FastGA Aligner #7666
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FastGA Aligner #7666
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SaimMomin12
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Feb 10, 2026
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@as042 Some preliminary comments inline. Please also add the missing .shed.yml file.
tools/fastga/fastga.xml
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| <tool id="fastga" name="FastGA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5" profile="21.05"> | |||
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| <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
tools/fastga/fastga.xml
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| <tool id="fastga" name="FastGA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5" profile="21.05"> | |||
| <description>: align long sequences</description> | |||
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| <description>: align long sequences</description> | |
| <description>align long sequences</description> |
tools/fastga/fastga.xml
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| <requirements> | ||
| <requirement type="package" version="@TOOL_VERSION@">fastga</requirement> | ||
| </requirements> |
tools/fastga/fastga.xml
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| </data> | ||
| </outputs> | ||
| <tests> | ||
| <test> |
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| <test> | |
| <test expect_num_outputs="1"> |
tools/fastga/fastga.xml
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| <param name="output_format" value="paf"/> | ||
| <output name="output1" file="chrM_HGvMM.paf"/> | ||
| </test> | ||
| <test> |
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| <test> | |
| <test expect_num_outputs="1"> |
tools/fastga/fastga.xml
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| <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"/> |
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Can we also check the ftype here?
tools/fastga/fastga.xml
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| <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"/> |
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| <macros> | |||
| <token name="@TOOL_VERSION@">1.3.1</token> | |||
| <token name="@VERSION_SUFFIX@">0</token> | |||
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| <token name="@VERSION_SUFFIX@">0</token> | |
| <token name="@VERSION_SUFFIX@">0</token> | |
| <token name="@PROFILE@">25.0</token> |
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| -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. | ||
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| -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 | ||
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| -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 |
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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.
tools/fastga/fastga.xml
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| <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> |
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This can also go to macros
I just want to push my changes, and git says I have to pull to do that first.
| <command detect_errors="exit_code"><
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Please use single quotes
| ln -s "$input1" "input1.${input1.ext}" && | ||
| ln -s "$input2" "input2.${input2.ext}" && | ||
| FastGA | ||
| #if str( $output_format ) == "paf": |
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You could just $output_format and use -paf and -psl as values of the select
| "input1.${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"/> |
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It's just fasta and fasta.gz.
Eher are gix, 1gdb and 1seq?
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Please add label to inputs
| <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"> |
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FOR CONTRIBUTOR:
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.