comparison stringtie.xml @ 20:cef79931dda5 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7f649c10c5d874f466122af0d24803a4c6affabb

19:333a6e13b622

        <test expect_num_outputs="1">
            <conditional name="input_options">
                <param name="input_mode" value="short_reads"/>
                <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
            </conditional>
            <output name="output_gtf" file="stringtie_out1.gtf" ftype="gtf" lines_diff="4" />
        </test>
        <!--Ensure fraction option works -->
        <test expect_num_outputs="1">
            <conditional name="input_options">
                <param name="input_mode" value="short_reads"/>
                <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
            </conditional>            
            <param name="fraction" value="0.17" />
            <output name="output_gtf" file="stringtie_out2.gtf" ftype="gtf" lines_diff="4" />
        </test>
        <!--Ensure guide option works -->
        <test expect_num_outputs="1">
            <conditional name="input_options">
                <param name="input_mode" value="short_reads"/>
                <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
            </conditional>            
            <param name="use_guide" value="yes" />
            <param name="guide_gff_select" value="history" />
            <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" />
            <output name="output_gtf" file="stringtie_out3.gtf" ftype="gtf" lines_diff="4"  />
        </test>
        <!--Ensure guide with fraction works -->
        <test expect_num_outputs="1">
            <conditional name="input_options">
                <param name="input_mode" value="short_reads"/>

            </conditional>            
            <param name="use_guide" value="yes" />
            <param name="guide_gff_select" value="history" />
            <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" />
            <param name="fraction" value="0.17" />
            <output name="output_gtf" file="stringtie_out4.gtf" ftype="gtf" lines_diff="4" />
        </test>
        <!--Ensure coverage and output for Ballgown works -->
        <test expect_num_outputs="7">
            <conditional name="input_options">
                <param name="input_mode" value="short_reads"/>

            <output name="exon_expression" file="./ballgown/e_data.ctab" ftype="tabular" />
            <output name="intron_expression" file="./ballgown/i_data.ctab" ftype="tabular" />
            <output name="transcript_expression" file="./ballgown/t_data.ctab" ftype="tabular" />
            <output name="exon_transcript_mapping" file="./ballgown/e2t.ctab" ftype="tabular" />
            <output name="intron_transcript_mapping" file="./ballgown/i2t.ctab" ftype="tabular" />
            <output name="output_gtf" file="stringtie_out5.gtf" ftype="gtf" lines_diff="4" />
            <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gtf" />
        </test>
        <!--Ensure output for edgeR works -->
        <test expect_num_outputs="5">
            <conditional name="input_options">
                <param name="input_mode" value="short_reads"/>

            <param name="coverage_file" value="true" />
            <param name="clustering" value="true" />
            <output name="gene_counts" file="gene_counts_edger.tsv" ftype="tabular" />
            <output name="transcript_counts" file="transcript_counts_edger.tsv" ftype="tabular" />
            <output name="legend" file="legend.tsv" ftype="tabular" />
            <output name="output_gtf" file="stringtie_out6.gtf" ftype="gtf" lines_diff="4" />
            <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gtf" />
        </test>
        <!--Ensure gene abundances output works -->
        <test expect_num_outputs="2">
            <conditional name="input_options">
                <param name="input_mode" value="short_reads"/>

            <param name="use_guide" value="yes" />
            <param name="guide_gff_select" value="history" />
            <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" />
            <param name="fraction" value="0.17" />
            <param name="abundance_estimation" value="true" />
            <output name="output_gtf" file="stringtie_out4.gtf" ftype="gtf" lines_diff="4" />
            <output name="gene_abundance_estimation" file="stringtie_out7.tsv" ftype="tabular" lines_diff="2" />
        </test>
        <!--Ensure another fraction value works -->
        <test expect_num_outputs="1">
            <conditional name="input_options">

