FastGA Aligner by as042 · Pull Request #7666 · galaxyproject/tools-iuc

as042 · 2026-02-09T23:08:44Z

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)

There are two labels that allow to ignore specific (false positive) tool linter errors:

skip-version-check: Use it if only a subset of the tools has been updated in a suite.
skip-url-check: Use it if github CI sees 403 errors, but the URLs work.

SaimMomin12

@as042 Some preliminary comments inline. Please also add the missing .shed.yml file.

SaimMomin12 · 2026-02-10T08:35:32Z

tools/fastga/fastga.xml

@@ -0,0 +1,99 @@
+<tool id="fastga" name="FastGA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5" profile="21.05">


Suggested change

<tool id="fastga" name="FastGA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5" profile="21.05">

<tool id="fastga" name="FastGA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">

@Profile@ token can be introduced here

SaimMomin12 · 2026-02-10T08:35:44Z

tools/fastga/fastga.xml

@@ -0,0 +1,99 @@
+<tool id="fastga" name="FastGA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5" profile="21.05">
+    <description>: align long sequences</description>


Suggested change

<description>: align long sequences</description>

<description>align long sequences</description>

SaimMomin12 · 2026-02-10T08:36:00Z

tools/fastga/fastga.xml

+    <requirements>
+    	<requirement type="package" version="@TOOL_VERSION@">fastga</requirement>
+    </requirements>


This can go to macros

SaimMomin12 · 2026-02-10T08:39:00Z

tools/fastga/fastga.xml

+        </data>
+    </outputs>
+    <tests>
+        <test>


Suggested change

<test>

<test expect_num_outputs="1">

SaimMomin12 · 2026-02-10T08:39:11Z

tools/fastga/fastga.xml

+            <param name="output_format" value="paf"/>
+            <output name="output1" file="chrM_HGvMM.paf"/>
+        </test>
+        <test>


Suggested change

<test>

<test expect_num_outputs="1">

SaimMomin12 · 2026-02-10T08:39:28Z

tools/fastga/fastga.xml

+            <param name="input1" value="chrM_hg38.fa.gz"/>
+            <param name="input2" value="chrM_mm39.fa.gz"/>
+            <param name="output_format" value="paf"/>
+            <output name="output1" file="chrM_HGvMM.paf"/>


Can we also check the ftype here?

SaimMomin12 · 2026-02-10T08:39:35Z

tools/fastga/fastga.xml

+            <param name="input1" value="chrM_hg38.fa.gz"/>
+            <param name="input2" value="chrM_mm39.fa.gz"/>
+            <param name="output_format" value="psl"/>
+            <output name="output1" file="chrM_HGvMM.psl"/>


SaimMomin12 · 2026-02-10T08:40:03Z

tools/fastga/fastga_macros.xml

@@ -0,0 +1,4 @@
+<macros>
+    <token name="@TOOL_VERSION@">1.3.1</token>
+    <token name="@VERSION_SUFFIX@">0</token>


Suggested change

<token name="@VERSION_SUFFIX@">0</token>

<token name="@VERSION_SUFFIX@">0</token>

<token name="@PROFILE@">25.0</token>

SaimMomin12 · 2026-02-10T08:41:25Z

tools/fastga/fastga.xml

+      -v: Verbose mode, output statistics as proceed.
+      -k: Keep any generated .1gdb's and .gix's.
+      -M: Use soft mask information if available.
+      -S: Use symmetric seeding (not recommended).
+      -L: Output log to specified file.
+      -T: Number of threads to use.
+      -P: Directory to use for temporary files.
+
+      -paf: Stream PAF output
+        -pafx: Stream PAF output with CIGAR string with X's
+        -pafm: Stream PAF output with CIGAR string with ='s
+        -pafs: Stream PAF output with CS string in short form
+        -pafS: Stream PAF output with CS string in long form
+      -psl: Stream PSL output
+      -1: Generate 1-code output to specified file
+
+      -f: adaptive seed count cutoff
+      -c: minimum seed chain coverage in both genomes
+      -s: threshold for starting a new seed chain
+      -l: minimum alignment length
+      -i: minimum alignment identity
+      -S: seed adaptamers from both genomes


I think many of these parameters are not part of the wrapper. Do you plan to include them? If not, this can be removed. More help about input, outputs and what the tool does could be beneficial here.

SaimMomin12 · 2026-02-10T08:41:39Z

tools/fastga/fastga.xml

+    <citations>
+        <citation type="bibtex">
+@misc{githubFASTGA,
+  author = {Gene Myers and Chenxi Zhou},
+  year = {2025},
+  title = {FASTGA},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {https://github.com/thegenemyers/FASTGA},
+}</citation>
+    </citations>


This can also go to macros

I just want to push my changes, and git says I have to pull to do that first.

bernt-matthias · 2026-02-12T05:51:00Z

tools/fastga/fastga.xml

+    <command detect_errors="exit_code"><![CDATA[
+        ## FastGA directly string matches the file extensions
+        ## symlinks are used to bypass that restriction
+        ln -s "$input1" "input1.${input1.ext}" &&


Please use single quotes

bernt-matthias · 2026-02-12T05:54:30Z

tools/fastga/fastga.xml

+        ln -s "$input1" "input1.${input1.ext}" &&
+        ln -s "$input2" "input2.${input2.ext}" &&
+        FastGA 
+        #if str( $output_format ) == "paf":


You could just $output_format and use -paf and -psl as values of the select

bernt-matthias · 2026-02-12T05:56:31Z

tools/fastga/fastga.xml

+        "input1.${input1.ext}" "input2.${input2.ext}" > output
+    ]]></command>
+    <inputs>
+        <param type="data" name="input1" format="gix,1gdb,fa,fna,fasta,fa.gz,fna.gz,fasta.gz,1seq"/>


It's just fasta and fasta.gz.

Eher are gix, 1gdb and 1seq?

Please add label to inputs

bernt-matthias · 2026-02-12T05:57:23Z

tools/fastga/fastga.xml

+    <inputs>
+        <param type="data" name="input1" format="gix,1gdb,fa,fna,fasta,fa.gz,fna.gz,fasta.gz,1seq"/>
+        <param type="data" name="input2" format="gix,1gdb,fa,fna,fasta,fa.gz,fna.gz,fasta.gz,1seq"/>
+        <param name="output_format" type="select" display="radio" label="Specify the output format">


Avoid radio

as042 and others added 2 commits February 9, 2026 18:04

first

c965d44

Merge branch 'galaxyproject:main' into FastGA

297c154

SaimMomin12 reviewed Feb 10, 2026

View reviewed changes

as042 and others added 3 commits February 11, 2026 13:33

xml edits

f0a86c2

Merge branch 'galaxyproject:main' into FastGA

13eacb6

Merge branch 'FastGA' of github.com:as042/tools-iuc into FastGA

64564d2

I just want to push my changes, and git says I have to pull to do that first.

bernt-matthias reviewed Feb 12, 2026

View reviewed changes

more options

986cb69

		@@ -0,0 +1,99 @@
		<tool id="fastga" name="FastGA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5" profile="21.05">

		@@ -0,0 +1,99 @@
		<tool id="fastga" name="FastGA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5" profile="21.05">
		<description>: align long sequences</description>

	<description>: align long sequences</description>
	<description>align long sequences</description>

	<token name="@VERSION_SUFFIX@">0</token>
	<token name="@VERSION_SUFFIX@">0</token>
	<token name="@PROFILE@">25.0</token>

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as042 commented Feb 9, 2026 •

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