New Tool addition: Haltools #7488

Maed0x · 2025-11-25T15:23:24Z

FOR CONTRIBUTOR:

I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
License permits unrestricted use (educational + commercial)
This PR adds a new tool or tool collection
This PR updates an existing tool or tool collection
This PR does something else (explain below)

Adding the first tool of haltools

SaimMomin12

@Maed0x Congrats on your first contribution to IUC 🎉 .Some comments inline.

SaimMomin12 · 2025-11-25T15:28:16Z

tools/haltools/.shed.yml

+long_description: |
+  A set of tools to for manipulating HAL alignment files


Please write a long description

SaimMomin12 · 2025-11-25T15:28:29Z

tools/haltools/.shed.yml

+- Sequence Analysis
+auto_tool_repositories:
+  name_template: "{{ tool_id }}"
+  description_template: "Wrapper for hal tool suite: {{ tool_name }}"


Suggested change

description_template: "Wrapper for hal tool suite: {{ tool_name }}"

description_template: "Wrapper for haltools suite: {{ tool_name }}"

SaimMomin12 · 2025-11-25T15:28:43Z

tools/haltools/.shed.yml

+  name: "suite_haltools"
+  description: "A set of tools to for manipulating HAL alignment files"
+  long_description: |
+    A set of tools to for manipulating HAL alignment files


SaimMomin12 · 2025-11-25T15:29:04Z

tools/haltools/hal_halStats.xml

@@ -0,0 +1,238 @@
+<tool id="hal_halstats" name="HAL halStats" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="25.0">


Suggested change

<tool id="hal_halstats" name="HAL halStats" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="25.0">

<tool id="hal_halstats" name="HAL halStats" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">

Define a PROFILE token in macros.xml

SaimMomin12 · 2025-11-25T15:30:06Z

tools/haltools/macros.xml

+    </xml>
+    <token name="@TOOL_VERSION@">2.9.9</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <xml name="in_hal_file">


Suggested change

<xml name="in_hal_file">

<xml name="input_hal">

SaimMomin12 · 2025-11-25T15:37:20Z

tools/haltools/hal_halStats.xml

+                <param name="allCoverage" type="boolean" truevalue="--allCoverage" falsevalue="" checked="false" 
+                    label="All Coverage" 
+                    help="Print histogram of coverage from all genomes to all genomes" />


SaimMomin12 · 2025-11-25T15:38:36Z

tools/haltools/hal_halStats.xml

+                <param name="baseComp" type="text" value="" 
+                    label="Base composition" 
+                    help="Print base composition for given genome by sampling every step bases. Parameter value is of the form genome,step. Ex: human,1000. The output is of the form fraction_of_As fraction_of_Gs fraction_of_Cs  fraction_of_Ts" />


Maybe specify an example and considering defining a sanitizer

SaimMomin12 · 2025-11-25T15:39:29Z

tools/haltools/hal_halStats.xml

+        <test expect_num_outputs="1">
+            <param name="in_hal_file" value="halTest.hal"/>
+            <output name="out_file_txt" file="halStats_output.txt"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="in_hal_file" value="halTest.hal"/>
+            <conditional name="mode">
+                <param name="option" value="--allCoverage"/>
+                <param name="allCoverage" value="true"/>
+            </conditional>
+            <output name="out_file_csv" file="halStats_allCoverage_output.csv"/>
+        </test>
+    </tests>


Please extend your test for other parameters.

SaimMomin12 · 2025-11-25T15:42:17Z

tools/haltools/hal_halStats.xml

+        </test>
+    </tests>
+    <help><![CDATA[
+Some global information from a HAL file can be quickly obtained using halStats. It will return the number of genomes, their phylogenetic tree, and the size of each array in each genome.


Some other help text would be benefits

SaimMomin12 · 2025-11-25T15:43:43Z

tools/haltools/macros.xml

+        </requirements>
+    </xml>
+    <token name="@TOOL_VERSION@">2.9.9</token>
+    <token name="@VERSION_SUFFIX@">0</token>


Introduce @Profile@ Token

SaimMomin12 · 2025-11-25T15:46:36Z

tools/haltools/hal_halStats.xml

+        <data name="out_file_txt" format="txt" from_work_dir="stats.txt" label="${tool.name} on ${on_string}: Stats">
+            <filter>mode['option'] != '--allCoverage'</filter>
+        </data>
+        <data name="out_file_csv" format="tabular" from_work_dir="stats.csv" label="${tool.name} on ${on_string}: CSV Stats">


Suggested change

<data name="out_file_csv" format="tabular" from_work_dir="stats.csv" label="${tool.name} on ${on_string}: CSV Stats">

<data name="out_file_csv" format="csv" from_work_dir="stats.csv" label="${tool.name} on ${on_string}: CSV Stats">

SaimMomin12 · 2025-11-26T12:47:04Z

tools/haltools/hal_halStats.xml

@@ -0,0 +1,238 @@
+<tool id="hal_halstats" name="HAL halStats" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="25.0">


Suggested change

<tool id="hal_halstats" name="HAL halStats" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="25.0">

<tool id="hal_halstats" name="halStats" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="25.0">

SaimMomin12 · 2025-11-26T12:47:23Z

tools/haltools/hal_halStats.xml

@@ -0,0 +1,238 @@
+<tool id="hal_halstats" name="HAL halStats" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="25.0">
+    <description>retrieves basic statistics from a hal file</description>


