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Merge pull request #17231 from mvdbeek/convert_test_backport

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[23.1] Backport #17188: Fix for converter tests
This commit is contained in:
Björn Grüning
2023-12-23 12:43:56 +01:00
committed by GitHub
parent 4d07aa974d 07bf0d6955
commit 687bcf9d01
2 changed files with 10 additions and 11 deletions
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lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml
+9 -10
View File
@@ -41,7 +41,7 @@
<test>
<param name="input1" ftype="bed" value="droPer1.bed"/>
<output name="output1" ftype="bgzip" value="droPer1.bgzip" decompress="true">
<expand macro="assert_size" value="131"/>
<expand macro="assert_size" value="120"/>
</output>
<assert_command>
<has_text text="-k1,1 -k2,2n -k3,3n"/>
@@ -49,7 +49,7 @@
</test>
<test>
<param name="input1" ftype="encodepeak" value="encode.broad.peak"/>
<output name="output1" ftype="bgzip">
<output name="output1" ftype="bgzip" decompress="true">
<expand macro="assert_size" value="143">
<has_text_matching expression="^#" negate="true"/>
</expand>
@@ -61,7 +61,7 @@
<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">
<expand macro="assert_size" value="638"/>
<expand macro="assert_size" value="3824"/>
</output>
<assert_command>
<has_text text="-k1,1 -k4,4n"/>
@@ -71,7 +71,7 @@
<test>
<param name="input1" ftype="interval" value="2.interval"/>
<output name="output1" ftype="bgzip" value="2.bgzip" decompress="true">
<expand macro="assert_size" value="208"/>
<expand macro="assert_size" value="501"/>
</output>
<assert_command>
<has_text text="-k1,1 -k2,2n -k3,3n"/>
@@ -80,10 +80,9 @@
<test>
<param name="input1" ftype="vcf" value="vcf_to_maf_in.vcf"/>
<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 +91,9 @@
</test>
<test>
<param name="input1" ftype="gtf" value="cufflinks_out1.gtf"/>
<output name="output1" ftype="bgzip" >
<output name="output1" ftype="bgzip" decompress="true">
<assert_contents>
<has_size value="270" delta="10" />
<has_size value="887"/>
</assert_contents>
</output>
<assert_command>
lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml
+1 -1
View File
@@ -17,7 +17,7 @@
<param name="input1" ftype="vcf" value="vcf_to_maf_in.vcf"/>
<output name="output1" ftype="vcf_bgzip" value="vcf_bgzip_to_maf_in.vcf_bgzip" decompress="true">
<assert_contents>
<has_size value="717" delta="10"/>
<has_size value="1182"/>
</assert_contents>
</output>
</test>