, convert, dir, ext, no_quant_files, out, out_lib, out_lib_copy, prefix, temp, threads, use-quant -->
        <section name="input" expanded="true" title="Input files">

                <param name="reannotate" type="boolean" truevalue="--reannotate" falsevalue="" checked="false" label="Reannotate the spectral library with protein information from the FASTA database" help="Reannotate the spectral library with protein information from the FASTA database, using the specified digest specificity"/>
                <param name="ref" type="text" optional="true" label="Reference run" help="(Experimental) Specify a special (small) spectral library which will be used exclusively for calibration - this function can speed up calibration in library-free searches"/>
            </section>
            <section name="fasta_db_options" title="FASTA database">
                <!-- ToDo fasta: use multiple fasta commands to specify multiple databases -->
                <param name="fasta" type="data" format="fasta" multiple="true" label="Sequence database" help="Specify a sequence database in FASTA format"/>
                <param name="fasta_filter" type="data" format="txt" optional="true" label="Fasta filter" help="Only consider peptides matching the stripped sequences specified in the text file provided, when processing a sequence database"/>
                <param name="fasta_search" type="boolean" truevalue="--fasta-search" falsevalue="" checked="false" label="Perform in silico digest of the sequence database" help="Instructs DIA-NN to perform an in silico digest of the sequence database"/>
            </section>
        </section>
        <section name="algo_options" title="Algorithm">

            <param name="verbose" type="integer" min="0" max="4" value="1" label="Verbose level" help="Sets the level of detail of the log"/>
        </section>
    </inputs>
    <outputs>
        <data format="tabular" name="output_report" label="${tool.name} on ${on_string}: report.tsv">
            <filter>input['f'] != None</filter>
        </data>
        <data format="tabular" name="output_report_lib" label="${tool.name} on ${on_string}: report-lib.tsv">
            <filter>input['spectral_lib_options']['gen_spec_lib'] == True</filter>
        </data>
        <data format="data" name="output_report_speclib" label="${tool.name} on ${on_string}: report-lib.tsv.speclib">
            <filter>input['spectral_lib_options']['gen_spec_lib'] == True</filter>
        </data>
        <data format="data" name="output_report_pred_speclib" label="${tool.name} on ${on_string}: report-lib.predicted.speclib">
            <filter>input['spectral_lib_options']['gen_spec_lib'] == True</filter>
        </data>
    </outputs>
    <tests>
        <!-- test for default run -->
        <test expect_num_outputs="4">
            <section name="input">
                <param name="f" value="small-peakpicking-cwt-allMS.mzML" />
                <section name="spectral_lib_options">
                    <param name="gen_spec_lib" value="True"/>
                    <param name="predictor" value="True"/>

                </assert_contents>
            </output>
            <output name="output_report_lib" file="report-lib.tsv">
                <assert_contents>
                    <has_text text="PrecursorMz"/>
                </assert_contents>
            </output>
            <output name="output_report_speclib" file="report-lib.tsv.speclib" compare="sim_size" delta="100"/>
            <output name="output_report_pred_speclib" file="report-lib.predicted.speclib" compare="sim_size" delta="100"/>
        </test>
        <!-- test for multiple fastas -->
        <test expect_num_outputs="1">
            <section name="input">
                <param name="f" value="small-peakpicking-cwt-allMS.mzML" />
                <section name="fasta_db_options">
                    <param name="fasta" value="bsa.fasta,bsa2.fasta"/>
                    <param name="fasta_search" value="True"/>
                </section>
            </section>
            <output name="output_report" file="report.tsv">
                <assert_contents>
                    <has_text text="PG.Normalised"/>
                </assert_contents>
            </output>
        </test>
        <!-- test for Bruker data -->
<!--        <test expect_num_outputs="2">-->