--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastga.xml	Fri Feb 20 07:47:05 2026 +0000
@@ -0,0 +1,217 @@
+<tool id="fastga" name="FastGA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>align whole genomes</description>
+    <macros>
+        <import>fastga_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <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}' &&
+        ln -s '$input2' 'input2.${input2.ext}' &&
+        FastGA
+        '${output_settings.out.format}'
+        #if str( $output_settings.out.format ) == "-paf":
+            #if str( $output_settings.out.cigar_string ) != "no":
+                '${output_settings.out.cigar_string}'
+            #end if
+            #if str( $output_settings.out.cs_string ) != "no":
+                '${output_settings.out.cs_string}'
+            #end if
+        #end if
+        $use_soft_mask
+        $use_sym_seeding
+        -f${adaptive_seed_count_cutoff}
+        -c${minimum_seed_coverage}
+        -s${new_seed_threshold}
+        -l${minimum_alignment_length}
+        -i${minimum_alignment_identity}
+        'input1.${input1.ext}' 'input2.${input2.ext}' 
+        #if str( $output_settings.out.format ) != "-1:output":
+            > output
+        #end if
+    ]]></command>
+    <inputs>
+        <param name="input1" type="data" label="FASTA sequence" format="fasta,fasta.gz"/>
+        <param name="input2" type="data" label="FASTA sequence" format="fasta,fasta.gz"/>
+        <param name="use_soft_mask" type="boolean" label="Use soft mask information if available (-M)" checked="false" truevalue="-M" falsevalue=""/>
+        <param name="use_sym_seeding" type="boolean" label="Use symmetric seeding (-S)" checked="false" truevalue="-S" falsevalue=""/>
+        <param name="adaptive_seed_count_cutoff" type="integer" label="Adaptive seed count cutoff (-f)" value="10" min="0" max="255"/>
+        <param name="minimum_seed_coverage" type="integer" label="Minimum seed chain coverage in both genomes (-c)" value="85" min="0"/>
+        <param name="new_seed_threshold" type="integer" label="Threshold for starting a new seed chain (-s)" value="1000" min="0"/>
+        <param name="minimum_alignment_length" type="integer" label="Minimum alignment length (-l)" value="100" min="0"/>
+        <param name="minimum_alignment_identity" type="float" label="Minimum alignment identity (-i)" value="0.7" min="0.55" max="0.99999999999999994"/>
+        <section name="output_settings" expanded="False" title="Output">
+            <conditional name="out">
+                <param name="format" type="select" label="Specify the output format">
+                    <option value="-paf" selected="true">paf (-paf)</option>
+                    <option value="-psl">psl (-psl)</option>
+                    <option value="-1:output">1aln (-1)</option>
+                </param>
+                <when value="-paf">
+                    <param name="cigar_string" type="select" label="Use CIGAR string?">
+                        <option value="no" selected="true">No CIGAR string</option>
+                        <option value="-pafx">CIGAR string with X's (-pafx)</option>
+                        <option value="-pafm">CIGAR string with ='s (-pafm)</option>
+                    </param>
+                    <param name="cs_string" type="select" label="Use CS string?">
+                        <option value="no" selected="true">No CS string</option>
+                        <option value="-pafs">CS string in short form (-pafs)</option>
+                        <option value="-pafS">CS string in long form (-pafS)</option>
+                    </param>
+                </when>
+                <when value="-psl"/>
+                <when value="-1:output"/>
+            </conditional>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="output" format="paf" from_work_dir="output">
+            <change_format>
+                <when input="output_settings.out.format" value="-paf" format="paf"/>
+                <when input="output_settings.out.format" value="-psl" format="psl"/>
+                <when input="output_settings.out.format" value="-1:output" format="txt"/>
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input1" value="chrM_hg38.fa.gz"/>
+            <param name="input2" value="chrM_mm39.fa.gz"/>
+            <section name="output_settings">
+                <conditional name="out">
+                    <param name="format" value="-paf"/>
+                </conditional>
+            </section>
+            <output name="output" file="chrM_HGvMM.paf" ftype="paf"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input1" value="chrM_hg38.fa.gz"/>
+            <param name="input2" value="chrM_mm39.fa.gz"/>
+            <section name="output_settings">
+                <conditional name="out">
+                    <param name="format" value="-psl"/>
+                </conditional>
+            </section>
+            <output name="output" file="chrM_HGvMM.psl" ftype="psl"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input1" value="chrM_hg38.fa.gz"/>