Suggested change

<description>retrieves basic statistics from a hal file</description>

<description>retrieve basic statistics from a HAL file</description>

SaimMomin12 · 2025-12-01T13:06:05Z

tools/haltools/macros.xml

+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">25.0</token>
+    <xml name="input_hal">
+        <param name="input_hal" type="data" format="hal" label="Input hal file to analyze" optional="false"/>


Suggested change

<param name="input_hal" type="data" format="hal" label="Input hal file to analyze" optional="false"/>

<param name="input_hal" type="data" format="hal" label="Input hal file to analyze"/>

SaimMomin12 · 2025-12-01T13:07:20Z

tools/haltools/macros.xml

+            <citation type="bibtex">
+                @misc{githubhal,
+                title = {HAL GitHub page},
+                url = {https://github.com/ComparativeGenomicsToolkit/hal},
+                }
+            </citation>


Suggested change

<citation type="bibtex">

@misc{githubhal,

title = {HAL GitHub page},

url = {https://github.com/ComparativeGenomicsToolkit/hal},

}

</citation>

SaimMomin12 · 2025-12-01T13:10:00Z

tools/haltools/macros.xml

+    <xml name="input_hal">
+        <param name="input_hal" type="data" format="hal" label="Input hal file to analyze" optional="false"/>
+    </xml>
+    <xml name="params_inputFormat">


Suggested change

<xml name="params_inputFormat">

<xml name="hal_backend_format">

Perhaps a better name?

SaimMomin12 · 2025-12-01T13:11:40Z

tools/haltools/hal_halStats.xml

+    ]]></command>
+    <inputs>
+        <expand macro="input_hal"/>
+        <expand macro="params_inputFormat"/>


Suggested change

<expand macro="params_inputFormat"/>

<expand macro="hal_backend_format"/>

SaimMomin12 · 2025-12-01T13:13:14Z

tools/haltools/hal_halStats.xml

+        (
+        #if $mode.option == "--baseComp":
+            echo -e "fraction_of_As\tfraction_of_Gs\tfraction_of_Cs\tfraction_of_Ts";
+        #else if $mode.option == "--numSegments":
+            echo "numTopSegments numBottomSegments";
+        #end if


Is there some reason, why this is echoed? Is it part of the tool?

SaimMomin12 · 2025-12-01T13:15:55Z

tools/haltools/hal_halStats.xml

+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="out_file" format="txt" label="${tool.name} on ${on_string}: Stats">


The tool outputs different file formats? (csv,tsv is fine, but why bed file)?

SaimMomin12 · 2025-12-01T14:19:00Z

tools/haltools/hal_halStats.xml

+        </test>
+    </tests>
+    <help><![CDATA[
+halStats lets you inspect the contents of a HAL database and pull out essential details about genomes, sequences, coverage, identity, and alignment structure. It provides quick checks on genome relationships, segment layout, metadata, and sequence level stats. 


Maybe a bit more info on what are the inputs, outputs, etc

Niklas M. added 3 commits November 24, 2025 16:02

halStats Added

9713939

Add first tool halStats

2d5c926

Removed old hal folder

7e2af1a

SaimMomin12 reviewed Nov 25, 2025

View reviewed changes

SaimMomin12 assigned Maed0x Nov 25, 2025

SaimMomin12 added this to Galaxy Tool Developers SIG Board Nov 25, 2025

github-project-automation bot moved this to Planned in Galaxy Tool Developers SIG Board Nov 25, 2025

SaimMomin12 moved this from Planned to In progress in Galaxy Tool Developers SIG Board Nov 25, 2025

SaimMomin12 reviewed Nov 26, 2025

View reviewed changes

Updates to halStats

15fbbed

Maed0x requested a review from SaimMomin12 November 27, 2025 13:14

SaimMomin12 reviewed Dec 1, 2025

View reviewed changes

		long_description: \|
		A set of tools to for manipulating HAL alignment files

	description_template: "Wrapper for hal tool suite: {{ tool_name }}"
	description_template: "Wrapper for haltools suite: {{ tool_name }}"

		@@ -0,0 +1,238 @@
		<tool id="hal_halstats" name="HAL halStats" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="25.0">

	<data name="out_file_csv" format="tabular" from_work_dir="stats.csv" label="${tool.name} on ${on_string}: CSV Stats">
	<data name="out_file_csv" format="csv" from_work_dir="stats.csv" label="${tool.name} on ${on_string}: CSV Stats">

	<tool id="hal_halstats" name="HAL halStats" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="25.0">
	<tool id="hal_halstats" name="halStats" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="25.0">

		@@ -0,0 +1,238 @@
		<tool id="hal_halstats" name="HAL halStats" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="25.0">
		<description>retrieves basic statistics from a hal file</description>

	<description>retrieves basic statistics from a hal file</description>
	<description>retrieve basic statistics from a HAL file</description>

	<param name="input_hal" type="data" format="hal" label="Input hal file to analyze" optional="false"/>
	<param name="input_hal" type="data" format="hal" label="Input hal file to analyze"/>

	<xml name="params_inputFormat">
	<xml name="hal_backend_format">

	<expand macro="params_inputFormat"/>
	<expand macro="hal_backend_format"/>

New Tool addition: Haltools #7488

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New Tool addition: Haltools #7488

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Maed0x commented Nov 25, 2025

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