# HG changeset patch
# User iuc
# Date 1761639327 0
# Node ID 8673617e7e092762742e801a257db17fc30d8c40
# Parent  9de6b5e570df84a813c24198a0e464039df9d3a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6

diff -r 9de6b5e570df -r 8673617e7e09 macros.xml
--- a/macros.xml	Tue Mar 25 15:52:22 2025 +0000
+++ b/macros.xml	Tue Oct 28 08:15:27 2025 +0000
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">2.0.2</token>
+    <token name="@TOOL_VERSION@">2.1.0</token>
     <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">21.01</token>
     <xml name="biotools">
@@ -48,6 +48,23 @@
             </when>
         </conditional>
     </xml>
+    <xml name="mode_fasta_strobealign">
+        <conditional name="mode">
+            <expand macro="mode_select"/>
+            <when value="single">
+                <expand macro="input-fasta-single"/>
+                <expand macro="input-txt"/>
+            </when>
+            <when value="co">
+                <expand macro="input-fasta-single"/>
+                <expand macro="input-txt"/>
+            </when>
+            <when value="multi">
+                <expand macro="input-fasta-multi"/>
+                <expand macro="input-txt"/>
+            </when>
+        </conditional>
+    </xml>
     <xml name="mode_select">
         <param name="select" type="select" label="Binning mode">
             <option value="single" selected="true">Single sample binning (each sample is assembled and binned independently)</option>
@@ -55,8 +72,14 @@
             <option value="multi">Multi-sample binning (multiple samples are assembled and binned individually, but information from multiple samples is used together)</option>
         </param>
     </xml>
+    <xml name="bam_or_strobealign">
+        <param name="align_select" type="select" label="Use bam or strobealign abundance files?" help="Strobealign abundance files can only be used when samples used in binning above or equal 5">
+            <option value="bam">BAM</option>
+            <option value="txt">Strobealign-aemb file(s)</option>
+        </param>
+    </xml>
     <xml name="input-fasta-single">
-        <param argument="--input-fasta" type="data" format="fasta,fasta.gz" label="Contig sequences"/>
+        <param argument="--input-fasta" type="data" format="fasta,fasta.gz,fasta.bz2" label="Contig sequences"/>
     </xml>
     <xml name="input-fasta-multi">
         <conditional name="multi_fasta">
@@ -65,11 +88,11 @@
                 <option value="multi">1 contig file per sample</option>
             </param>
             <when value="concatenated">
-                <param argument="--input-fasta" type="data" format="fasta,fasta.gz" label="Combined contig sequences"/>
+                <param argument="--input-fasta" type="data" format="fasta,fasta.gz,fasta.bz2" label="Combined contig sequences"/>
                 <expand macro="separator"/>
             </when>
             <when value="multi">
-                <param argument="--input-fasta" type="data" multiple="true" format="fasta,fasta.gz" label="Contig sequences"/>
+                <param argument="--input-fasta" type="data" multiple="true" format="fasta,fasta.gz,fasta.bz2" label="Contig sequences"/>
                 <expand macro="concat_min_len"/>
             </when>
         </conditional>
@@ -78,39 +101,27 @@
         <param name="min_len" type="integer" min="0" value="0" label="Minimal length for contigs to be kept"/>
     </xml>
     <token name="@SINGLE_FASTA_FILES@"><![CDATA[
-#if $input_fasta.ext.endswith(".gz")
-gunzip -c '$input_fasta' > 'contigs.fasta' &&
-#else
-ln -s '$input_fasta' 'contigs.fasta' &&
-#end if
+ln -s '$input_fasta' 'contigs.$input_fasta.ext' &&
     ]]></token>
     <token name="@FASTA_FILES@"><![CDATA[
 #if $mode.select == 'single' or $mode.select == 'co'
-    #if $mode.input_fasta.ext.endswith(".gz")
-gunzip -c '$mode.input_fasta' > 'contigs.fasta' &&
-    #else
-ln -s '$mode.input_fasta' 'contigs.fasta' &&
-    #end if
+ln -s '$input_fasta' 'contigs.$input_fasta.ext' &&
 #else
     #if $mode.multi_fasta.select == 'concatenated'
-        #if $mode.multi_fasta.input_fasta.ext.endswith(".gz")
