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Minor tool updates to tools/hicstuff #6589

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merged 3 commits into from
Nov 25, 2024
Merged

Minor tool updates to tools/hicstuff #6589

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908a0f4
Updating tools/hicstuff from version 3.2.3 to 3.2.4
Nov 25, 2024
a529d26
Profile version update and minor fixes
SaimMomin12 Nov 25, 2024
c526834
macros comment cleanup
SaimMomin12 Nov 25, 2024
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28 changes: 14 additions & 14 deletions tools/hicstuff/hicstuff_pipeline.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
<import>macros.xml</import>
<token name="@VERSION_SUFFIX@">0</token>
</macros>
<expand macro="requirements" />
<expand macro="requirements"/>
<command detect_errors="exit_code"><![CDATA[
hicstuff pipeline
--genome '$genome'
Expand Down Expand Up @@ -79,10 +79,10 @@ hicstuff pipeline
</outputs>
<tests>
<test expect_num_outputs="3">
<param name="genome" value="seq.fa.gz" />
<param name="genome" value="seq.fa.gz"/>
<param name="paired_cond|paired_select" value="separate"/>
<param name="paired_cond|forward_reads" value="sample.reads_for.fastq.gz" />
<param name="paired_cond|reverse_reads" value="sample.reads_rev.fastq.gz" />
<param name="paired_cond|forward_reads" value="sample.reads_for.fastq.gz"/>
<param name="paired_cond|reverse_reads" value="sample.reads_rev.fastq.gz"/>
<output name="abs_fragments_contacts_weighted_graal">
<assert_contents>
<has_n_lines n="77"/>
Expand All @@ -97,15 +97,15 @@ hicstuff pipeline
</output>
<output name="info_contigs" file="info_contigs.txt"/>
<assert_stderr>
<has_text text="Contact map generated" />
<has_text text="Contact map generated"/>
</assert_stderr>
</test>
<!-- bg2 format -->
<test expect_num_outputs="3">
<param name="genome" value="seq.fa.gz" />
<param name="genome" value="seq.fa.gz"/>
<param name="paired_cond|paired_select" value="separate"/>
<param name="paired_cond|forward_reads" value="sample.reads_for.fastq.gz" />
<param name="paired_cond|reverse_reads" value="sample.reads_rev.fastq.gz" />
<param name="paired_cond|forward_reads" value="sample.reads_for.fastq.gz"/>
<param name="paired_cond|reverse_reads" value="sample.reads_rev.fastq.gz"/>
<param name="matfmt" value="bg2"/>
<output name="abs_fragments_contacts_weighted_bg2">
<assert_contents>
Expand All @@ -121,15 +121,15 @@ hicstuff pipeline
</output>
<output name="info_contigs" file="info_contigs.txt"/>
<assert_stderr>
<has_text text="Contact map generated" />
<has_text text="Contact map generated"/>
</assert_stderr>
</test>
<!-- cool format -->
<test expect_num_outputs="3">
<param name="genome" value="seq.fa.gz" />
<param name="genome" value="seq.fa.gz"/>
<param name="paired_cond|paired_select" value="separate"/>
<param name="paired_cond|forward_reads" value="sample.reads_for.fastq.gz" />
<param name="paired_cond|reverse_reads" value="sample.reads_rev.fastq.gz" />
<param name="paired_cond|forward_reads" value="sample.reads_for.fastq.gz"/>
<param name="paired_cond|reverse_reads" value="sample.reads_rev.fastq.gz"/>
<param name="matfmt" value="cool"/>
<output name="abs_fragments_contacts_weighted_cool">
<assert_contents>
Expand All @@ -144,7 +144,7 @@ hicstuff pipeline
</output>
<output name="info_contigs" file="info_contigs.txt"/>
<assert_stderr>
<has_text text="Contact map generated" />
<has_text text="Contact map generated"/>
</assert_stderr>
</test>
</tests>
Expand All @@ -170,5 +170,5 @@ Output files
* Contig info.txt: Contains chromosome names, theirs length and number of bins.

]]></help>
<expand macro="citations" />
<expand macro="citations"/>
</tool>
7 changes: 2 additions & 5 deletions tools/hicstuff/macros.xml
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Original file line number Diff line number Diff line change
@@ -1,12 +1,9 @@
<macros>
<token name="@TOOL_VERSION@">3.2.3</token><!-- TODO remove cooler and biopython requirement on update -->
<token name="@PROFILE@">21.09</token>
<token name="@TOOL_VERSION@">3.2.4</token>
<token name="@PROFILE@">23.02</token>
<xml name="requirements">
<requirements>
<requirement type="package" version="@TOOL_VERSION@">hicstuff</requirement>
<requirement type="package" version="0.10.2">cooler</requirement>
<requirement type="package" version="1.84">biopython</requirement>
<yield/>
</requirements>
</xml>
<xml name="citations">
Expand Down