comparison cuffdiff_wrapper.xml @ 2:fdf01b3c1841

Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output

1:ebb9a992508d

<tool id="cuffdiff_cummerbund" name="Cuffdiff" version="0.0.6">
    <!-- Wrapper supports Cuffdiff versions v1.3.0-v2.0 -->
    <description>find significant changes in transcript expression, splicing, and promoter use</description>
    <requirements>
        <requirement type="package">cufflinks</requirement>
    </requirements>
    <command interpreter="python">
        #set sel_outputs = $output_sel.__str__.split(',')
        cuffdiff_wrapper.py
            --FDR=$fdr
            --num-threads="4"
            --min-alignment-count=$min_alignment_count

            #if 'cuffdata' in $sel_outputs or not $output_sel:
                --cuffdatadir=$cuffdata.extra_files_path
            #end if
            #if 'cummeRbund_db' in $sel_outputs:
                --cummeRbund_db=$cummeRbund_db
            #end if

            #if 'isoforms_fpkm_tracking' in $sel_outputs:
                --isoforms_fpkm_tracking_output=$isoforms_fpkm_tracking
            #end if
            #if 'genes_fpkm_tracking' in $sel_outputs:
                --genes_fpkm_tracking_output=$genes_fpkm_tracking
            #end if
            #if 'cds_fpkm_tracking' in $sel_outputs:
                --cds_fpkm_tracking_output=$cds_fpkm_tracking
            #end if
            #if 'tss_groups_fpkm_tracking' in $sel_outputs:
                --tss_groups_fpkm_tracking_output=$tss_groups_fpkm_tracking
            #end if
            #if 'isoforms_exp_diff' in $sel_outputs:
                --isoforms_exp_output=$isoforms_exp_diff
            #end if
            #if 'genes_exp_diff' in $sel_outputs:
                --genes_exp_output=$genes_exp_diff
            #end if
            #if 'tss_groups_exp_diff' in $sel_outputs:
                --tss_groups_exp_output=$tss_groups_exp_diff
            #end if
            #if 'cds_exp_fpkm_tracking' in $sel_outputs:
                --cds_exp_fpkm_tracking_output=$cds_exp_fpkm_tracking
            #end if
            #if 'splicing_diff' in $sel_outputs:
                --splicing_diff_output=$splicing_diff
            #end if
            #if 'cds_diff' in $sel_outputs:
                --cds_diff_output=$cds_diff
            #end if
            #if 'promoters_diff' in $sel_outputs:
                --promoters_diff_output=$promoters_diff
            #end if
            #if 'cds_read_group_tracking' in $sel_outputs:
                --cds_read_group_tracking=$cds_read_group_tracking
            #end if
            #if 'tss_groups_read_group_tracking' in $sel_outputs:
                --tss_groups_read_group_tracking=$tss_groups_read_group_tracking
            #end if
            #if 'genes_read_group_tracking' in $sel_outputs:
                --genes_read_group_tracking=$genes_read_group_tracking
            #end if
            #if 'isoforms_read_group_tracking' in $sel_outputs:
                --isoforms_read_group_tracking=$isoforms_read_group_tracking
            #end if
            
            ## Set advanced data parameters?
            #if $additional.sAdditional == "Yes":
                -m $additional.frag_mean_len
                -s $additional.frag_len_std_dev
            #end if

            ## Normalization?
            #if str($do_normalization) == "Yes":
            -N
            #end if

            ## Multi-read correct?
            #if str($multiread_correct) == "Yes":
            -u
            #end if

            ## Bias correction?
            #if $bias_correction.do_bias_correction == "Yes":
	        -b
                #if $bias_correction.seq_source.index_source == "history":
                    --ref_file=$bias_correction.seq_source.ref_file
                #else:
                    --ref_file="None"
                #end if
                --dbkey=${gtf_input.metadata.dbkey}
                --index_dir=${GALAXY_DATA_INDEX_DIR}
            #end if
                