-gunzip -c '$mode.multi_fasta.input_fasta' > 'contigs.fasta' &&
-        #else
-ln -s '$mode.multi_fasta.input_fasta' 'contigs.fasta' &&
-        #end if
+ln -s '$input_fasta' 'contigs.$input_fasta.ext' &&
 #set $separator = $mode.multi_fasta.separator
     #else
         #for $e in $mode.multi_fasta.input_fasta
-            #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($e.element_identifier))
-            #if $e.ext.endswith(".gz")
-gunzip -c '$e' > '${identifier}.fasta' &&
-            #else
-ln -s '$e' '${identifier}.fasta' &&
-            #end if
+            #set $identifier = re.sub('[^\s\w\-]', '_', str($e.element_identifier))
+ln -s '$e' '${identifier}.$e.ext' &&
         #end for
 #set $separator = ':'
 SemiBin2 concatenate_fasta
-    --input-fasta *.fasta
+    --input-fasta
+    #for $e in $mode.multi_fasta.input_fasta
+        #set $identifier = re.sub('[^\s\w\-]', '_', str($e.element_identifier))
+        '${identifier}.$e.ext'
+    #end for
     --output 'output'
     --separator '$separator'
     --compression none
@@ -129,17 +140,27 @@
     <xml name="input-bam-multi">
         <param argument="--input-bam" type="data" format="bam" multiple="true" label="Read mapping to the contigs" help="One file per sample, sorted BAM files"/>
     </xml>
+    <!-- Strobealign files -->
+    <xml name="input-txt">
+        <param argument="--abundance" type="data" format="txt" label="Read mapping to the contigs" multiple="true" help="Strobealign abundance files"/>
+    </xml>
     <token name="@BAM_FILES@"><![CDATA[
 #if $mode.select == 'single'
-#set $identifier = re.sub('[^\s\w\-\\.]', '_', str($input_bam.element_identifier))
-ln -s '$input_bam' '${identifier}.bam' &&
+#set $identifier = re.sub('[^\s\w\-]', '_', str($mode.input_bam.element_identifier))
+ln -s '$mode.input_bam' '${identifier}.bam' &&
 #else
-    #for $e in $input_bam
-        #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($e.element_identifier))
+    #for $e in $mode.input_bam
+        #set $identifier = re.sub('[^\s\w\-]', '_', str($e.element_identifier))
 ln -s '$e' '${identifier}.bam' &&
     #end for
 #end if
     ]]></token>
+    <token name="@STROBEALIGN_FILES@"><![CDATA[
+#for $e in $mode.align_select.abundance
+    #set $identifier = re.sub('[^\s\w\-]', '_', str($e.element_identifier))
+    ln -s '$e' '${identifier}.txt' &&
+#end for
+    ]]></token>
     <xml name="ref_select_cannot">
         <param name="select" type="select" label="Reference database">
             <option value="cached">Cached database</option>
@@ -257,7 +278,6 @@
         <param argument="--orf-finder" type="select" label="ORF finder used to estimate the number of bins">
             <option value="fast-naive" selected="true">Fast-Naive</option>
             <option value="prodigal">Prodigal</option>
-            <option value="fraggenescan">Fraggenescan</option>
         </param>
     </xml>
     <xml name="max-node">
@@ -293,58 +313,153 @@
     </xml>
     <xml name="data_output_single">
         <data name="single_data" format="csv" from_work_dir="output/data.csv" label="${tool.name} on ${on_string}: Training data">
-            <filter>mode["select"]=="single" or mode["select"]=="co"</filter>
+            <filter>input_type_select['mode']['select']=="single" or input_type_select['mode']['select']=="co"</filter>
         </data>
         <data name="single_data_split" format="csv" from_work_dir="output/data_split.csv" label="${tool.name} on ${on_string}: Split training data">
-            <filter>mode["select"]=="single" or mode["select"]=="co"</filter>
+            <filter>input_type_select['mode']['select']=="single" or input_type_select['mode']['select']=="co"</filter>
         </data>
     </xml>
-    <xml name="data_output_multi">
+    <xml name="data_output_multi"> 
         <collection name="multi_data" type="list" label="${tool.name} on ${on_string}: Training data per sample">
-            <filter>mode["select"]=="multi"</filter>
+            <filter>input_type_select['mode']['select']=="multi"</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
         </collection>