            </conditional>            
            <param name="use_guide" value="yes" />
            <param name="guide_gff_select" value="history" />
            <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" />
            <param name="fraction" value="0.15" />
            <output name="output_gtf" file="stringtie_out8.gtf" ftype="gtf" lines_diff="4" />
        </test>
        <!--Ensure built-in GTFs work -->
        <test expect_num_outputs="1">
            <conditional name="input_options">
                <param name="input_mode" value="short_reads"/>
                <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
            </conditional>            
            <param name="use_guide" value="yes" />
            <param name="guide_gff_select" value="cached" />
            <param name="fraction" value="0.15" />
            <output name="output_gtf" file="stringtie_out9.gtf" ftype="gtf" lines_diff="4" />
        </test>
        <!-- Test long reads input -->
        <test expect_num_outputs="1">
            <conditional name="input_options">
                <param name="input_mode" value="long_reads"/>
                <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
            </conditional>            
            <param name="use_guide" value="yes" />
            <param name="guide_gff_select" value="cached" />
            <param name="fraction" value="0.15" />
            <output name="output_gtf" file="stringtie_out10.gtf" ftype="gtf" lines_diff="4" />
        </test>
        <!-- Test error splice option -->
        <test expect_num_outputs="1">
            <conditional name="input_options">
                <param name="input_mode" value="long_reads"/>

                <param name="error_splice" value="30" />
            </conditional>            
            <param name="use_guide" value="yes" />
            <param name="guide_gff_select" value="cached" />
            <param name="fraction" value="0.15" />
            <output name="output_gtf" file="stringtie_out11.gtf" ftype="gtf" lines_diff="4" />
        </test>
        <!-- Test mixed reads input -->
        <test expect_num_outputs="1">
            <conditional name="input_options">
                <param name="input_mode" value="mixed_reads"/>
                <param name="input_bam_short" ftype="bam" value="short_reads.bam" />
                <param name="input_bam_long" ftype="bam" value="long_reads.bam" />
            </conditional>            
            <output name="output_gtf" file="stringtie_out12.gtf" ftype="gtf" lines_diff="4" />
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

20:cef79931dda5

        <test expect_num_outputs="1">
            <conditional name="input_options">
                <param name="input_mode" value="short_reads"/>
                <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
            </conditional>
            <output name="output_gtf" file="stringtie_out1_re.gtf" ftype="gtf" compare="re_match" sort="true"/>
        </test>
        <!--Ensure fraction option works -->
        <test expect_num_outputs="1">
            <conditional name="input_options">
                <param name="input_mode" value="short_reads"/>
                <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
            </conditional>            
            <param name="fraction" value="0.17" />
            <output name="output_gtf" file="stringtie_out2_re.gtf" ftype="gtf" compare="re_match" sort="true"/>
        </test>
        <!--Ensure guide option works -->
        <test expect_num_outputs="1">
            <conditional name="input_options">
                <param name="input_mode" value="short_reads"/>
                <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
            </conditional>            
            <param name="use_guide" value="yes" />
            <param name="guide_gff_select" value="history" />
            <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" />
            <output name="output_gtf" file="stringtie_out3_re.gtf" ftype="gtf" compare="re_match" sort="true"/>
        </test>
        <!--Ensure guide with fraction works -->
        <test expect_num_outputs="1">
            <conditional name="input_options">
                <param name="input_mode" value="short_reads"/>

            </conditional>            
            <param name="use_guide" value="yes" />
            <param name="guide_gff_select" value="history" />
            <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" />
            <param name="fraction" value="0.17" />
            <output name="output_gtf" file="stringtie_out4_re.gtf" ftype="gtf" compare="re_match" sort="true"/>
        </test>
        <!--Ensure coverage and output for Ballgown works -->
        <test expect_num_outputs="7">
            <conditional name="input_options">
                <param name="input_mode" value="short_reads"/>