            ## Inputs.
            --inputA=$gtf_input
            #if $group_analysis.do_groups == "No":
                --input1=$aligned_reads1
                --input2=$aligned_reads2
            #else:
                ## Replicates.
                --labels
                #for $group in $group_analysis.groups
                    ${group.group}
                #end for
                --files
                #for $group in $group_analysis.groups
                    #for $file in $group.files:
                        ${file.file}
                    #end for
                    ,
                #end for
            #end if

    </command>
    <inputs>
        <param format="gtf,gff3" name="gtf_input" type="data" label="Transcripts" help="A transcript GFF3 or GTF file produced by cufflinks, cuffcompare, or other source."/>
        <conditional name="group_analysis"> 
            <param name="do_groups" type="select" label="Perform replicate analysis" help="Perform cuffdiff with replicates in each group.">
                <option value="No">No</option>
                <option value="Yes">Yes</option>
            </param>
            <when value="Yes">
                <repeat name="groups" title="Group">
                    <param name="group" title="Group name" type="text" label="Group name (no spaces or commas)"/>
                    <repeat name="files" title="Replicate">
                        <param name="file" label="Add file" type="data" format="sam,bam"/>
                    </repeat>
                </repeat>
            </when>
            <when value="No">
                <param format="sam,bam" name="aligned_reads1" type="data" label="SAM or BAM file of aligned RNA-Seq reads" help=""/>
                <param format="sam,bam" name="aligned_reads2" type="data" label="SAM or BAM file of aligned RNA-Seq reads" help=""/>
            </when>
        </conditional>

        <param name="fdr" type="float" value="0.05" label="False Discovery Rate" help="The allowed false discovery rate."/>

        <param name="min_alignment_count" type="integer" value="10" label="Min Alignment Count" help="The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples."/>

        <param name="do_normalization" type="select" label="Perform quartile normalization" help="Removes top 25% of genes from FPKM denominator to improve accuracy of differential expression calls for low abundance transcripts.">
            <option value="No">No</option>
            <option value="Yes">Yes</option>
        </param>

        <param name="multiread_correct" type="select" label="Use multi-read correct" help="Tells Cufflinks to do an initial estimation procedure to more accurately weight reads mapping to multiple locations in the genome.">
            <option value="No" selected="true">No</option>
            <option value="Yes">Yes</option>
        </param>

                </conditional>
            </when>
            <when value="No"></when>
        </conditional>

        <conditional name="additional">
            <param name="sAdditional" type="select" label="Set Additional Parameters? (not recommended)">
                <option value="No">No</option>
                <option value="Yes">Yes</option>
            </param>
            <when value="No"></when>
            <when value="Yes">
                <param name="frag_mean_len" type="integer" value="200" label="Average Fragment Length"/>
                <param name="frag_len_std_dev" type="integer" value="80" label="Fragment Length Standard Deviation"/>
            </when>
        </conditional>

        <param name="output_sel" type="select" multiple="true" display="checkboxes" force_select="true" label="Select outputs for history datasets">
            <option value="cuffdata">cuffdata - html page with links to cuffdiff outputs</option>
            <option value="cummeRbund_db">cummeRbund database</option>
            <option value="run_info">run.info</option>
            <option value="read_groups_info">read_groups.info</option>
            <option value="splicing_diff">splicing.diff</option>
            <option value="promoters_diff">promoters.diff</option>
            <option value="genes_exp_diff">genes_exp.diff</option>
            <option value="genes_fpkm_tracking">genes.fpkm_tracking</option>
            <option value="genes_count_tracking">genes.count_tracking</option>
            <option value="genes_read_group_tracking">genes.read_group_tracking</option>
            <option value="isoforms_exp_diff">isoforms.exp_diff</option>
            <option value="isoforms_fpkm_tracking">isoforms.fpkm_tracking</option>
            <option value="isoforms_count_tracking">isoforms.count_tracking</option>
            <option value="isoforms_read_group_tracking">isoforms.read_group_tracking</option>
            <option value="cds_diff">cds.diff</option>
            <option value="cds_exp_diff">cds_exp.diff</option>
            <option value="cds_fpkm_tracking">cds.fpkm_tracking</option>
            <option value="cds_count_tracking">cds.count_tracking</option>
            <option value="cds_read_group_tracking">cds.read_group_tracking</option>
            <option value="tss_groups_exp_diff">tss_groups_exp.diff</option>
            <option value="tss_groups_fpkm_tracking">tss_groups.fpkm_tracking</option>
            <option value="tss_groups_count_tracking">tss_groups.count_tracking</option>
            <option value="tss_groups_read_group_tracking">tss_groups.read_group_tracking</option>
        </param>
        