         <collection name="multi_data_split" type="list" label="${tool.name} on ${on_string}: Split training data per sample">
-            <filter>mode["select"]=="multi"</filter>
+            <filter>input_type_select['mode']['select']=="multi"</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_split.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
         </collection>
     </xml>
     <xml name="generate_sequence_features_extra_outputs">
         <data name="single_cov" format="csv" from_work_dir="output/*_data_cov.csv" label="${tool.name} on ${on_string}: Coverage">
-            <filter>mode["select"]=="single" and extra_output and "coverage" in extra_output</filter>
+            <filter>input_type_select['mode']['select']=="single" and extra_output and "coverage" in extra_output</filter>
+            <filter>input_type_select['input_type']=="bam"</filter>
         </data>
         <data name="single_split_cov" format="csv" from_work_dir="output/*_data_split_cov.csv" label="${tool.name} on ${on_string}: Coverage (split data)">
-            <filter>mode["select"]=="single" and extra_output and "coverage" in extra_output</filter>
+            <filter>input_type_select['mode']['select']=="single" and extra_output and "coverage" in extra_output</filter>
+            <filter>input_type_select['input_type']=="bam"</filter>
         </data>
         <collection name="co_cov" type="list" label="${tool.name} on ${on_string}: Coverage (co_cov)">
-            <filter>mode["select"]=="co" and extra_output and "coverage" in extra_output</filter>
+            <filter>input_type_select['mode']['select']=="co" and extra_output and "coverage" in extra_output</filter>
+            <filter>input_type_select['input_type']=="bam"</filter>
             <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_cov\.csv" format="csv" directory="output/" />
         </collection>
         <collection name="co_split_cov" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample">
-            <filter>mode["select"]=="co" and extra_output and "coverage" in extra_output</filter>
+            <filter>input_type_select['mode']['select']=="co" and extra_output and "coverage" in extra_output</filter>
+            <filter>input_type_select['input_type']=="bam"</filter>
             <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_split_cov\.csv" format="csv" directory="output/" />
         </collection>
+        <data name="cov_txt" label="${tool.name} on ${on_string}: Coverage (split data) per sample (aemb)" from_work_dir="output/cov_split.csv" format="csv">
+            <filter>input_type_select['mode']['select']=="single" or input_type_select['mode']['select']=="co" and extra_output and "coverage" in extra_output</filter>
+            <filter>input_type_select['input_type']=="txt"</filter>
+        </data>
+        <data name="co_cov_txt" label="${tool.name} on ${on_string}: Coverage (aemb)" format="csv" from_work_dir="output/cov.csv">
+            <filter>input_type_select['mode']['select']=="single" or input_type_select['mode']['select']=="co" and extra_output and "coverage" in extra_output</filter>
+            <filter>input_type_select['input_type']=="txt"</filter>
+        </data>
+        <collection name="multi_split_cov_txt" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample (multi_split_cov) (aemb)">
+            <filter>input_type_select['mode']['select']=="multi" and extra_output and "coverage" in extra_output</filter>
+            <filter>input_type_select['input_type']=="txt"</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_split_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
+        </collection>
         <collection name="multi_cov" type="list" label="${tool.name} on ${on_string}: Coverage (multi_cov)">
-            <filter>mode["select"]=="multi" and extra_output and "coverage" in extra_output</filter>
-            <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_cov.csv" format="csv" directory="output/samples/" />
+            <filter>input_type_select['mode']['select']=="multi" and extra_output and "coverage" in extra_output</filter>
+            <filter>input_type_select['input_type']=="bam"</filter>
