comparison cuffnorm_wrapper.xml @ 4:6cbfede05833 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnorm commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"

3:f5b2ee725d34

    <description>Create normalized expression levels</description>
    <macros>
      <import>cuff_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <version_command>cuffnorm 2>&amp;1 | head -n 1</version_command>
    <command detect_errors="aggressive">
        cuffnorm
            --no-update-check
            --num-threads="\${GALAXY_SLOTS:-4}"
            --library-norm-method=$library_norm_method
            --output-format=$output_format

                        --library-type=$advanced_settings.library_type
                #end if
                $advanced_settings.hits_norm
            #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">
            <option value="geometric" selected="True">geometric</option>

        <data format="tabular" name="isoforms_count_table" label="${tool.name} on ${on_string}: transcript count table" from_work_dir="isoforms.count_table" >
            <filter>(output_format == 'simple-table')</filter>
        </data>
    </outputs>
    <tests>
        <!-- 
        <test>
                NOTE: as of version 0.0.6 of the wrapper, tests cannot be run because multiple inputs to a repeat
                element are not supported.
        </test>
        -->
    </tests>

    <help>
**Cuffnorm Overview**

  --library-norm-method          Library Normalization method : Geometric (default), classic-fpkm, quartile
  --library-type                 ff-firststrand,ff-secondstrand,ff-unstranded,fr-firstrand,fr-secondstrand,fr-unstranded,transfrags
  --compatible-hits-norm         With this option, Cufflinks counts only those fragments compatible with some reference transcript towards the number of mapped fragments used in the FPKM denominator. Using this mode is generally recommended in Cuffdiff to reduce certain types of bias caused by differential amounts of ribosomal reads which can create the impression of falsely differentially expressed genes.
  --total-hits-norm              With this option, Cufflinks counts all fragments, including those not compatible with any reference transcript, towards the number of mapped fragments used in the FPKM denominator
    </help>
    <citations>
        <citation type="doi">10.1038/nbt.1621</citation>
    </citations>
</tool>

4:6cbfede05833

    <description>Create normalized expression levels</description>
    <macros>
      <import>cuff_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <version_command><![CDATA[cuffnorm 2>&1 | head -n 1]]></version_command>
    <command detect_errors="aggressive"><![CDATA[
        cuffnorm
            --no-update-check
            --num-threads="\${GALAXY_SLOTS:-4}"
            --library-norm-method=$library_norm_method
            --output-format=$output_format

                        --library-type=$advanced_settings.library_type
                #end if
                $advanced_settings.hits_norm
            #end if
            ## Inputs.
            '$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">
            <option value="geometric" selected="True">geometric</option>

        <data format="tabular" name="isoforms_count_table" label="${tool.name} on ${on_string}: transcript count table" from_work_dir="isoforms.count_table" >
            <filter>(output_format == 'simple-table')</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="8">
            <param name="gtf_input" value="cuffcompare_out5.gtf" ftype="gtf"/>
            <conditional name="in_type">
                <param name="set_in_type" value="BAM"/>
                <repeat name="conditions">
                    <param name="name" value="in1"/>
                    <param name="samples" value="cuffdiff_in1.sam" ftype="sam"/>
                </repeat>
                <repeat name="conditions">
                    <param name="name" value="in2"/>
                    <param name="samples" value="cuffdiff_in2.sam" ftype="sam"/>
                </repeat>
            </conditional>
            <output ftype="tabular" name="cds_fpkm_table" value="cds.fpkm_table"/>
            <output ftype="tabular" name="cds_count_table" value="cds.count_table"/>
            <output ftype="tabular" name="tss_groups_fpkm_table" value="tss_groups.fpkm_table"/>
            <output ftype="tabular" name="tss_groups_count_table" value="tss_groups.count_table"/>
            <output ftype="tabular" name="genes_fpkm_table" value="genes.fpkm_table"/>
            <output ftype="tabular" name="genes_count_table" value="genes.count_table"/>
            <output ftype="tabular" name="isoforms_fpkm_table" value="isoforms.fpkm_table"/>
            <output ftype="tabular" name="isoforms_count_table" value="isoforms.count_table"/>
        </test>
    </tests>

    <help>
**Cuffnorm Overview**

  --library-norm-method          Library Normalization method : Geometric (default), classic-fpkm, quartile
  --library-type                 ff-firststrand,ff-secondstrand,ff-unstranded,fr-firstrand,fr-secondstrand,fr-unstranded,transfrags
  --compatible-hits-norm         With this option, Cufflinks counts only those fragments compatible with some reference transcript towards the number of mapped fragments used in the FPKM denominator. Using this mode is generally recommended in Cuffdiff to reduce certain types of bias caused by differential amounts of ribosomal reads which can create the impression of falsely differentially expressed genes.
  --total-hits-norm              With this option, Cufflinks counts all fragments, including those not compatible with any reference transcript, towards the number of mapped fragments used in the FPKM denominator
    </help>
    <expand macro="citations"/>
</tool>