    </inputs>

    <outputs>
        <data format="text" name="run_info" label="${tool.name} on ${on_string}: run.info">
            <filter>output_sel and 'run_info' in output_sel</filter>
        </data>
        <data format="tabular" name="read_groups_info" label="${tool.name} on ${on_string}: read_groups.info">
            <filter>output_sel and 'read_groups_info' in output_sel</filter>
        </data>
        <data format="tabular" name="splicing_diff" label="${tool.name} on ${on_string}: splicing differential expression testing">
            <filter>output_sel and 'splicing_diff' in output_sel</filter>
        </data>
        <data format="tabular" name="promoters_diff" label="${tool.name} on ${on_string}: promoters differential expression testing">
            <filter>output_sel and 'promoters_diff' in output_sel</filter>
        </data>
        <data format="tabular" name="cds_diff" label="${tool.name} on ${on_string}: CDS overloading diffential expression testing">
            <filter>output_sel and 'cds_diff' in output_sel</filter>
        </data>
        <data format="tabular" name="cds_exp_diff" label="${tool.name} on ${on_string}: CDS differential expression testing">
            <filter>output_sel and 'cds_exp_diff' in output_sel</filter>
        </data>
        <data format="tabular" name="cds_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM tracking">
            <filter>output_sel and 'cds_fpkm_tracking' in output_sel</filter>
        </data>
        <data format="tabular" name="cds_count_tracking" label="${tool.name} on ${on_string}: CDS counts">
            <filter>output_sel and 'cds_count_tracking' in output_sel</filter>
        </data>
        <data format="tabular" name="cds_read_group_tracking" label="${tool.name} on ${on_string}: CDS Read Group tracking">
            <filter>output_sel and 'cds_read_group_tracking' in output_sel</filter>
        </data>
        <data format="tabular" name="tss_groups_exp_diff" label="${tool.name} on ${on_string}: TSS groups differential expression testing">
            <filter>output_sel and 'tss_groups_exp_diff' in output_sel</filter>
        </data>
        <data format="tabular" name="tss_groups_fpkm_tracking" label="${tool.name} on ${on_string}: TSS groups FPKM tracking">
            <filter>output_sel and 'tss_groups_fpkm_tracking' in output_sel</filter>
        </data>
        <data format="tabular" name="tss_groups_count_tracking" label="${tool.name} on ${on_string}: TSS groups counts">
            <filter>output_sel and 'tss_groups_count_tracking' in output_sel</filter>
        </data>
        <data format="tabular" name="tss_groups_read_group_tracking" label="${tool.name} on ${on_string}: TSS groups Read Group tracking">
            <filter>output_sel and 'tss_groups_read_group_tracking' in output_sel</filter>
        </data>
        <data format="tabular" name="isoforms_exp_diff" label="${tool.name} on ${on_string}: transcript differential expression testing">
            <filter>output_sel and 'isoforms_exp_diff' in output_sel</filter>
        </data>
        <data format="tabular" name="isoforms_fpkm_tracking" label="${tool.name} on ${on_string}: transcript FPKM tracking">
            <filter>output_sel and 'isoforms_fpkm_tracking' in output_sel</filter>
        </data>
        <data format="tabular" name="isoforms_count_tracking" label="${tool.name} on ${on_string}: transcript counts">
            <filter>output_sel and 'isoforms_count_tracking' in output_sel</filter>
        </data>
        <data format="tabular" name="isoforms_read_group_tracking" label="${tool.name} on ${on_string}: transcript Read Group tracking">
            <filter>output_sel and 'isoforms_read_group_tracking' in output_sel</filter>
        </data>
        <data format="tabular" name="genes_exp_diff" label="${tool.name} on ${on_string}: gene differential expression testing">
            <filter>output_sel and 'genes_exp_diff' in output_sel</filter>
        </data>
        <data format="tabular" name="genes_fpkm_tracking" label="${tool.name} on ${on_string}: gene FPKM tracking">
            <filter>output_sel and 'genes_fpkm_tracking' in output_sel</filter>
        </data>
        <data format="tabular" name="genes_count_tracking" label="${tool.name} on ${on_string}: gene counts">
            <filter>output_sel and 'genes_count_tracking' in output_sel</filter>
        </data>
        <data format="tabular" name="genes_read_group_tracking" label="${tool.name} on ${on_string}: gene Read Group tracking">
            <filter>output_sel and 'genes_read_group_tracking' in output_sel</filter>
        </data>
        <data format="cuffdata" name="cuffdata" label="${tool.name} on ${on_string}: cuffdata" >
            <filter>not output_sel or output_sel and 'cuffdata' in output_sel</filter>
        </data>
        <data format="cuffdatadb" name="cummeRbund_db" label="${tool.name} on ${on_string}: cummeRbund sqlite Database" >
            <filter>output_sel and 'cummeRbund_db' in output_sel</filter>
        </data>
    </outputs>
    <stdio>
        <exit_code range="1:"  level="fatal"   description="Cufflinks Err" />
    </stdio>