+            <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_cov.csv" format="csv" directory="output/samples/" recurse="true"/>
         </collection>
         <collection name="multi_cov_sample" type="list" label="${tool.name} on ${on_string}: Coverage per sample">
-            <filter>mode["select"]=="multi" and extra_output and "coverage" in extra_output</filter>
+            <filter>input_type_select['mode']['select']=="multi" and extra_output and "coverage" in extra_output</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
         </collection>
         <collection name="multi_split_cov" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample (multi_split_cov)">
-            <filter>mode["select"]=="multi" and extra_output and "coverage" in extra_output</filter>
+            <filter>input_type_select['mode']['select']=="multi" and extra_output and "coverage" in extra_output</filter>
+            <filter>input_type_select['input_type']=="bam"</filter>
             <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_split_cov.csv" format="csv" directory="output/samples/" />
         </collection>
         <collection name="multi_split_cov_sample" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample (multi_split_cov_sample)">
-            <filter>mode["select"]=="multi" and extra_output and "coverage" in extra_output</filter>
-            <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_split_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
+            <filter>input_type_select['mode']['select']=="multi" and extra_output and "coverage" in extra_output</filter>
+            <filter>input_type_select['input_type']=="bam"</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_split_cov.csv" format="csv" directory="output/samples/" match_relative_path="true" recurse="true"/>
         </collection>
         <collection name="multi_contigs" type="list" label="${tool.name} on ${on_string}: Contigs">
-            <filter>mode["select"]=="multi" and extra_output and "contigs" in extra_output</filter>
+            <filter>input_type_select['mode']['select']=="multi" and extra_output and "contigs" in extra_output</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/samples/" />
         </collection>
-        
+    </xml>
+    <xml name="generate_sequence_features_extra_outputs_main">
+    <!-- Single -->
+        <data name="single_cov" format="csv" from_work_dir="output/*_data_cov.csv" label="${tool.name} on ${on_string}: Coverage">
+            <filter>mode['select']=="single" and extra_output and "coverage" in extra_output</filter>
+        </data>
+        <data name="single_split_cov" format="csv" from_work_dir="output/*_data_split_cov.csv" label="${tool.name} on ${on_string}: Coverage (split data)">
+            <filter>mode['select']=="single" and extra_output and "coverage" in extra_output</filter>
+        </data>
+    <!-- Bam co aligned -->
+        <collection name="co_cov_bam" type="list" label="${tool.name} on ${on_string}: Coverage (co_cov)">
+            <filter>mode['select']=="co" and extra_output and "coverage" in extra_output</filter>
+            <filter>mode['align_select']</filter>
+            <filter>mode['align_select']['align_select']=="bam"</filter>
+            <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_cov\.csv" format="csv" directory="output/" />
+        </collection>
+        <collection name="co_split_cov_bam" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample">
+            <filter>mode['select']=="co" and extra_output and "coverage" in extra_output</filter>
+            <filter>mode['align_select']</filter>
+            <filter>mode['align_select']['align_select']=="bam"</filter>
+            <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_split_cov\.csv" format="csv" directory="output/" />
+        </collection>
+
+    <!-- Bam Multi aligned -->
+        <collection name="multi_cov_bam" type="list" label="${tool.name} on ${on_string}: Coverage (multi_cov)">
+            <filter>mode['select']=="multi" and extra_output and "coverage" in extra_output</filter>
