Updating tools/fastga from version 1.3.1 to 1.5 (#7882)

Author: RZ9082

tools/fastga/fastga.xml

@@ -19,7 +19,7 @@
                 '${output_settings.out.cs_string}'
             #end if
         #end if
-        $use_soft_mask
+        $disable_soft_mask
         $use_sym_seeding
         -f${adaptive_seed_count_cutoff}
         -c${minimum_seed_coverage}
@@ -36,8 +36,8 @@
             help="FASTA or gzip-compressed FASTA file of a high-quality genome assembly (Q40 or better). The order of inputs can affect results—FastGA is not commutative unless symmetric seeding (-S) is enabled."/>
         <param name="input2" type="data" label="FASTA sequence 2" format="fasta,fasta.gz"
             help="FASTA or gzip-compressed FASTA file of a high-quality genome assembly (Q40 or better). The order of inputs can affect results—FastGA is not commutative unless symmetric seeding (-S) is enabled."/>
-        <param argument="-M" name="use_soft_mask" type="boolean" label="Use soft mask information if available" checked="false" truevalue="-M" falsevalue=""
-            help="Use soft-masked regions (lowercase nucleotides) encoded in the genome index to guide alignment. Helps reduce spurious alignments in repeat-rich genomes by down-weighting repetitive regions during seed finding."/>
+        <param argument="-N" name="disable_soft_mask" type="boolean" label="Do not soft mask" checked="false" truevalue="-N" falsevalue="" 
+            help="Ignore masking information encoded in the genome index. By default, masking from the GIX is applied during alignment to reduce spurious matches in repeat-rich regions."/>
         <param argument="-S" name="use_sym_seeding" type="boolean" label="Use symmetric seeding" checked="false" truevalue="-S" falsevalue=""
             help="Generate seeds from both genomes instead of only from genome 1. Makes alignment results independent of input order at the cost of extra computation time. Generally not recommended for standard use."/>
         <param argument="-f" name="adaptive_seed_count_cutoff" type="integer" label="Adaptive seed count cutoff" value="10" min="0" max="255"
@@ -123,7 +123,7 @@
         <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="disable_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"/>

tools/fastga/fastga_macros.xml

@@ -1,6 +1,6 @@
 <macros>
-    <token name="@TOOL_VERSION@">1.3.1</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@TOOL_VERSION@">1.5</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">25.0</token>
     <xml name="requirements">
         <requirements>

tools/fastga/test-data/chrM_HGvMM.paf

@@ -1,2 +1,2 @@
-chrM	16569	596	3105	+	chrM	16299	18	2547	2209	5038	255	dv:f:.1195	df:i:620
-chrM	16569	3112	16020	+	chrM	16299	2553	15420	11087	25775	255	dv:f:.1410	df:i:3601
+chrM	16569	596	3105	+	chrM	16299	18	2547	2209	5038	255	dv:f:0.1195	df:i:620
+chrM	16569	3112	16020	+	chrM	16299	2553	15420	11087	25775	255	dv:f:0.1410	df:i:3601