comparison recentrifuge.xml @ 1:fe733f05c2f8 draft

planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 9142693589056424fb64869b69dbc08b179f57ee

0:09b7b0b2e2c2

        Robust comparative analysis and contamination removal for metagenomics
    </description>
    <macros>
        <import>macro.xml</import>
    </macros>
    <expand macro='xrefs'/>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="aggressive"><![CDATA[
        #*======================================
                  database input
        ======================================*#
        rcf
        -n $database.database_name.fields.path
        #*======================================
                  Recentrifuge input file
        ======================================*#
        #if $file_type.filetype == "centrifuge"
            -f '$input_file'
            #set $default_scoring = 'SHEL'
        #else if $file_type.filetype == "lmat"
            -l '$input_file'
            #set $default_scoring = 'LMAT'
        #else if $file_type.filetype == "clark"
            -r '$input_file'
            #set $default_scoring = 'SHEL'
        #else if $file_type.filetype == "kraken"
            -k '$input_file'
            #set $default_scoring = 'KRAKEN'
        #else if $file_type.filetype == "generic"
            -g '$input_file'
            --format '$file_type.format'
            #set $default_scoring = 'GENERIC'
        #end if
        #*======================================
                  Output options
        ======================================*#
        -e $output_option.extra
        -o output

        $more_advanced_option.strain
        $more_advanced_option.sequential
        #*======================================
                  Log file output
        ======================================*#
        &> $logfile
        ]]>
    </command>
    <inputs>
        <!-- INPUT FILES -->
        <param name="input_file" type="data" format="tabular" label="Select taxonomy file tabular formated"/>
        <conditional name="file_type">
            <param name="filetype" type="select" display="radio" label="Type of input file (Centrifuge, CLARK, Generic, Kraken, LMAT)" help="(-f, -r, -g, -k, -l)">
                <option value="centrifuge">Centrifuge</option>
                <option value="clark">CLARK</option>
                <option value="generic">Generic</option>

                <option value="DYNOMICS">DYNOMICS</option>
                <option value="FULL">FULL</option>
                <option value="TSV" >TSV</option>
            </param>
            <param argument="--nohtml" type="boolean" truevalue="--nohtml" falsevalue="" label="Suppress saving the HTML output file" help="remove html output"/>
        </section>
    <!-- ADVANCED OPTIONS -->
        <section name="advanced_option" title="Coarse tuning of algorithm parameters">
            <param name="controls" type="integer" optional="true" value="0" label="Number of first samples will be treated as negative controls" help="Add control samples (default is 0)"/>
            <param name="scoring" type="select" optional="true" label="Type of scoring to be applied" help="Scoring algorithm, depending of the input files, see the help section of the tools">

  <!-- OUTPUT FILE, TYPE DEPENDING ON extra PARAMETER -->
    <outputs>
        <data name="html_report" format="html" from_work_dir="output.rcf.html" label="${tool.name} on ${on_string}: html report">
            <filter> output_option['nohtml'] == False</filter>
        </data>
        <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log file"/>
        <data name="data_csv" format="tabular" from_work_dir="output.rcf.data.csv" label="${tool.name} on ${on_string}: data.csv">
            <filter> output_option['extra']  == 'CSV' </filter>
        </data>
        <data name="stat_csv" format="tabular" from_work_dir="output.rcf.stat.csv" label="${tool.name} on ${on_string}: stat.csv">
            <filter> output_option['extra']  == 'CSV' </filter>

                <param name="strain" value="true"/>
            </section>
            <output name="data_tsv" file="kraken_test/test3_rcf.data.tsv" lines_diff="2"/>
            <output name="stat_tsv" file="kraken_test/test3_rcf.stat.tsv" lines_diff="2"/>
            <output name="logfile" file="kraken_test/test3_tsv.log" lines_diff="12"/>
        </test>
    </tests>
  <help><![CDATA[
**What it does**

1:fe733f05c2f8

        Robust comparative analysis and contamination removal for metagenomics
    </description>
    <macros>
        <import>macro.xml</import>
    </macros>
    <expand macro='edam'/>
    <expand macro='xrefs'/>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="aggressive"><![CDATA[
      #import re
      #*======================================
            Make a dir with all input files
      ======================================*#
        mkdir input_dir &&
        #for $input in $input_file
            #set input_identifier = re.sub('[^\s\w\-]', '_', str($input.element_identifier))
            #if $file_type.filetype == "centrifuge"
                ln -s '$input' 'input_dir/${input_identifier}.out' &&
            #else if $file_type.filetype == "clark"
                ln -s '$input' 'input_dir/${input_identifier}.csv' &&
            #else if $file_type.filetype == "kraken"
                ln -s '$input' 'input_dir/${input_identifier}.krk' &&
            #else
                ln -s '$input' 'input_dir/$input_identifier' &&
            #end if
        #end for
        #*======================================
                  database input
        ======================================*#
        rcf
        -n $database.database_name.fields.path
        #*======================================
                  Recentrifuge input file
        ======================================*#

