comparison maxbin2.xml @ 4:9d11c2c0ff24 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26

3:9bfc53fc35aa

<tool id="maxbin2" name="MaxBin2" version="@MAXBIN_VERSION@+galaxy2">
    <description>clusters metagenomic contigs into bins</description>
    <xrefs>
        <xref type="bio.tools">masigpro</xref>
    </xrefs>
    <macros>
        <token name="@MAXBIN_VERSION@">2.2.7</token>
    </macros>
    <requirements>
        <requirement type="package" version="@MAXBIN_VERSION@">maxbin2</requirement>
    </requirements>
    <version_command><![CDATA[run_MaxBin.pl -version | head -n 1]]></version_command>
    <command detect_errors="exit_code"><![CDATA[
    ## generate read or abundance files	
    #if $intype_cond.intype_select == 'rds':
        #for $r in $intype_cond.reads
            #if $r
                echo '$r' >> reads_list &&
            #end if
        #end for
    #else if $intype_cond.intype_select == 'abdc':
        #for $a in $intype_cond.abund
            #if $a
                echo '$a' >> abund_list &&
            #end if
        #end for
    #end if

    ## in case of reassembly the IBDA out and err is appended
    ## to differentiate this a header is added also befor the
    ## MaxBin2 outputs
    #if $intype_cond.intype_select == 'rds' and $intype_cond.reassembly != ""
        echo "==== MaxBin2 stdout ====" &&
        echo "==== MaxBin2 stderr ====" 1>&2 &&
    #end if

    run_MaxBin.pl
    -contig '$contig'
    -out out
    #if $intype_cond.intype_select == 'rds':
        -reads_list reads_list
        $intype_cond.reassembly
    #else if $intype_cond.intype_select == 'abdc':
        -abund_list abund_list
    #end if
    #if $adv_cond.adv_select == 'yes':
        -min_contig_length $adv_cond.min_contig_length
        -max_iteration $adv_cond.max_iteration
        -prob_threshold $adv_cond.prob_threshold
        $adv_cond.plotmarker
        -markerset $adv_cond.markerset
    #end if
    -thread \${GALAXY_SLOTS:-1}

    && gzip -cd out.marker_of_each_bin.tar.gz | tar -xf -

    ## redirect the idba out and err file content to stdout and err
    ## since this is also wanted in case the error case ';' is used here to 
    ## separate commands
    #if $intype_cond.intype_select == 'rds' and $intype_cond.reassembly != ""
        ; echo "==== IDBA stdout ===="
        && if [[ -f out.idba.out ]]; then cat out.idba.out; fi
        && echo "==== IDBA stderr ====" 1>&2
        && if [[ -f out.idba.err ]]; then cat out.idba.err 1>&2; fi
    #end if
    ]]></command>
    <inputs>
        <param argument="-contig" type="data" format="fasta,fasta.gz" label="Contig file"/>
          <conditional name="intype_cond">
              <param name="intype_select" type="select" label="Input type">
                  <option value="rds" selected="true">Sequencing Reads</option>
                  <option value="abdc">Abundances</option>
              </param>
              <when value="rds">
                  <param name="reads" type="data" format="fasta,fastq" multiple="true" label="Reads file(s)" help="(-read/-read2/...)"/>
                  <param name="output_abundances" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output abundances" help="" />
                  <param argument="--reassembly" type="boolean" truevalue="-reassembly" falsevalue="" checked="false" label="Reassembly" help="Reassembly option is still highly experimental. To use this function, you need to feed MaxBin interleaved paired-end fastq or fasta file." />
              </when>
              <when value="abdc">
                  <param name="abund" type="data" format="tabular" multiple="true" label="Abundance file(s)" help="(-abund/-abund2/...)" />
              </when>
          </conditional>
          <conditional name="adv_cond">
            <param name="adv_select" type="select" label="Advanced options">
                <option value="yes">Yes</option>
                <option value="no" selected="true">No</option>
            </param>
            <when value="no"/>
            <when value="yes">
                <param argument="-min_contig_length" type="integer" min="0" value="1000" label="minimum contig length" />
                <param argument="-max_iteration" type="integer" min="0" value="50" label="Maximum Expectation-Maximization algorithm iteration number" />
                <param argument="-prob_threshold" type="float" min="0" max="1.0" value="0.5" label="Probability threshold for EM final classification" />
                <param argument="-plotmarker" type="boolean" truevalue="-plotmarker" falsevalue="" checked="false" label="Generate visualization of the marker gene presence numbers" />
                <param name="output_marker" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output marker gene presence for bins table" />
                <param name="output_markers" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output marker genes for each bin as fasta" />
                <param name="output_log" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output log" />
                <param argument="-markerset" type="select" label="Marker gene set">
                    <option value="107" selected="true">107 marker genes present in >95% of bacteria</option>
                    <option value="40">40 marker gene sets that are universal among bacteria and archaea</option>
                </param>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <!-- default outputs -->
        <collection name="bins" type="list" label="${tool.name} on ${on_string} (bins)">
            <discover_datasets pattern="out.(?P&lt;designation&gt;[0-9]+).fasta" format="fasta" visible="false" />
        </collection>
        <data name="noclass" format="fasta" label="${tool.name} on ${on_string} (unclassified sequences)" from_work_dir="out.noclass"/>
        <data name="toshort" format="fasta" label="${tool.name} on ${on_string} (to short sequences)" from_work_dir="out.tooshort"/>
        <data name="summary" format="tabular" label="${tool.name} on ${on_string} (summary)" from_work_dir="out.summary"/>