    <tests>
        <test>
                <!--
                    cuffdiff cuffcompare_out5.gtf cuffdiff_in1.sam cuffdiff_in2.sam 
                -->
                <param name="gtf_input" value="cuffcompare_out5.gtf" ftype="gtf" />
                <param name="do_groups" value="No" />
                <param name="aligned_reads1" value="cuffdiff_in1.sam" ftype="sam" />
                <param name="aligned_reads2" value="cuffdiff_in2.sam" ftype="sam" />
                <!-- Defaults. -->
                <param name="fdr" value="0.05" />
                <param name="min_alignment_count" value="0" />
                <param name="do_bias_correction" value="No" />
                <param name="do_normalization" value="No" />
                <param name="multiread_correct" value="No"/>
                <param name="sAdditional" value="No"/>
                <!-- 
                    Line diffs are needed because cuffdiff does not produce deterministic output.
                    TODO: can we find datasets that lead to deterministic behavior?
                -->
                <output name="splicing_diff" file="cuffdiff_out9.txt"/>
                <output name="promoters_diff" file="cuffdiff_out10.txt"/>
                <output name="cds_diff" file="cuffdiff_out11.txt"/>
                <output name="cds_exp_fpkm_tracking" file="cuffdiff_out4.txt"/>
                <output name="cds_fpkm_tracking" file="cuffdiff_out8.txt"/>

                <output name="tss_groups_fpkm_tracking" file="cuffdiff_out7.txt"/>
                <output name="genes_exp" file="cuffdiff_out2.txt" lines_diff="200"/>
                <output name="genes_fpkm_tracking" file="cuffdiff_out6.txt" lines_diff="200"/>
                <output name="isoforms_exp" file="cuffdiff_out1.txt" lines_diff="200"/>
                <output name="isoforms_fpkm_tracking" file="cuffdiff_out5.txt" lines_diff="200"/>
        </test>
    </tests>