        #if $file_type.filetype == "centrifuge"
            -f input_dir
            #set $default_scoring = 'SHEL'
        #else if $file_type.filetype == "kraken"
            -k input_dir
            #set $default_scoring = 'KRAKEN'
        #else if $file_type.filetype == "clark"
            -r input_dir
            #set $default_scoring = 'SHEL'
        #else if $file_type.filetype == "lmat"
            -l input_dir
            #set $default_scoring = 'LMAT'
        #else if $file_type.filetype == "generic"
            -g input_dir
            --format '$file_type.format'
            #set $default_scoring = 'GENERIC'
        #end if

        #*======================================
                  Output options
        ======================================*#
        -e $output_option.extra
        -o output

        $more_advanced_option.strain
        $more_advanced_option.sequential
        #*======================================
                  Log file output
        ======================================*#
        | tee "$logfile"
        ]]>
    </command>
    <inputs>
        <!-- INPUT FILES -->
        <param name="input_file" type="data" format="tabular" multiple="true" optional="false" label="Select taxonomy file tabular formated"/>
        <conditional name="file_type">
            <param name="filetype" type="select" display="radio" label="Type of input file (Centrifuge, CLARK, Generic, Kraken, LMAT)" help="(-f, -r, -g, -k, -l)">
                <option value="centrifuge">Centrifuge</option>
                <option value="clark">CLARK</option>
                <option value="generic">Generic</option>

                <option value="DYNOMICS">DYNOMICS</option>
                <option value="FULL">FULL</option>
                <option value="TSV" >TSV</option>
            </param>
            <param argument="--nohtml" type="boolean" truevalue="--nohtml" falsevalue="" label="Suppress saving the HTML output file" help="remove html output"/>
            <param name="no_logfile" type="boolean" truevalue="True" falsevalue="False" label="Remove the log file"/>
        </section>
    <!-- ADVANCED OPTIONS -->
        <section name="advanced_option" title="Coarse tuning of algorithm parameters">
            <param name="controls" type="integer" optional="true" value="0" label="Number of first samples will be treated as negative controls" help="Add control samples (default is 0)"/>
            <param name="scoring" type="select" optional="true" label="Type of scoring to be applied" help="Scoring algorithm, depending of the input files, see the help section of the tools">

  <!-- OUTPUT FILE, TYPE DEPENDING ON extra PARAMETER -->
    <outputs>
        <data name="html_report" format="html" from_work_dir="output.rcf.html" label="${tool.name} on ${on_string}: html report">
            <filter> output_option['nohtml'] == False</filter>
        </data>
        <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log file">
            <filter> output_option['no_logfile'] == False </filter>
        </data>
        <data name="data_csv" format="tabular" from_work_dir="output.rcf.data.csv" label="${tool.name} on ${on_string}: data.csv">
            <filter> output_option['extra']  == 'CSV' </filter>
        </data>
        <data name="stat_csv" format="tabular" from_work_dir="output.rcf.stat.csv" label="${tool.name} on ${on_string}: stat.csv">
            <filter> output_option['extra']  == 'CSV' </filter>

                <param name="strain" value="true"/>
            </section>
            <output name="data_tsv" file="kraken_test/test3_rcf.data.tsv" lines_diff="2"/>
            <output name="stat_tsv" file="kraken_test/test3_rcf.stat.tsv" lines_diff="2"/>
            <output name="logfile" file="kraken_test/test3_tsv.log" lines_diff="12"/>
        </test>
        <test expect_num_outputs="3"> <!-- Test sumarized output TEST_4 -->
            <section name="database">
                <param name="database_name" value="test-db-2022"/>
            </section>
            <param name="input_file" value="centrifuge_test/centrifuge.out,centrifuge_test/centrifuge_1.out,centrifuge_test/centrifuge_2.out"/>
            <conditional name="file_type">
                <param name="filetype" value="centrifuge"/>
            </conditional>
            <section name="output_option" >
                <param name="extra" value="TSV"/>
                <param name="no_logfile" value="True"/>
            </section>
            <section name="advanced_option">
                <param name="scoring" value="LENGTH"/>
            </section>
            <section name="more_advanced_option">
                <param name="summary" value="ADD"/>
                <param name="strain" value="true"/>
            </section>
            <output name="data_tsv" file="centrifuge_test/test4_rcf.data.tsv" lines_diff="2"/>
            <output name="stat_tsv" file="centrifuge_test/test4_rcf.stat.tsv" lines_diff="2"/>
            <output name="html_report" file="centrifuge_test/test4_tsv.html" lines_diff="12"/>
        </test>
    </tests>
  <help><![CDATA[
**What it does**