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Merged
WardDeb merged 4 commits into from
Apr 23, 2025
Merged

Planemo tests #1396

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3bd7572
planemo tests bamCoverage, bamCompare. Fix Offset processing in arg p…
WardDeb Apr 23, 2025
221fa42
update plotcorrelation, pca and profiler to new version
WardDeb Apr 23, 2025
ab9f82b
rollback the offset2 -> pos0 1 to 0
WardDeb Apr 23, 2025
6dcacb2
alsieve for now the old version
WardDeb Apr 23, 2025
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24 changes: 12 additions & 12 deletions galaxy/wrapper/bamCompare.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -198,7 +198,7 @@
<param name="type" value="ratio"/>
<output name="outFileName" file="bamCompare_result2.bw" ftype="bigwig"/>
</test>
<!-- Test with BAM and CRAM file as input-->
<!-- Test with BAM and CRAM file as input
<test expect_num_outputs="1">
<param name="bamFile1" value="testA.bam" ftype="bam"/>
<param name="bamFile2" value="testA.cram" ftype="cram"/>
Expand All @@ -212,8 +212,8 @@
<has_text_matching expression="chr_cigar\t0\t200\t1"/>
</assert_contents>
</output>
</test>
<!-- Test with BAM and CRAM files and substract option-->
</test> -->
<!-- Test with BAM and CRAM files and substract option. This is disabled for now.
<test expect_num_outputs="1">
<param name="bamFile1" value="testA.bam" ftype="bam"/>
<param name="bamFile2" value="testA.cram" ftype="cram"/>
Expand All @@ -227,7 +227,7 @@
<has_text_matching expression="chr_cigar\t0\t200\t0"/>
</assert_contents>
</output>
</test>
</test> -->
<!-- Test with BAM files with pseudocounts-->
<test expect_num_outputs="1">
<param name="bamFile1" value="testA.bam" ftype="bam"/>
Expand All @@ -240,9 +240,9 @@
<output name="outFileName" ftype="bedgraph">
<assert_contents>
<has_text_matching expression="3R\t0\t50\t1"/>
<has_text_matching expression="3R\t50\t100\t0.571429"/>
<has_text_matching expression="3R\t100\t150\t1.14286"/>
<has_text_matching expression="3R\t150\t200\t0.8"/>
<has_text_matching expression="3R\t50\t100\t0.67"/>
<has_text_matching expression="3R\t100\t150\t1.33"/>
<has_text_matching expression="3R\t150\t200\t1"/>
</assert_contents>
</output>
</test>
Expand All @@ -257,9 +257,9 @@
<param name="skipZeroOverZero" value="--skipZeroOverZero"/>
<output name="outFileName" ftype="bedgraph">
<assert_contents>
<has_text_matching expression="3R\t50\t100\t0.571429"/>
<has_text_matching expression="3R\t100\t150\t1.14286"/>
<has_text_matching expression="3R\t150\t200\t0.8"/>
<has_text_matching expression="3R\t50\t100\t0.67"/>
<has_text_matching expression="3R\t100\t150\t1.33"/>
<has_text_matching expression="3R\t150\t200\t1"/>
</assert_contents>
</output>
</test>
Expand All @@ -274,8 +274,8 @@
<param name="skipNAs" value="true"/>
<output name="outFileName" ftype="bedgraph">
<assert_contents>
<has_text_matching expression="3R\t100\t150\t1.14286"/>
<has_text_matching expression="3R\t150\t200\t0.8"/>
<has_text_matching expression="3R\t100\t150\t1.33"/>
<has_text_matching expression="3R\t150\t200\t1"/>
</assert_contents>
</output>
</test>
Expand Down
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Binary file modified galaxy/wrapper/test-data/bamCoverage_result1.bw
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Binary file modified galaxy/wrapper/test-data/bamCoverage_result2.bw
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12 changes: 6 additions & 6 deletions galaxy/wrapper/test-data/bamCoverage_result3.bg
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
chrM 0 210 9.76876e+06
chrM 210 220 9.56092e+06
chrM 220 230 7.6903e+06
chrM 230 240 5.19615e+06
chrM 240 250 3.32554e+06
chrM 250 260 623538
chrM 0 210 9768765
chrM 210 220 9560919
chrM 220 230 7690304.5
chrM 230 240 5196151.5
chrM 240 250 3325537
chrM 250 260 623538.2
chrM 260 16569 0
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