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unintrusive fix for converter tests

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This commit is contained in:
Matthias Bernt
2023-12-23 10:27:00 +01:00
committed by mvdbeek
parent 1ffcf8e334
commit e4993e6d88
1 changed files with 28 additions and 9 deletions
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lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml
+28 -9
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@@ -40,9 +40,12 @@
<tests>
<test>
<param name="input1" ftype="bed" value="droPer1.bed"/>
<output name="output1" ftype="bgzip" value="droPer1.bgzip" decompress="true">
<output name="output1" ftype="bgzip" value="droPer1.bgzip">
<expand macro="assert_size" value="131"/>
</output>
<output name="output1" ftype="bgzip" decompress="true">
<expand macro="assert_size" value="120"/>
</output>
<assert_command>
<has_text text="-k1,1 -k2,2n -k3,3n"/>
</assert_command>
@@ -50,6 +53,9 @@
<test>
<param name="input1" ftype="encodepeak" value="encode.broad.peak"/>
<output name="output1" ftype="bgzip">
<expand macro="assert_size" value="141"/>
</output>
<output name="output1" ftype="bgzip" decompress="true">
<expand macro="assert_size" value="143">
<has_text_matching expression="^#" negate="true"/>
</expand>
@@ -60,9 +66,12 @@
</test>
<test>
<param name="input1" ftype="gff" value="gff_filter_by_feature_count_out2.gff"/>
<output name="output1" ftype="bgzip" value="bgzip_filter_by_feature_count_out2.bgzip" decompress="true">
<output name="output1" ftype="bgzip">
<expand macro="assert_size" value="638"/>
</output>
<output name="output1" ftype="bgzip" value="bgzip_filter_by_feature_count_out2.bgzip" decompress="true">
<expand macro="assert_size" value="3824"/>
</output>
<assert_command>
<has_text text="-k1,1 -k4,4n"/>
<has_text text="-k5,5" negate="true"/>
@@ -70,20 +79,25 @@
</test>
<test>
<param name="input1" ftype="interval" value="2.interval"/>
<output name="output1" ftype="bgzip" value="2.bgzip" decompress="true">
<output name="output1" ftype="bgzip">
<expand macro="assert_size" value="208"/>
</output>
<output name="output1" ftype="bgzip" value="2.bgzip" decompress="true">
<expand macro="assert_size" value="501"/>
</output>
<assert_command>
<has_text text="-k1,1 -k2,2n -k3,3n"/>
</assert_command>
</test>
<test>
<param name="input1" ftype="vcf" value="vcf_to_maf_in.vcf"/>
<output name="output1" ftype="bgzip">
<expand macro="assert_size" value="321"/>
</output>
<output name="output1" ftype="bgzip" decompress="true">
<expand macro="assert_size" value="322">
<!-- will only work with https://github.com/galaxyproject/galaxy/pull/15085
<has_n_lines n="3"/>
<has_text_matching expression="^#" negate="true"/> -->
<expand macro="assert_size" value="507">
<has_n_lines n="5"/>
<has_text_matching expression="^#" negate="true"/>
</expand>
</output>
<assert_command>
@@ -92,9 +106,14 @@
</test>
<test>
<param name="input1" ftype="gtf" value="cufflinks_out1.gtf"/>
<output name="output1" ftype="bgzip" >
<output name="output1" ftype="bgzip">
<assert_contents>
<has_size value="270" delta="10" />
<has_size value="270" delta="10"/>
</assert_contents>
</output>
<output name="output1" ftype="bgzip" decompress="true">
<assert_contents>
<has_size value="887"/>
</assert_contents>
</output>
<assert_command>