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Merge pull request galaxyproject#6449 from SaimMomin12/tools/cutesv
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Updating tools/cutesv
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@bgruening
bgruening authored Oct 11, 2024
2 parents dcb5fdc + 798dbc0 commit 963634c
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Showing 2 changed files with 23 additions and 23 deletions.
42 changes: 21 additions & 21 deletions tools/cutesv/cutesv.xml
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Expand Up @@ -8,7 +8,7 @@
</xrefs>
<requirements>
<requirement type="package" version="@TOOL_VERSION@">cutesv</requirement>
<requirement type="package" version="1.10">samtools</requirement>
<requirement type="package" version="1.21">samtools</requirement>
</requirements>
<command detect_errors="exit_code"><![CDATA[
ln -s '$input_sample_file' ./sample.bam &&
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--diff_ratio_filtering_TRA '$sel_method.adv_settings.diff_ratio_filtering_TRA'
]]></command>
<inputs>
<param name="input_sample_file" type="data" format="bam" label="Sample file" help="Sample file in .BAM format." />
<param name="input_sample_file" type="data" format="bam" label="Sample file" help="Sample file in .BAM format."/>
<expand macro="reference_interface" />
<param name="sample" type="text" value="Sample" label="Sample name/id" help="">
<validator type="length" min="1" message="Please enter a sample name/id"/>
Expand All @@ -66,30 +66,30 @@
</param>
<when value="pb_clr">
<section name="adv_settings" title="Advanced settings" expanded="false">
<expand macro="adv_shared_1" />
<expand macro="adv_pb_clr" />
<expand macro="adv_shared_2" />
<expand macro="adv_shared_1"/>
<expand macro="adv_pb_clr"/>
<expand macro="adv_shared_2"/>
</section>
</when>
<when value="pb_ccs">
<section name="adv_settings" title="Advanced settings" expanded="false">
<expand macro="adv_shared_1" />
<expand macro="adv_pb_ccs" />
<expand macro="adv_shared_2" />
<expand macro="adv_shared_1"/>
<expand macro="adv_pb_ccs"/>
<expand macro="adv_shared_2"/>
</section>
</when>
<when value="pb_ont">
<section name="adv_settings" title="Advanced settings" expanded="false">
<expand macro="adv_shared_1" />
<expand macro="adv_ont" />
<expand macro="adv_shared_2" />
<expand macro="adv_shared_1"/>
<expand macro="adv_ont"/>
<expand macro="adv_shared_2"/>
</section>
</when>
<when value="other">
<section name="adv_settings" title="Advanced settings" expanded="true">
<expand macro="adv_shared_1" />
<expand macro="adv_other" />
<expand macro="adv_shared_2" />
<expand macro="adv_shared_1"/>
<expand macro="adv_other"/>
<expand macro="adv_shared_2"/>
</section>
</when>
</conditional>
Expand All @@ -101,14 +101,14 @@
<test expect_num_outputs="1">
<conditional name="reference_source">
<param name="ref_selector" value="history"/>
<param name="ref" ftype="fasta" value="genome.fasta" />
<param name="ref" ftype="fasta" value="genome.fasta"/>
</conditional>
<param name="sel_method|meth_selector" value="pb_ccs" />
<param name="input_sample_file" ftype="bam" value="sample.bam" />
<param name="sel_method|meth_selector" value="pb_ccs"/>
<param name="input_sample_file" ftype="bam" value="sample.bam"/>
<output name="out_sample">
<assert_contents>
<has_text text="##fileformat=VCFv4.2"/>
<has_text text="##source=cuteSV-1.0.8"/>
<has_text text="##contig=&lt;ID=chrM,length=16571&gt;"/>
</assert_contents>
</output>
</test>
Expand All @@ -117,12 +117,12 @@
<param name="ref_selector" value="cached"/>
<param name="ref" value="test_buildid"/>
</conditional>
<param name="sel_method|meth_selector" value="pb_ccs" />
<param name="input_sample_file" ftype="bam" value="sample.bam" />
<param name="sel_method|meth_selector" value="pb_ccs"/>
<param name="input_sample_file" ftype="bam" value="sample.bam"/>
<output name="out_sample">
<assert_contents>
<has_text text="##fileformat=VCFv4.2"/>
<has_text text="##source=cuteSV-1.0.8"/>
<has_text text="##contig=&lt;ID=chrM,length=16571&gt;"/>
</assert_contents>
</output>
</test>
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4 changes: 2 additions & 2 deletions tools/cutesv/macros.xml
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@@ -1,6 +1,6 @@
<macros>
<token name="@VERSION_SUFFIX@">1</token>
<token name="@TOOL_VERSION@">1.0.8</token>
<token name="@VERSION_SUFFIX@">0</token>
<token name="@TOOL_VERSION@">2.1.1</token>
<xml name="reference_interface">
<conditional name="reference_source">
<param name="ref_selector" type="select" label="Choose the source for the reference genome">
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