    <help>
**Cuffdiff Overview**

2:fdf01b3c1841

<tool id="cuffdiff_cummerbund" name="Cuffdiff for cummeRbund" version="0.0.7">
    <!-- Wrapper supports Cuffdiff versions 2.1.0-2.1.1 -->
    <description>find significant changes in transcript expression, splicing, and promoter use</description>
    <requirements>
        <requirement type="package" version="2.1.1">cufflinks</requirement>
    </requirements>
    <version_command>cuffdiff 2>&amp;1 | head -n 1</version_command>
    <command>
        cuffdiff
            --no-update-check
            --FDR=$fdr
            --num-threads="4"
            --min-alignment-count=$min_alignment_count
            --library-norm-method=$library_norm_method
            --dispersion-method=$dispersion_method

            ## Set advanced data parameters?
            #if $additional.sAdditional == "Yes":
                #if $additional.frag_mean_len:
                    -m $additional.frag_mean_len
                #end if
                #if $additional.frag_len_std_dev:
                    -s $additional.frag_len_std_dev
                #end if
                #if $additional.max_bundle_frags:
                    --max-bundle-frags="$additional.max_bundle_frags"
                #end if
            #end if

            ## Multi-read correct?
            #if str($multiread_correct) == "Yes":
            -u
            #end if

            ## Bias correction?
            #if $bias_correction.do_bias_correction == "Yes":
               -b
                #if $bias_correction.seq_source.index_source == "history":
                    ## Custom genome from history.
                    $bias_correction.seq_source.ref_file
                #else:
                    ## Built-in genome.
                    ${__get_data_table_entry__('sam_fa_indexes', 'value', $gtf_input.dbkey, 'path')}
                #end if
            #end if

            #set labels = '\'' + '\',\''.join( [ str( $condition.name ) for $condition in $conditions ] ) + '\''
            --labels $labels

            ## Inputs.
            $gtf_input
            #for $condition in $conditions:
                #set samples = ','.join( [ str( $sample.sample ) for $sample in $condition.samples ] )
                $samples
            #end for
 
            ## If build cummerbund db
            #if $build_cummerbund_db:
                &amp;&amp; echo 'library(cummeRbund)' > cuffData.r 
                #if $bias_correction.do_bias_correction == "Yes":
                    #if $bias_correction.seq_source.index_source == "history":
                        ## Custom genome from history.
                        &amp;&amp; echo 'cuff&lt;-readCufflinks( dbFile = "cuffdata.db", gtfFile = "$gtf_input", genome = "$bias_correction.seq_source.ref_file", rebuild = T)' >> cuffData.r
                    #else:
                        ## Built-in genome.
                        ${__get_data_table_entry__('sam_fa_indexes', 'value', $gtf_input.dbkey, 'path')}
                        &amp;&amp; echo 'cuff&lt;-readCufflinks( dbFile = "cuffdata.db", gtfFile = "$gtf_input", genome = "${__get_data_table_entry__('sam_fa_indexes', 'value', $gtf_input.dbkey, 'path')}", rebuild = T)' >> cuffData.r
                    #end if
                #else 
                    &amp;&amp; echo 'cuff&lt;-readCufflinks( dbFile = "cuffdata.db", rebuild = T)' >> cuffData.r
                #end if
                &amp;&amp; Rscript --vanilla cuffData.r
                &amp;&amp; cp cuffdata.db $cummerbund_db
            #end if
    </command>
    <inputs>
        <param format="gtf,gff3" name="gtf_input" type="data" label="Transcripts" help="A transcript GFF3 or GTF file produced by cufflinks, cuffcompare, or other source."/>

        <repeat name="conditions" title="Condition" min="2">
            <param name="name" title="Condition name" type="text" label="Name"/>
            <repeat name="samples" title="Replicate" min="1">
                <param name="sample" label="Add replicate" type="data" format="sam,bam"/>
            </repeat>
        </repeat>
        <param name="time_series" type="boolean" checked="false" truevalue="--time-series" falsevalue="" optional="true" label="treat samples as a time-series">
            <help>
            Instructs Cuffdiff to analyze the provided samples as a time series, rather than testing for differences between all pairs of samples. 
            Samples should be provided in increasing time order at the command line (e.g first time point SAM, second timepoint SAM, etc.)
            </help>
        </param>