            <output name="exon_expression" file="./ballgown/e_data.ctab" ftype="tabular" />
            <output name="intron_expression" file="./ballgown/i_data.ctab" ftype="tabular" />
            <output name="transcript_expression" file="./ballgown/t_data.ctab" ftype="tabular" />
            <output name="exon_transcript_mapping" file="./ballgown/e2t.ctab" ftype="tabular" />
            <output name="intron_transcript_mapping" file="./ballgown/i2t.ctab" ftype="tabular" />
            <output name="output_gtf" file="stringtie_out5.gtf" ftype="gtf" compare="re_match" sort="true"/>
            <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gtf" compare="re_match" sort="true"/>
        </test>
        <!--Ensure output for edgeR works -->
        <test expect_num_outputs="5">
            <conditional name="input_options">
                <param name="input_mode" value="short_reads"/>

            <param name="coverage_file" value="true" />
            <param name="clustering" value="true" />
            <output name="gene_counts" file="gene_counts_edger.tsv" ftype="tabular" />
            <output name="transcript_counts" file="transcript_counts_edger.tsv" ftype="tabular" />
            <output name="legend" file="legend.tsv" ftype="tabular" />
            <output name="output_gtf" file="stringtie_out6.gtf" ftype="gtf" compare="re_match" sort="true"/>
            <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gtf" compare="re_match" sort="true"/>
        </test>
        <!--Ensure gene abundances output works -->
        <test expect_num_outputs="2">
            <conditional name="input_options">
                <param name="input_mode" value="short_reads"/>

            <param name="use_guide" value="yes" />
            <param name="guide_gff_select" value="history" />
            <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" />
            <param name="fraction" value="0.17" />
            <param name="abundance_estimation" value="true" />
            <output name="output_gtf" file="stringtie_out4_re.gtf" ftype="gtf" compare="re_match" sort="true"/>
            <output name="gene_abundance_estimation" file="stringtie_out7.tsv" ftype="tabular" lines_diff="2" />
        </test>
        <!--Ensure another fraction value works -->
        <test expect_num_outputs="1">
            <conditional name="input_options">

            </conditional>            
            <param name="use_guide" value="yes" />
            <param name="guide_gff_select" value="history" />
            <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" />
            <param name="fraction" value="0.15" />
            <output name="output_gtf" file="stringtie_out8.gtf" ftype="gtf" compare="re_match" sort="true"/>
        </test>
        <!--Ensure built-in GTFs work -->
        <test expect_num_outputs="1">
            <conditional name="input_options">
                <param name="input_mode" value="short_reads"/>
                <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
            </conditional>            
            <param name="use_guide" value="yes" />
            <param name="guide_gff_select" value="cached" />
            <param name="fraction" value="0.15" />
            <output name="output_gtf" file="stringtie_out9.gtf" ftype="gtf" compare="re_match" sort="true"/>
        </test>
        <!-- Test long reads input -->
        <test expect_num_outputs="1">
            <conditional name="input_options">
                <param name="input_mode" value="long_reads"/>
                <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
            </conditional>            
            <param name="use_guide" value="yes" />
            <param name="guide_gff_select" value="cached" />
            <param name="fraction" value="0.15" />
            <output name="output_gtf" file="stringtie_out10.gtf" ftype="gtf" compare="re_match" sort="true"/>
        </test>
        <!-- Test error splice option -->
        <test expect_num_outputs="1">
            <conditional name="input_options">
                <param name="input_mode" value="long_reads"/>

                <param name="error_splice" value="30" />
            </conditional>            
            <param name="use_guide" value="yes" />
            <param name="guide_gff_select" value="cached" />
            <param name="fraction" value="0.15" />
            <output name="output_gtf" file="stringtie_out11.gtf" ftype="gtf"  compare="re_match" sort="true"/>
        </test>
        <!-- Test mixed reads input -->
        <test expect_num_outputs="1">
            <conditional name="input_options">
                <param name="input_mode" value="mixed_reads"/>
                <param name="input_bam_short" ftype="bam" value="short_reads.bam" />
                <param name="input_bam_long" ftype="bam" value="long_reads.bam" />
            </conditional>            
            <output name="output_gtf" file="stringtie_out12.gtf" ftype="gtf" compare="re_match" sort="true"/>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark