comparison cuffdiff_wrapper.xml @ 8:a10919766c11 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 80b06e80066b32ad53ed418628992f056444256f

7:456797205473

<tool id="cuffdiff" name="Cuffdiff" version="@VERSION@.6">
    <description>find significant changes in transcript expression, splicing, and promoter use</description>
    <macros>
        <import>cuff_macros.xml</import>
    </macros>
    <expand macro="requirements">

            <filter>generate_sqlite</filter>
        </data>
    </outputs>

    <tests>
        <test>
            <!--
                cuffdiff cuffcompare_out5.gtf cuffdiff_in1.sam cuffdiff_in2.sam
            -->
            <param name="gtf_input" value="cuffdiff_in1.gtf" ftype="gtf" />
            <param name="generate_sqlite" value="yes" />

            <param name="do_bias_correction" value="No" />
            <param name="multiread_correct" value="No"/>
            <param name="sAdditional" value="No"/>
            <output name="output_cummerbund" ftype="sqlite" file="cuffdiff_out.sqlite" compare="sim_size" />
        </test>
        <test>
            <!--
                Use a list collection as conditions input
                cuffdiff cuffcompare_out5.gtf cuffdiff_in1.sam cuffdiff_in2.sam
            -->
            <param name="gtf_input" value="cuffdiff_in1.gtf" ftype="gtf" />

            <param name="do_bias_correction" value="No" />
            <param name="multiread_correct" value="No"/>
            <param name="sAdditional" value="No"/>
            <output name="output_cummerbund" ftype="sqlite" file="cuffdiff_out.sqlite" compare="sim_size" />
        </test>
        <test>
            <!--
                cuffdiff cuffcompare_out5.gtf cuffdiff_in1.sam cuffdiff_in2.sam
            -->
            <param name="gtf_input" value="cuffdiff_in1.gtf" ftype="gtf" />
            <param name="omit_tabular_output" value="no" />

8:a10919766c11

<tool id="cuffdiff" name="Cuffdiff" version="@TOOL_VERSION@.7" profile="@PROFILE@">
    <description>find significant changes in transcript expression, splicing, and promoter use</description>
    <macros>
        <import>cuff_macros.xml</import>
    </macros>
    <expand macro="requirements">

            <filter>generate_sqlite</filter>
        </data>
    </outputs>

    <tests>
        <test expect_num_outputs="1">
            <!--
                cuffdiff cuffcompare_out5.gtf cuffdiff_in1.sam cuffdiff_in2.sam
            -->
            <param name="gtf_input" value="cuffdiff_in1.gtf" ftype="gtf" />
            <param name="generate_sqlite" value="yes" />

            <param name="do_bias_correction" value="No" />
            <param name="multiread_correct" value="No"/>
            <param name="sAdditional" value="No"/>
            <output name="output_cummerbund" ftype="sqlite" file="cuffdiff_out.sqlite" compare="sim_size" />
        </test>
        <test expect_num_outputs="1">
            <!--
                Use a list collection as conditions input
                cuffdiff cuffcompare_out5.gtf cuffdiff_in1.sam cuffdiff_in2.sam
            -->
            <param name="gtf_input" value="cuffdiff_in1.gtf" ftype="gtf" />

            <param name="do_bias_correction" value="No" />
            <param name="multiread_correct" value="No"/>
            <param name="sAdditional" value="No"/>
            <output name="output_cummerbund" ftype="sqlite" file="cuffdiff_out.sqlite" compare="sim_size" />
        </test>
        <test expect_num_outputs="11">
            <!--
                cuffdiff cuffcompare_out5.gtf cuffdiff_in1.sam cuffdiff_in2.sam
            -->
            <param name="gtf_input" value="cuffdiff_in1.gtf" ftype="gtf" />
            <param name="omit_tabular_output" value="no" />