Unverified Commit 02d389f8 authored by mvdbeek's avatar mvdbeek
Browse files

Drop size assertions on tabix index 

That's none of our business. We know index is valid if the chromosome
names are printed to stdout.
parent ada69149

lib/galaxy/datatypes/converters/interval_to_tabix_converter.xml

+16 −43
Original line number Diff line number Diff line
@@ -42,11 +42,6 @@ 
        <test>

            <param name="input1" ftype="bed" value="droPer1.bed" />

            <param name="bgzip" ftype="bgzip" value="droPer1.bed.gz" />

            <output name="output1" ftype="tabix">

                <assert_contents>

                    <has_size value="133"/>

                </assert_contents>

            </output>

            <assert_command>

                <has_text text="-p bed"/>

            </assert_command>
@@ -57,11 +52,6 @@ 
        <test>

            <param name="input1" ftype="encodepeak" value="encode.broad.peak" />

            <param name="bgzip" ftype="bgzip" value="encode.broad.peak.gz" />

            <output name="output1" ftype="tabix">

                <assert_contents>

                    <has_size value="110" delta="10"/>

                </assert_contents>

            </output>

            <assert_command>

                <has_text text="-p" negate="true"/>

            </assert_command>
@@ -72,11 +62,6 @@ 
        <test>

            <param name="input1" ftype="gff" value="gff_filter_by_feature_count_out2.gff" />

            <param name="bgzip" ftype="bgzip" value="gff_filter_by_feature_count_out2.gff.gz" />

            <output name="output1" ftype="tabix">

                <assert_contents>

                    <has_size value="120"/>

                </assert_contents>

            </output>

            <assert_command>

                <has_text text="-p gff"/>

            </assert_command>
@@ -87,11 +72,6 @@ 
        <test>

            <param name="input1" ftype="interval" value="2.interval" />

            <param name="bgzip" ftype="bgzip" value="2.interval.gz" />

            <output name="output1" ftype="tabix">

                <assert_contents>

                    <has_size value="247"/>

                </assert_contents>

            </output>

            <assert_command>

                <has_text text="-p" negate="true"/>

            </assert_command>
@@ -102,11 +82,6 @@ 
        <test>

            <param name="input1" ftype="vcf" value="vcf_to_maf_in.vcf" />

            <param name="bgzip" ftype="bgzip" value="vcf_to_maf_in.vcf.gz" />

            <output name="output1" ftype="tabix">

                <assert_contents>

                    <has_size value="143"/>

                </assert_contents>

            </output>

            <assert_command>

                <has_text text="-p vcf"/>

            </assert_command>
@@ -117,14 +92,12 @@ 
        <test>

            <param name="input1" ftype="gtf" value="cufflinks_out1.gtf" />

            <param name="bgzip" ftype="bgzip" value="cufflinks_out1.gtf.gz" />

            <output name="output1" ftype="tabix">

                <assert_contents>

                    <has_size value="125"/>

                </assert_contents>

            </output>

            <assert_command>

                <has_text text="-p gff" />

            </assert_command>

            <assert_stdout>

                <has_line line="test_chromosome" />

            </assert_stdout>

        </test>

    </tests>

    <help>