        <!-- optional outputs -->
        <data name="log" format="txt" label="${tool.name} on ${on_string} (log)" from_work_dir="out.log">
            <filter>adv_cond['adv_select']=='yes' and adv_cond['output_log']</filter>
        </data>
        <data name="marker" format="tabular" label="${tool.name} on ${on_string} (marker gene presence)" from_work_dir="out.marker">
            <filter>adv_cond['adv_select']=='yes' and adv_cond['output_marker']</filter>
        </data>
        <data name="abundout" format="tabular" label="${tool.name} on ${on_string} (abundances)" from_work_dir="out.abund1">
            <filter>intype_cond['intype_select']=='rds' and intype_cond['output_abundances']</filter>
        </data>
        <data name="plot" format="pdf" label="${tool.name} on ${on_string} (marker gene presence plot)" from_work_dir="out.marker.pdf">
            <filter>adv_cond['adv_select']=='yes' and adv_cond['plotmarker']</filter>
        </data>
        <collection name="markers" type="list" label="${tool.name} on ${on_string} (markers prediced for bins)">
            <discover_datasets pattern="out.(?P&lt;designation&gt;[0-9]+).marker.fasta" format="fasta" visible="false" />
            <filter>adv_cond['adv_select']=='yes' and adv_cond['output_markers']</filter>
        </collection>

        <!-- additional output in case of reassembly -->
        <collection name="reassembly_bins" type="list" label="${tool.name} on ${on_string} (reassembly bins)">
            <discover_datasets directory="out.reassem" pattern="out.(?P&lt;designation&gt;[0-9]+).fasta" format="fasta" visible="false" />
            <filter>intype_cond['intype_select']=='rds' and intype_cond['reassembly']</filter>
        </collection>
        <collection name="reassembly_reads" type="list" label="${tool.name} on ${on_string} (reassembly reads)">
            <discover_datasets directory="out.reassem" pattern="out.reads.(?P&lt;designation&gt;[0-9]+)" format="fasta" visible="false" />
            <filter>intype_cond['intype_select']=='rds' and intype_cond['reassembly']</filter>
        </collection>
        <data name="reassembly_noclass" format="fasta" label="${tool.name} on ${on_string} (reassembly unclassified sequences)" from_work_dir="out.reassem/out.reads.noclass">
            <filter>intype_cond['intype_select']=='rds' and intype_cond['reassembly']</filter>
        </data>
        <data name="reassembly_n50" format="txt" label="${tool.name} on ${on_string} (reassembly N50)" from_work_dir="out.reassem/N50.txt">
            <filter>intype_cond['intype_select']=='rds' and intype_cond['reassembly']</filter>
        </data>
    </outputs>
    <tests>
        <!-- test w contigs and reads as input -->
        <test expect_num_outputs="4">
            <param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" />
            <conditional name="intype_cond">
                <param name="intype_select" value="rds"/>
                <param name="reads" value="interleavedPE_unmapped_Sample3_small.fasta" ftype="fasta"/>
            </conditional>
            <conditional name="adv_cond">
                <param name="adv_select" value="no"/>
            </conditional>
            <output_collection name="bins" type="list" count="2">
                <element name="001" file="1/out.001.fasta" ftype="fasta"/>
                <element name="002" file="1/out.002.fasta" ftype="fasta"/>
            </output_collection>
            <output name="summary" file="1/out.summary" ftype="tabular" />
            <output name="noclass" file="1/out.noclass" ftype="fasta" />
            <output name="toshort" file="1/out.tooshort" ftype="fasta" />
        </test>
        <!-- test w contigs and reads as input test for optional outputs -->
        <test expect_num_outputs="9">
            <param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" />
            <conditional name="intype_cond">
                <param name="intype_select" value="rds"/>
                <param name="reads" value="interleavedPE_unmapped_Sample3_small.fasta" ftype="fasta"/>
                <param name="output_abundances" value="true" />
            </conditional>
            <conditional name="adv_cond">
                <param name="adv_select" value="yes"/>
                <param name="plotmarker" value="true" />
                <param name="output_marker" value="true" />
                <param name="output_markers" value="true" />
                <param name="output_log" value="true" />
            </conditional>
            <output_collection name="bins" type="list" count="2">
                <element name="001" file="1/out.001.fasta" ftype="fasta"/>
                <element name="002" file="1/out.002.fasta" ftype="fasta"/>
            </output_collection>
            <output name="summary" file="1/out.summary" ftype="tabular" />
            <output name="noclass" file="1/out.noclass" ftype="fasta" />
            <output name="toshort" file="1/out.tooshort" ftype="fasta" />
            <output name="log" file="1/out.log" ftype="txt" compare="diff" lines_diff="21" />
            <output name="abundout" file="1/out.abund1" ftype="tabular" />
            <output name="marker" file="1/out.marker" ftype="tabular" />
            <output name="plot" file="1/out.marker.pdf" ftype="pdf" compare="sim_size" />
            <output_collection name="markers" type="list" count="1">
                <element name="001" file="1/out.001.marker.fasta" ftype="fasta"/>
            </output_collection>
        </test>
        <!--test w contigs and abundances as input + advanced options -->
        <test expect_num_outputs="5">
            <param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" />
            <conditional name="intype_cond">
                <param name="intype_select" value="abdc"/>
                <param name="abund" value="abundances.tsv" ftype="tabular"/>
            </conditional>
            <conditional name="adv_cond">
                <param name="adv_select" value="yes"/>
                <param name="min_contig_length" value="500"/>
                <param name="max_iteration" value="10"/>
                <param name="prob_threshold" value="0.95"/>
                <param name="plotmarker" value="-plotmarker"/>
                <param name="markerset" value="107"/>
            </conditional>
            <output_collection name="bins" type="list" count="2">
                <element name="001" file="2/out.001.fasta" ftype="fasta"/>
                <element name="002" file="2/out.002.fasta" ftype="fasta"/>
            </output_collection>
            <output name="summary" file="2/out.summary" ftype="tabular" />

            <output name="plot" file="2/out.marker.pdf" ftype="pdf" compare="sim_size" />
        </test>
        <!-- test w contigs and reads as input + reassembly-->
        <test expect_num_outputs="8">
            <param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" />
            <conditional name="intype_cond">
                <param name="intype_select" value="rds"/>
                <param name="reads" value="interleavedPE_unmapped_Sample3_small.fasta" ftype="fasta"/>
                <param name="reassembly" value="-reassembly"/>
            </conditional>
            <conditional name="adv_cond">
                <param name="adv_select" value="no"/>
            </conditional>
            <output_collection name="bins" type="list" count="2">
                <element name="001" file="3/out.001.fasta" ftype="fasta"/>
                <element name="002" file="3/out.002.fasta" ftype="fasta"/>
            </output_collection>
            <output name="summary" file="3/out.summary" ftype="tabular" />
            <output name="noclass" file="3/out.noclass" ftype="fasta" />
            <output name="toshort" file="3/out.tooshort" ftype="fasta" />
            <output_collection name="reassembly_bins" type="list" count="2">
                <element name="001" file="3/out.reassem/out.001.fasta" ftype="fasta"/>
                <element name="002" file="3/out.reassem/out.002.fasta" ftype="fasta"/>
            </output_collection>
            <output_collection name="reassembly_reads" type="list" count="2">
                <element name="001" file="3/out.reassem/out.reads.001" ftype="fasta"/>
                <element name="002" file="3/out.reassem/out.reads.002" ftype="fasta"/>
            </output_collection>
            <output name="reassembly_noclass" file="3/out.reassem/out.reads.noclass" ftype="fasta" />
            <output name="reassembly_n50" file="3/out.reassem/N50.txt" ftype="txt" />
        </test>
    </tests>
    <help><![CDATA[
MaxBin is a software that clusters metagenomic contigs into different bins,
each consists (hopefully) of contigs from one species. MaxBin uses the

4:9d11c2c0ff24

<tool id="maxbin2" name="MaxBin2" version="@MAXBIN_VERSION@+galaxy3">
    <description>clusters metagenomic contigs into bins</description>
    <xrefs>
        <xref type="bio.tools">masigpro</xref>
    </xrefs>
    <macros>
        <token name="@MAXBIN_VERSION@">2.2.7</token>
        <xml name="contig">
            <param argument="-contig" type="data" format="fasta,fasta.gz" label="Contig file"/>
        </xml>
        <xml name="input_type">
            <param name="type" type="select" label="Input type">
                <option value="reads" selected="true">Sequencing Reads</option>
                <option value="abund">Abundances</option>
            </param>
        </xml>
        <xml name="reads_extra_params">
            <param name="output_abundances" type="boolean" checked="false" label="Output abundances" help="" />
            <param argument="--reassembly" type="boolean" truevalue="-reassembly" falsevalue="" checked="false" label="Reassembly" help="Reassembly option is still highly experimental. To use this function, you need to feed MaxBin interleaved paired-end fastq or fasta file." />
        </xml>
    </macros>
    <requirements>
        <requirement type="package" version="@MAXBIN_VERSION@">maxbin2</requirement>
    </requirements>
    <version_command><![CDATA[run_MaxBin.pl -version | head -n 1]]></version_command>
    <command detect_errors="exit_code"><![CDATA[
## generate read or abundance files
#if $assembly.inputs.type == 'reads'
    #if $assembly.type == 'individual'
echo '$assembly.inputs.reads' >> reads_list &&
    #else
        #for $r in $assembly.inputs.reads
            #if $r
echo '$r' >> reads_list &&
            #end if
        #end for
    #end if
#else if $assembly.inputs.type == 'abund'
    #if $assembly.type == 'individual'
echo '$assembly.inputs.abund' >> abund_list &&
    #else
        #for $a in $assembly.inputs.abund
            #if $a
echo '$a' >> abund_list &&
            #end if
        #end for
    #end if
#end if

## in case of reassembly the IBDA out and err is appended
## to differentiate this a header is added also befor the
## MaxBin2 outputs
#if $assembly.inputs.type == 'reads' and $assembly.inputs.reassembly != ""
echo "==== MaxBin2 stdout ====" &&
echo "==== MaxBin2 stderr ====" 1>&2 &&
#end if

run_MaxBin.pl
    -contig '$contig'
    -out out
#if $assembly.inputs.type == 'reads':
    -reads_list reads_list
    $assembly.inputs.reassembly
#else if $assembly.inputs.type == 'abund':
    -abund_list abund_list
#end if
    -min_contig_length $adv.min_contig_length
    -max_iteration $adv.max_iteration
    -prob_threshold $adv.prob_threshold
    $output.plotmarker
    -markerset $output.markerset
    -thread \${GALAXY_SLOTS:-1}