+            <param name="input2" value="chrM_mm39.fa.gz"/>
+            <section name="output_settings">
+                <conditional name="out">
+                    <param name="format" value="-paf"/>
+                    <param name="cigar_string" value="-pafx"/>
+                </conditional>
+            </section>
+            <output name="output" file="pafx.paf" ftype="paf"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input1" value="chrM_hg38.fa.gz"/>
+            <param name="input2" value="chrM_mm39.fa.gz"/>
+            <param name="use_soft_mask" value="True"/>
+            <param name="use_sym_seeding" value="True"/>
+            <param name="adaptive_seed_count_cutoff" value="9"/>
+            <param name="minimum_seed_coverage" value="100"/>
+            <param name="new_seed_threshold" value="750"/>
+            <param name="minimum_alignment_length" value="90"/>
+            <param name="minimum_alignment_identity" value="0.6"/>
+            <section name="output_settings">
+                <conditional name="out">
+                    <param name="format" value="-paf"/>
+                    <param name="cigar_string" value="-pafm"/>
+                    <param name="cs_string" value="-pafS"/>
+                </conditional>
+            </section>
+            <output name="output" file="pafmS_options.paf" ftype="paf"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input1" value="chrM_hg38.fa.gz"/>
+            <param name="input2" value="chrM_mm39.fa.gz"/>
+            <section name="output_settings">
+                <conditional name="out">
+                    <param name="format" value="-1:output"/>
+                </conditional>
+            </section>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+FastGA compares two high-quality genomes and outputs a ``.1aln``, ``.paf``, or ``.psl`` file containing all local alignments found.
+
+It is based on a novel adaptive seed finding algorithm as well as the first wave-based local aligner developed for daligner (2012).
+
+FastGA uses a number of temporary, hidden files such as ONEcode genome databases (.1gdb) and genome indices (.gix) to achieve its high speed and space efficiency.
+
+-----
+
+Input
+*****
+
+This tool takes two ``fasta`` or ``fasta.gz`` input files to align.
+
+It is a core assumption of FastGA that the input genomes are nearly complete and are of high quality (Q40 or better).
+
+FastGA is not commutative by default (see *Use symmetric seeding* below).
+
+-----
+
+Options
+*******
+
+    ===============================  ========  ===========  ===========================
+    **Option**                       **Flag**  **Default**  **Description**
+    -------------------------------  --------  -----------  ---------------------------
+    Use soft mask information        -M        False        Use soft-masked regions if
+                                                            present in the input FASTA
+    Use symmetric seeding            -S        False        Enables symmetric seeding
+                                                            (not recommended)
+    Adaptive seed count cutoff       -f        10           Range: 0–255
+    Minimum seed chain coverage      -c        85           Range: ≥ 0
+    Threshold for new seed chain     -s        1000         Range: ≥ 0
+    Minimum alignment length         -l        100          Range: ≥ 0
+    Minimum alignment identity       -i        0.7          Range: 0.55–<1.0
+    ===============================  ========  ===========  ===========================
+
+-----
+
+Output
+******
+
+**Output format**
+
+    ==========  ========  ===========  ===============================
+    **Format**  **Flag**  **Default**  **Notes**
+    ----------  --------  -----------  -------------------------------
+    PAF         -paf      Yes          
+    PSL         -psl      No
+    1ALN        -1        No           Output is nondeterministic
+    ==========  ========  ===========  ===============================
+
+**CIGAR string options**  
+
+(available only when output format is PAF)
+
+    ==============================  ========  ===========
+    **Option**                      **Flag**  **Default**
+    ------------------------------  --------  -----------
+    No CIGAR string                           Yes
+    CIGAR string with X's           -pafx     No
+    CIGAR string with ='s           -pafm     No
+    ==============================  ========  ===========
+
+**CS string options**  
+
+(available only when output format is PAF)
+
+    ==============================  ========  ===========
+    **Option**                      **Flag**  **Default**
+    ------------------------------  --------  -----------
+    No CS string                              Yes
+    CS string (short form)          -pafs     No
+    CS string (long form)           -pafS     No
+    ==============================  ========  ===========
+
+]]></help>
+    <expand macro="citations" />
+</tool>