+            <filter>mode['align_select']</filter>
+            <filter>mode['align_select']['align_select']=="bam"</filter>
+            <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_cov.csv" format="csv" directory="output/samples/" />
+        </collection>
+        <collection name="multi_cov_sample_bam" type="list" label="${tool.name} on ${on_string}: Coverage per sample">
+            <filter>mode['select']=="multi" and extra_output and "coverage" in extra_output</filter>
+            <filter>mode['align_select']</filter>
+            <filter>mode['align_select']['align_select']=="bam"</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
+        </collection>
+        <collection name="multi_split_cov_bam" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample (multi_split_cov)">
+            <filter>mode['select']=="multi" and extra_output and "coverage" in extra_output</filter>
+            <filter>mode['align_select']</filter>
+            <filter>mode['align_select']['align_select']=="bam"</filter>
+            <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_split_cov.csv" format="csv" directory="output/samples/" />
+        </collection>
+        <collection name="multi_split_cov_sample_bam" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample (multi_split_cov_sample)">
+            <filter>mode['select']=="multi" and extra_output and "coverage" in extra_output</filter>
+            <filter>mode['align_select']</filter>
+            <filter>mode['align_select']['align_select']=="bam"</filter>
+            <discover_datasets pattern=".*\.bam_(?P&lt;designation&gt;.*)_data_split_cov.csv" format="csv" directory="output/samples/" />
+        </collection>
+        <collection name="multi_contigs" type="list" label="${tool.name} on ${on_string}: Contigs">
+            <filter>mode['select']=="multi" and extra_output and "contigs" in extra_output</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/samples/" />
+        </collection>
+        <!-- Txt co aligned -->
+        <data name="co_split_cov_txt" label="${tool.name} on ${on_string}: Coverage (split data) per sample (aemb)" from_work_dir="output/cov_split.csv" format="csv">
+            <filter>mode['select']=="co" and extra_output and "coverage" in extra_output</filter>
+            <filter>mode['align_select']</filter>
+            <filter>mode['align_select']['align_select']=="txt"</filter>
+        </data>
+        <data name="co_cov_txt" label="${tool.name} on ${on_string}: Coverage (aemb)" format="csv" from_work_dir="output/cov.csv">
+            <filter>mode['select']=="co" and extra_output and "coverage" in extra_output</filter>
+            <filter>mode['align_select']</filter>
+            <filter>mode['align_select']['align_select']=="txt"</filter>
+        </data>
+        <!-- Txt multi aligned -->
+        <collection name="multi_cov_txt" type="list" label="${tool.name} on ${on_string}: Coverage per sample (aemb)">
+            <filter>mode['select']=="multi" and extra_output and "coverage" in extra_output</filter>
+            <filter>mode['align_select']</filter>
+            <filter>mode['align_select']['align_select'] =="txt"</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
+        </collection>
+        <collection name="multi_split_cov_txt" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample (multi_split_cov) (aemb)">
+            <filter>mode['select']=="multi" and extra_output and "coverage" in extra_output</filter>
+            <filter>mode['align_select']</filter>
+            <filter>mode['align_select']['align_select']=="txt"</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_split_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
+        </collection>
     </xml>
     <xml name="train_output">
         <data name="model" format="h5" from_work_dir="output/model.h5" label="${tool.name} on ${on_string}: Semi-supervised deep learning model" />
@@ -353,34 +468,37 @@
         <data name="cannot" format="txt" from_work_dir="output/cannot/cannot.txt" label="${tool.name} on ${on_string}: Cannot-link constraints" />
     </xml>
     <token name="@HELP_HEADER@"><![CDATA[
+
 What it does