&& gzip -cd out.marker_of_each_bin.tar.gz | tar -xf -

## redirect the idba out and err file content to stdout and err
## since this is also wanted in case the error case ';' is used here to
## separate commands
#if $assembly.inputs.type == 'reads' and $assembly.inputs.reassembly != ""
; echo "==== IDBA stdout ===="
&& if [[ -f out.idba.out ]]; then cat out.idba.out; fi
&& echo "==== IDBA stderr ====" 1>&2
&& if [[ -f out.idba.err ]]; then cat out.idba.err 1>&2; fi
#end if
    ]]></command>
    <inputs>
        <expand macro="contig"/>
        <conditional name="assembly">
            <param name="type" type="select" label="Assembly type used to generate contig(s)">
                <option value="individual">Assembly of sample(s) one by one (individual assembly)</option>
                <option value="coassembly">Assembly of different samples together (co-assembly)</option>
            </param>
            <when value="individual">
                <conditional name="inputs">
                    <expand macro="input_type"/>
                    <when value="reads">
                        <param argument="-reads" type="data" format="fasta,fastq" label="Reads file"/>
                        <expand macro="reads_extra_params"/>
                    </when>
                    <when value="abund">
                        <param argument="-abund" type="data" format="tabular" label="Abundance file"/>
                    </when>
                </conditional>
            </when>
            <when value="coassembly">
                <conditional name="inputs">
                    <expand macro="input_type"/>
                    <when value="reads">
                        <param argument="-reads" type="data" multiple="true" format="fasta,fastq" label="Reads file(s)"/>
                        <expand macro="reads_extra_params"/>
                    </when>
                    <when value="abund">
                        <param argument="-abund" type="data" format="tabular" multiple="true" label="Abundance file(s)"/>
                    </when>
                </conditional>
            </when>
        </conditional>
        <section name="adv" title="Advanced options">
            <param argument="-min_contig_length" type="integer" min="0" value="1000" label="minimum contig length" />
            <param argument="-max_iteration" type="integer" min="0" value="50" label="Maximum Expectation-Maximization algorithm iteration number" />
            <param argument="-prob_threshold" type="float" min="0" max="1.0" value="0.5" label="Probability threshold for EM final classification" />
        </section>
        <section name="output" title="Outputs">
            <param argument="-plotmarker" type="boolean" truevalue="-plotmarker" falsevalue="" checked="false" label="Generate visualization of the marker gene presence numbers" />
            <param name="marker" type="boolean" checked="false" label="Output marker gene presence for bins table" />
            <param name="markers" type="boolean" checked="false" label="Output marker genes for each bin as fasta" />
            <param name="log" type="boolean" checked="false" label="Output log" />
            <param argument="-markerset" type="select" label="Marker gene set">
                <option value="107" selected="true">107 marker genes present in >95% of bacteria</option>
                <option value="40">40 marker gene sets that are universal among bacteria and archaea</option>
            </param>
        </section>
    </inputs>
    <outputs>
        <!-- default outputs -->
        <collection name="bins" type="list" label="${tool.name} on ${on_string}: Bins">
            <discover_datasets pattern="out.(?P&lt;designation&gt;[0-9]+).fasta" format="fasta" visible="false" />
        </collection>
        <data name="noclass" format="fasta" label="${tool.name} on ${on_string}: Unclassified sequences" from_work_dir="out.noclass"/>
        <data name="toshort" format="fasta" label="${tool.name} on ${on_string}: Too short sequences" from_work_dir="out.tooshort"/>
        <data name="summary" format="tabular" label="${tool.name} on ${on_string}: Summary" from_work_dir="out.summary"/>
        <!-- optional outputs -->
        <data name="log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="out.log">
            <filter>output['log']</filter>
        </data>
        <data name="marker" format="tabular" label="${tool.name} on ${on_string}: Marker gene presence" from_work_dir="out.marker">
            <filter>output['marker']</filter>
        </data>
        <data name="abundout" format="tabular" label="${tool.name} on ${on_string}: Abundances" from_work_dir="out.abund1">
            <filter>assembly['inputs']['type']=='reads' and assembly['inputs']['output_abundances']</filter>
        </data>
        <data name="plot" format="pdf" label="${tool.name} on ${on_string}: Marker gene presence plot" from_work_dir="out.marker.pdf">
            <filter>output['plotmarker']</filter>
        </data>
        <collection name="markers" type="list" label="${tool.name} on ${on_string}: Markers prediced for bins">
            <discover_datasets pattern="out.(?P&lt;designation&gt;[0-9]+).marker.fasta" format="fasta" visible="false" />
            <filter>output['markers']</filter>
        </collection>
        <!-- additional output in case of reassembly -->
        <collection name="reassembly_bins" type="list" label="${tool.name} on ${on_string}: Reassembly bins">
            <discover_datasets directory="out.reassem" pattern="out.(?P&lt;designation&gt;[0-9]+).fasta" format="fasta" visible="false" />
            <filter>assembly['inputs']['type']=='reads' and assembly['inputs']['reassembly']</filter>
        </collection>
        <collection name="reassembly_reads" type="list" label="${tool.name} on ${on_string}: Reassembly reads">
            <discover_datasets directory="out.reassem" pattern="out.reads.(?P&lt;designation&gt;[0-9]+)" format="fasta" visible="false" />
            <filter>assembly['inputs']['type']=='reads' and assembly['inputs']['reassembly']</filter>
        </collection>
        <data name="reassembly_noclass" format="fasta" label="${tool.name} on ${on_string}: Reassembly unclassified sequences" from_work_dir="out.reassem/out.reads.noclass">
