comparison cuffdiff_wrapper.xml @ 8:88fcac97c2a0 draft

Uploaded updated cuffdiff.

7:8da0eade1f59

<tool id="cuffdiff" name="Cuffdiff" version="@VERSION@.0">
    <description>find significant changes in transcript expression, splicing, and promoter use</description>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <macros>
      <import>cuff_macros.xml</import>
    </macros>
    <version_command>cuffdiff 2>&amp;1 | head -n 1</version_command>
    <command>
        cuffdiff
            --no-update-check
            --FDR=$fdr
            --num-threads="\${GALAXY_SLOTS:-4}"
            --min-alignment-count=$min_alignment_count

            #end if
            ## Inputs.
            $gtf_input

            @CONDITION_SAMPLES@
    </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."/>
        <expand macro="condition_inputs" />
        <param name="library_norm_method" type="select" label="Library normalization method">

                <param name="min_reps_for_js_test" type="integer" value="3" label="Minimal Replicates for isoform shift testing" help="Cuffdiff won't test genes for differential regulation unless the conditions in question have at least this many replicates. Default: 3." />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <!-- Optional read group datasets. -->
        <data format="tabular" name="isoforms_read_group" label="${tool.name} on ${on_string}: isoforms read group tracking" from_work_dir="isoforms.read_group_tracking" >
            <filter>(include_read_group_files == 'Yes')</filter>
        </data>
        <data format="tabular" name="genes_read_group" label="${tool.name} on ${on_string}: genes read group tracking" from_work_dir="genes.read_group_tracking" >
            <filter>(include_read_group_files == 'Yes')</filter>
        </data>
        <data format="tabular" name="cds_read_group" label="${tool.name} on ${on_string}: CDs read group tracking" from_work_dir="cds.read_group_tracking" >
            <filter>(include_read_group_files == 'Yes')</filter>
        </data>
        <data format="tabular" name="tss_groups_read_group" label="${tool.name} on ${on_string}: TSS groups read group tracking" from_work_dir="tss_groups.read_group_tracking" >
            <filter>(include_read_group_files == 'Yes')</filter>
        </data>
        <data format="text" name="read_group_info" label="${tool.name} on ${on_string}: read group info" from_work_dir="read_groups.info" >
            <filter>(include_read_group_files == 'Yes')</filter>
        </data>
        <data format="text" name="run_info" label="${tool.name} on ${on_string}: run info" from_work_dir="run.info" >
            <filter>(include_read_group_files == 'Yes')</filter>
        </data>
        <!-- Standard datasets. -->
        <data format="tabular" name="splicing_diff" label="${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 ${on_string}: CDS FPKM tracking" from_work_dir="cds.fpkm_tracking" />
        <data format="tabular" name="cds_count_tracking" label="${tool.name} on ${on_string}: CDS count tracking" from_work_dir="cds.count_tracking" >
                <filter>(include_count_files == 'Yes')</filter>
        </data>

        <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 ${on_string}: TSS groups FPKM tracking" from_work_dir="tss_groups.fpkm_tracking" />
        <data format="tabular" name="tss_groups_count_tracking" label="${tool.name} on ${on_string}: TSS count FPKM tracking" from_work_dir="tss_groups.count_tracking" >
                <filter>(include_count_files == 'Yes')</filter>
        </data>

        <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 ${on_string}: gene FPKM tracking" from_work_dir="genes.fpkm_tracking" />
        <data format="tabular" name="genes_count_tracking" label="${tool.name} on ${on_string}: gene count tracking" from_work_dir="genes.count_tracking" >
                <filter>(include_count_files == 'Yes')</filter>
        </data>

        <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 ${on_string}: transcript FPKM tracking" from_work_dir="isoforms.fpkm_tracking" />
        <data format="tabular" name="isoforms_count_tracking" label="${tool.name} on ${on_string}: transcript count tracking" from_work_dir="isoforms.count_tracking" >
                <filter>(include_count_files == 'Yes')</filter>
        </data>
    </outputs>

    <tests>
        <test>
                <!--

                <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_exp" file="cuffdiff_out3.txt" lines_diff="200"/>
                <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**

8:88fcac97c2a0

<tool id="cuffdiff" name="Cuffdiff" version="@VERSION@.1">
    <description>find significant changes in transcript expression, splicing, and promoter use</description>
    <requirements>
        <requirement type="set_environment">CUFFDIFF_SCRIPT_PATH</requirement>
        <requirement type="package" version="2.2.1">cufflinks</requirement>
        <requirement type="package" version="2.8.2">cummeRbund</requirement>
    </requirements>
    <expand macro="stdio" />
    <macros>
      <import>cuff_macros.xml</import>
    </macros>
    <version_command>cuffdiff 2>&amp;1 | head -n 1</version_command>
    <command><![CDATA[
        cuffdiff
            --no-update-check
            --FDR=$fdr
            --num-threads="\${GALAXY_SLOTS:-4}"
            --min-alignment-count=$min_alignment_count

            #end if
            ## Inputs.
            $gtf_input

            @CONDITION_SAMPLES@
            &&
            R --vanilla --no-save -f \$CUFFDIFF_SCRIPT_PATH/cummeRbund.R && mv cummeRbund.sqlite "${output_cummerbund}"
            ]]>
    </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."/>
        <expand macro="condition_inputs" />
        <param name="library_norm_method" type="select" label="Library normalization method">

                <param name="min_reps_for_js_test" type="integer" value="3" label="Minimal Replicates for isoform shift testing" help="Cuffdiff won't test genes for differential regulation unless the conditions in question have at least this many replicates. Default: 3." />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="sqlite" name="output_cummerbund" label="${tool.name} on ${on_string}: cummeRbund SQLite database" />
    </outputs>

    <tests>
        <test>
                <!--

                <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="output_cummerbund" ftype="sqlite" file="cuffdiff_out.sqlite"/>
        </test>
    </tests>
    <help>
**Cuffdiff Overview**