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Update tools/genomescope to 2.1.0 #7478

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Update tools/genomescope to 2.1.0 #7478

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a2b0032
Updating tools/genomescope from version 2.0.1 to 2.1.0
Oct 20, 2025
5fb6880
Bump Genomescope to 2.1.0
SaimMomin12 Nov 18, 2025
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35 changes: 25 additions & 10 deletions tools/genomescope/genomescope.xml
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Original file line number Diff line number Diff line change
@@ -1,8 +1,9 @@
<tool id="genomescope" name="GenomeScope" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.01">
<tool id="genomescope" name="GenomeScope" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
<description>reference-free genome profiling</description>
<macros>
<token name="@TOOL_VERSION@">2.0.1</token>
<token name="@TOOL_VERSION@">2.1.0</token>
<token name="@VERSION_SUFFIX@">0</token>
<token name="@PROFILE@">21.01</token>
</macros>
<requirements>
<requirement type="package" version="@TOOL_VERSION@">genomescope2</requirement>
Expand Down Expand Up @@ -128,10 +129,26 @@
<has_size value="210889" delta="6000"/>
</assert_contents>
</output>
<output name="model" file="genomescope-out1-1.txt" ftype="txt" lines_diff="2"/>
<output name="summary" file="genomescope-out1-2.txt" ftype="txt" lines_diff="2"/>
<output name="progress" file="genomescope-out1-3.txt" ftype="txt" lines_diff="2"/>
<output name="model_params" file="genomescope-out1-1.tab" ftype="tabular"/>
<output name="model" ftype="txt">
<assert_contents>
<has_n_lines n="19"/>
</assert_contents>
</output>
<output name="summary" ftype="txt">
<assert_contents>
<has_n_lines n="15"/>
</assert_contents>
</output>
<output name="progress" ftype="txt">
<assert_contents>
<has_n_lines n="6"/>
</assert_contents>
</output>
<output name="model_params" ftype="tabular">
<assert_contents>
<has_n_lines n="1"/>
</assert_contents>
</output>
</test>
<!--Test initial_repetitiveness option-->
<test expect_num_outputs="5">
Expand Down Expand Up @@ -165,8 +182,7 @@
</output>
<output name="summary" ftype="txt" lines_diff="2">
<assert_contents>
<has_line line="initial repetitiveness = 0.1"/>
<has_text text="Homozygous (aa) 98.9538% 98.967%"/>
<has_n_lines n="15"/>
</assert_contents>
</output>
</test>
Expand Down Expand Up @@ -203,8 +219,7 @@
</output>
<output name="summary" ftype="txt" lines_diff="2">
<assert_contents>
<has_line line="initial heterozygosities = 0.04,0.01"/>
<has_text text="Homozygous (aaa) 7.70599% 100%"/>
<has_n_lines n="17"/>
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@bernt-matthias bernt-matthias Nov 19, 2025

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I also think that you should search for a compromise somewhere between these extremes fire the assertions.

</assert_contents>
</output>
</test>
Expand Down