            <filter>assembly['inputs']['type']=='reads' and assembly['inputs']['reassembly']</filter>
        </data>
        <data name="reassembly_n50" format="txt" label="${tool.name} on ${on_string}: Reassembly N50" from_work_dir="out.reassem/N50.txt">
            <filter>assembly['inputs']['type']=='reads' and assembly['inputs']['reassembly']</filter>
        </data>
    </outputs>
    <tests>
        <!-- test w contigs and reads as input -->
        <test expect_num_outputs="4">
            <param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" />
            <conditional name="assembly">
                <param name="type" value="individual"/>
                <conditional name="inputs">
                    <param name="type" value="reads"/>
                    <param name="reads" value="interleavedPE_unmapped_Sample3_small.fasta" ftype="fasta"/>
                    <param name="output_abundances" value="false"/>
                    <param name="reassembly" value=""/>
                </conditional>
            </conditional>
            <section name="adv">
                <param name="min_contig_length" value="1000"/>
                <param name="max_iteration" value="50"/>
                <param name="prob_threshold" value="0.5"/>
            </section>
            <section name="output">
                <param name="plotmarker" value=""/>
                <param name="marker" value="false"/>
                <param name="markers" value="false" />
                <param name="log" value="false"/>
                <param name="markerset" value="107"/>
            </section>
            <output_collection name="bins" type="list" count="2">
                <element name="001" file="1/out.001.fasta" ftype="fasta"/>
                <element name="002" file="1/out.002.fasta" ftype="fasta"/>
            </output_collection>
            <output name="summary" file="1/out.summary" ftype="tabular" />
            <output name="noclass" file="1/out.noclass" ftype="fasta" />
            <output name="toshort" file="1/out.tooshort" ftype="fasta" />
        </test>
        <!-- test w co-assembled contigs and multiple reads and optional outputs -->
        <test expect_num_outputs="9">
            <param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" />
            <conditional name="assembly">
                <param name="type" value="coassembly"/>
                <conditional name="inputs">
                    <param name="type" value="reads"/>
                    <param name="reads" value="interleavedPE_unmapped_Sample3_small.fasta,interleavedPE_unmapped_Sample3_small.fasta" ftype="fasta"/>
                    <param name="output_abundances" value="true"/>
                    <param name="reassembly" value=""/>
                </conditional>
            </conditional>
            <section name="adv">
                <param name="min_contig_length" value="1000"/>
                <param name="max_iteration" value="50"/>
                <param name="prob_threshold" value="0.5"/>
            </section>
            <section name="output">
                <param name="plotmarker" value="true"/>
                <param name="marker" value="true"/>
                <param name="markers" value="true" />
                <param name="log" value="true"/>
                <param name="markerset" value="107"/>
            </section>
            <output_collection name="bins" type="list" count="2">
                <element name="001" file="1/out.001.fasta" ftype="fasta"/>
                <element name="002" file="1/out.002.fasta" ftype="fasta"/>
            </output_collection>
            <output name="summary" ftype="tabular">
                <assert_contents>
                    <has_text text="Completeness"/>
                    <has_text text="out.001.fasta"/>
                </assert_contents>
            </output>
            <output name="noclass" file="1/out.noclass" ftype="fasta" />
            <output name="toshort" file="1/out.tooshort" ftype="fasta" />
            <output name="log" ftype="txt" >
                <assert_contents>
                    <has_text text="Input contig"/>
                    <has_text text="Elapsed time"/>
                    <has_text text="Yielded 2 bins for contig (scaffold) file"/>
                </assert_contents>
            </output>
            <output name="abundout" file="1/out.abund1" ftype="tabular" />
            <output name="marker" file="1/out.marker" ftype="tabular" />
            <output name="plot" file="1/out.marker.pdf" ftype="pdf" compare="sim_size" />
            <output_collection name="markers" type="list" count="1">
                <element name="001" file="1/out.001.marker.fasta" ftype="fasta"/>
            </output_collection>
        </test>
        <!--test w contigs and abundances as input + advanced options -->
        <test expect_num_outputs="5">
            <param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" />
            <conditional name="assembly">
                <param name="type" value="individual"/>
                <conditional name="inputs">
                    <param name="type" value="abund"/>
                    <param name="abund" value="abundances.tsv" ftype="tabular"/>
                </conditional>
            </conditional>
            <section name="adv">
                <param name="min_contig_length" value="500"/>
                <param name="max_iteration" value="10"/>
                <param name="prob_threshold" value="0.95"/>
            </section>
            <section name="output">
                <param name="plotmarker" value="-plotmarker"/>
                <param name="marker" value="false"/>
                <param name="markers" value="false" />
                <param name="log" value="false"/>
                <param name="markerset" value="107"/>
            </section>
            <output_collection name="bins" type="list" count="2">
                <element name="001" file="2/out.001.fasta" ftype="fasta"/>
                <element name="002" file="2/out.002.fasta" ftype="fasta"/>
            </output_collection>
            <output name="summary" file="2/out.summary" ftype="tabular" />