        <param name="library_norm_method" type="select" label="Library normalization method">
            <option value="geometric" selected="True">geometric</option>
            <option value="classic-fpkm">classic-fpkm</option>
            <option value="quartile">quartile</option>
        </param>

        <param name="dispersion_method" type="select" label="Dispersion estimation method" help="If using only one sample per condition, you must use 'blind.'">
            <option value="pooled" selected="True">pooled</option>
            <option value="per-condition">per-condition</option>
            <option value="blind">blind</option>
        </param>

        <param name="fdr" type="float" value="0.05" label="False Discovery Rate" help="The allowed false discovery rate."/>

        <param name="min_alignment_count" type="integer" value="10" label="Min Alignment Count" help="The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples."/>

        <param name="multiread_correct" type="select" label="Use multi-read correct" help="Tells Cufflinks to do an initial estimation procedure to more accurately weight reads mapping to multiple locations in the genome.">
            <option value="No" selected="true">No</option>
            <option value="Yes">Yes</option>
        </param>

                </conditional>
            </when>
            <when value="No"></when>
        </conditional>

        <param name="include_read_group_files" type="select" label="Include Read Group Datasets" help="Read group datasets provide information on replicates.">
            <option value="No" selected="true">No</option>
            <option value="Yes">Yes</option>
        </param>
        <param name="build_cummerbund_db" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Build cummeRbund database"/>
        <conditional name="additional">
            <param name="sAdditional" type="select" label="Set Additional Parameters? (not recommended for paired-end reads)">
                <option value="No">No</option>
                <option value="Yes">Yes</option>
            </param>
            <when value="No"></when>
            <when value="Yes">
                <param name="frag_mean_len" type="integer" value="" optional="true" label="Average Fragment Length Default: 200">
                    <help>
                    Note: Cufflinks now learns the fragment length mean for each SAM file, 
                    so using this option is no longer recommended with paired-end reads.
                    </help>
                </param>
                <param name="frag_len_std_dev" type="integer" value="" optional="true" label="Fragment Length Standard Deviation Default: 80">
                    <help>
                    Note: Cufflinks now learns the fragment length mean for each SAM file, 
                    so using this option is no longer recommended with paired-end reads.
                    </help>
                </param>
                <param name="max_bundle_frags" type="integer" value="" optional="true" label="--max-bundle-frags">
                    <help>
                    Sets the maximum number of fragments a locus may have before being skipped. Skipped loci are listed in skipped.gtf. Default: 1000000
                    </help>
                    <validator type="in_range" message="Value greater than 0" min="1"/>
                </param>
            </when>
        </conditional>
    </inputs>

    <stdio>
        <regex match="Error" source="both" level="fatal" description="Error"/>
        <regex match=".*" source="both" level="log" description="tool progress"/>
    </stdio>

    <outputs>
        <!-- Optional read group datasets. -->
        <data format="cuffdatadb" name="cummerbund_db" label="${tool.name} on ${on_string}: cummeRbund sqlite Database" >
            <filter>build_cummerbund_db</filter>
        </data>
        <data format="tabular" name="isoforms_read_group" label="${tool.name} on ${on_string}: isoforms read group tracking" from_work_dir="isoforms.read_group_tracking" >
            <filter>(params['include_read_group_files'] == 'Yes'</filter>
        </data>
        <data format="tabular" name="genes_read_group" label="${tool.name} on ${on_string}: genes read group tracking" from_work_dir="genes.read_group_tracking" >
            <filter>(params['include_read_group_files'] == 'Yes'</filter>
        </data>
        <data format="tabular" name="cds_read_group" label="${tool.name} on ${on_string}: CDs read group tracking" from_work_dir="cds.read_group_tracking" >
            <filter>(params['include_read_group_files'] == 'Yes'</filter>
        </data>
        <data format="tabular" name="tss_groups_read_group" label="${tool.name} on ${on_string}: TSS groups read group tracking" from_work_dir="tss_groups.read_group_tracking" >
            <filter>(params['include_read_group_files'] == 'Yes'</filter>
        </data>

