comparison cuffmerge_wrapper.xml @ 14:6a6717a5f421 draft

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

13:cf747d1bd79a

<tool id="cuffmerge" name="Cuffmerge" version="@VERSION@.1">
    <description>merge together several Cufflinks assemblies</description>
    <macros>
      <import>cuff_macros.xml</import>
    </macros>
    <expand macro="requirements" />
     <version_command>cuffmerge -v</version_command>
    <command detect_errors="aggressive">
        python '$__tool_directory__/cuffmerge_wrapper.py'
            --num-threads="\${GALAXY_SLOTS:-4}"
            
            ## Use annotation reference?
            #if $annotation.use_ref_annotation == "Yes":
                -g '${annotation.reference_annotation}'
            #end if
            

                    --index '${seq_data.seq_source.index.fields.path}'
                #end if
            #end if

            --min-isoform-fraction="${min_isoform_fraction}"

            ## Outputs.
            --merged-transcripts '${merged_transcripts}'

            @CUFFLINKS_GTF_INPUTS@
    </command>
    <inputs>
        <expand macro="cufflinks_gtf_inputs" />
        <conditional name="annotation">
            <param name="use_ref_annotation" type="select" label="Use Reference Annotation">
                <option value="No">No</option>

        </conditional>
        <param name="min_isoform_fraction" type="float" min="0" max="1" value="0.05" label="Minimum isoform fraction" help="Discard isoforms with abundance below this value" />
    </inputs>

    <outputs>
        <data format="gtf" name="merged_transcripts" label="${tool.name} on ${on_string}: merged transcripts"/>
    </outputs>

    <tests>
        <!-- 
            cuffmerge -g cuffcompare_in3.gtf cuffcompare_in1.gtf cuffcompare_in2.gtf

Merged transcripts file:

Cuffmerge produces a GTF file that contains an assembly that merges together the input assemblies.
    </help>
    <citations>
        <citation type="doi">10.1038/nbt.1621</citation>
    </citations>
</tool>

14:6a6717a5f421

<tool id="cuffmerge" name="Cuffmerge" version="@VERSION@.2">
    <description>merge together several Cufflinks assemblies</description>
    <macros>
      <import>cuff_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <version_command>cuffmerge -v</version_command>
    <command detect_errors="aggressive"><![CDATA[
        @CUFFLINKS_LINK_GTF_INPUTS@
        echo @CUFFLINKS_GTF_INPUTS@ | sed 's/\s\+/\n/' > assembly_GTF_list.txt &&
        cuffmerge 
            -o output
            --num-threads="\${GALAXY_SLOTS:-4}"
            ## Use annotation reference?
            #if $annotation.use_ref_annotation == "Yes":
                -g '${annotation.reference_annotation}'
            #end if
            

                    --index '${seq_data.seq_source.index.fields.path}'
                #end if
            #end if

            --min-isoform-fraction="${min_isoform_fraction}"
            assembly_GTF_list.txt
    ]]></command>
    <inputs>
        <expand macro="cufflinks_gtf_inputs" />
        <conditional name="annotation">
            <param name="use_ref_annotation" type="select" label="Use Reference Annotation">
                <option value="No">No</option>

        </conditional>
        <param name="min_isoform_fraction" type="float" min="0" max="1" value="0.05" label="Minimum isoform fraction" help="Discard isoforms with abundance below this value" />
    </inputs>

    <outputs>
        <data format="gtf" name="merged_transcripts" label="${tool.name} on ${on_string}: merged transcripts" from_work_dir="output/merged.gtf"/>
    </outputs>

    <tests>
        <!-- 
            cuffmerge -g cuffcompare_in3.gtf cuffcompare_in1.gtf cuffcompare_in2.gtf

Merged transcripts file:

Cuffmerge produces a GTF file that contains an assembly that merges together the input assemblies.
    </help>
    <expand macro="citations"/>
</tool>