            <output name="plot" file="2/out.marker.pdf" ftype="pdf" compare="sim_size" />
        </test>
        <!-- test w contigs and reads as input + reassembly-->
        <test expect_num_outputs="8">
            <param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" />
            <conditional name="assembly">
                <param name="type" value="individual"/>
                <conditional name="inputs">
                    <param name="type" value="reads"/>
                    <param name="reads" value="interleavedPE_unmapped_Sample3_small.fasta" ftype="fasta"/>
                    <param name="output_abundances" value="false"/>
                    <param name="reassembly" value="-reassembly"/>
                </conditional>
            </conditional>
            <section name="adv">
                <param name="min_contig_length" value="1000"/>
                <param name="max_iteration" value="50"/>
                <param name="prob_threshold" value="0.5"/>
            </section>
            <section name="output">
                <param name="plotmarker" value=""/>
                <param name="marker" value="false"/>
                <param name="markers" value="false" />
                <param name="log" value="false"/>
                <param name="markerset" value="107"/>
            </section>
            <output_collection name="bins" type="list" count="2">
                <element name="001" file="3/out.001.fasta" ftype="fasta"/>
                <element name="002" file="3/out.002.fasta" ftype="fasta"/>
            </output_collection>
            <output name="summary" file="3/out.summary" ftype="tabular" />
            <output name="noclass" file="3/out.noclass" ftype="fasta" />
            <output name="toshort" file="3/out.tooshort" ftype="fasta" />
            <output_collection name="reassembly_bins" type="list" count="2">
                <element name="001" ftype="fasta">
                    <assert_contents>
                        <has_text text=">scaffold_0"/>
                        <has_text text=">scaffold_523"/>
                    </assert_contents>
                </element>
                <element name="002" ftype="fasta">
                    <assert_contents>
                        <has_text text=">scaffold_0"/>
                        <has_text text=">scaffold_523"/>
                    </assert_contents>
                </element>
            </output_collection>
            <output_collection name="reassembly_reads" type="list" count="2">
                <element name="001" file="3/out.reassem/out.reads.001" ftype="fasta"/>
                <element name="002" file="3/out.reassem/out.reads.002" ftype="fasta"/>
            </output_collection>
            <output name="reassembly_noclass" file="3/out.reassem/out.reads.noclass" ftype="fasta" />
            <output name="reassembly_n50" ftype="txt">
                <assert_contents>
                    <has_text text="N50 before reassem"/>
                    <has_text text="out.002.fasta"/>
                    <has_text text="2878"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
MaxBin is a software that clusters metagenomic contigs into different bins,
each consists (hopefully) of contigs from one species. MaxBin uses the