        <!-- Standard datasets. -->
        <data format="tabular" name="splicing_diff" label="${tool.name} on ${on_string}: splicing differential expression testing" from_work_dir="splicing.diff" />
        <data format="tabular" name="promoters_diff" label="${tool.name} on ${on_string}: promoters differential expression testing" from_work_dir="promoters.diff" />
        <data format="tabular" name="cds_diff" label="${tool.name} on ${on_string}: CDS overloading diffential expression testing" from_work_dir="cds.diff" />
        <data format="tabular" name="cds_exp_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM differential expression testing" from_work_dir="cds_exp.diff" />
        <data format="tabular" name="cds_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM tracking" from_work_dir="cds.fpkm_tracking" />
        <data format="tabular" name="tss_groups_exp" label="${tool.name} on ${on_string}: TSS groups differential expression testing" from_work_dir="tss_group_exp.diff" />
        <data format="tabular" name="tss_groups_fpkm_tracking" label="${tool.name} on ${on_string}: TSS groups FPKM tracking" from_work_dir="tss_groups.fpkm_tracking" />
        <data format="tabular" name="genes_exp" label="${tool.name} on ${on_string}: gene differential expression testing" from_work_dir="gene_exp.diff" />
        <data format="tabular" name="genes_fpkm_tracking" label="${tool.name} on ${on_string}: gene FPKM tracking" from_work_dir="genes.fpkm_tracking" />
        <data format="tabular" name="isoforms_exp" label="${tool.name} on ${on_string}: transcript differential expression testing" from_work_dir="isoform_exp.diff" />
        <data format="tabular" name="isoforms_fpkm_tracking" label="${tool.name} on ${on_string}: transcript FPKM tracking" from_work_dir="isoforms.fpkm_tracking" />
    </outputs>

    <tests>
        <test>
                <!--
                    cuffdiff cuffcompare_out5.gtf cuffdiff_in1.sam cuffdiff_in2.sam 
                -->
                <!-- 
                    NOTE: as of version 0.0.6 of the wrapper, tests cannot be run because multiple inputs to a repeat
                    element are not supported.
                <param name="gtf_input" value="cuffcompare_out5.gtf" ftype="gtf" />
                <param name="do_groups" value="No" />
                <param name="aligned_reads1" value="cuffdiff_in1.sam" ftype="sam" />
                <param name="aligned_reads2" value="cuffdiff_in2.sam" ftype="sam" />
                <param name="fdr" value="0.05" />
                <param name="min_alignment_count" value="0" />
                <param name="do_bias_correction" value="No" />
                <param name="do_normalization" value="No" />
                <param name="multiread_correct" value="No"/>
                <param name="sAdditional" value="No"/>
                <output name="splicing_diff" file="cuffdiff_out9.txt"/>
                <output name="promoters_diff" file="cuffdiff_out10.txt"/>
                <output name="cds_diff" file="cuffdiff_out11.txt"/>
                <output name="cds_exp_fpkm_tracking" file="cuffdiff_out4.txt"/>
                <output name="cds_fpkm_tracking" file="cuffdiff_out8.txt"/>

                <output name="tss_groups_fpkm_tracking" file="cuffdiff_out7.txt"/>
                <output name="genes_exp" file="cuffdiff_out2.txt" lines_diff="200"/>
                <output name="genes_fpkm_tracking" file="cuffdiff_out6.txt" lines_diff="200"/>
                <output name="isoforms_exp" file="cuffdiff_out1.txt" lines_diff="200"/>
                <output name="isoforms_fpkm_tracking" file="cuffdiff_out5.txt" lines_diff="200"/>
                -->
        </test>
    </tests>

    <help>
**Cuffdiff Overview**