 ============
 
 SemiBin is a Semi-supervised siamese neural network for metagenomic binning
-
-]]></token>
+    ]]></token>
     <token name="@HELP_INPUT_FASTA@"><![CDATA[
 - Contigs in fasta for 1 or several samples from single or co-assembly
-]]></token>
+    ]]></token>
     <token name="@HELP_INPUT_BAM@"><![CDATA[
 - BAM with reads mapping to the contigs
-]]></token>
+    ]]></token>
+    <token name="@HELP_INPUT_STROBEALIGN@"><![CDATA[
+- TXT alignment files that are the output of strobealign-aemb
+    ]]></token>
     <token name="@HELP_CANNOT@"><![CDATA[
 - Cannot-link constraints
-]]></token>
+    ]]></token>
     <token name="@HELP_DATA@"><![CDATA[
 - Training data and split training data for the model
-]]></token>
+    ]]></token>
     <token name="@HELP_MODEL@"><![CDATA[
 - Semi-supervised deep learning model
-]]></token>
+    ]]></token>
     <token name="@HELP_BINS@"><![CDATA[
 - Reconstructed bins after reclustering
 - Reconstructed bins before reclustering
-]]></token>
+    ]]></token>
     <xml name="citations">
         <citations>
             <citation type="doi">10.1038/s41467-022-29843-y</citation>
         </citations>
     </xml>
-</macros>
+</macros>
\ No newline at end of file
diff -r 9de6b5e570df -r 8673617e7e09 semibin.xml
--- a/semibin.xml	Tue Mar 25 15:52:22 2025 +0000
+++ b/semibin.xml	Tue Oct 28 08:15:27 2025 +0000
@@ -10,7 +10,15 @@
     <expand macro="version"/>
     <command detect_errors="exit_code"><![CDATA[
 #import re
-@BAM_FILES@
+#if $mode.select != "single":
+    #if $mode.align_select.align_select == "bam":
+        @BAM_FILES@
+    #else:
+        @STROBEALIGN_FILES@
+    #end if
+#else:
+    @BAM_FILES@
+#end if
 @FASTA_FILES@
 SemiBin2
 #if $mode.select == 'single' or $mode.select == 'co'
@@ -37,8 +45,16 @@
         #end for
     #end if
 #end if
-    --input-fasta 'contigs.fasta'
-    --input-bam *.bam
+    --input-fasta 'contigs.$input_fasta.ext'
+    #if $mode.select == "single":
+        --input-bam *.bam
+    #else:
+        #if $mode.align_select.align_select == "bam":
+            --input-bam *.bam
+        #else:
+            -a *.txt
+        #end if
+    #end if
     --output 'output'
     --cannot-name 'cannot'
     @MIN_LEN@
@@ -68,18 +84,34 @@
             <expand macro="mode_select"/>
             <when value="single">
                 <expand macro="input-fasta-single"/>
-                <expand macro="input-bam-single"/>
+                    <expand macro="input-bam-single"/>
                 <expand macro="ref-single"/>
                 <expand macro="environment"/>
             </when>
             <when value="co">
                 <expand macro="input-fasta-single"/>
-                <expand macro="input-bam-multi"/>
+                <conditional name="align_select">
+                    <expand macro="bam_or_strobealign"/>
+                    <when value="bam">
+                        <expand macro="input-bam-multi"/>
+                    </when>
+                    <when value="txt">
+                        <expand macro="input-txt"/>
+                    </when>
+                </conditional>
                 <expand macro="ref-single"/>
             </when>
             <when value="multi">
                 <expand macro="input-fasta-multi"/>
-                <expand macro="input-bam-multi"/>
+                <conditional name="align_select">
+                    <expand macro="bam_or_strobealign"/>
+                    <when value="bam">
+                        <expand macro="input-bam-multi"/>
+                    </when>
+                    <when value="txt">
+                        <expand macro="input-txt"/>
+                    </when>
+                </conditional>
                 <expand macro="ref-multi"/>
             </when>
         </conditional>
@@ -107,42 +139,42 @@
     </inputs>
     <outputs>
         <collection name="output_pre_recluster_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins before reclustering">
-            <filter>mode["select"]!="multi" and extra_output and "pre_reclustering_bins" in extra_output</filter>
+            <filter>mode['select']!="multi" and extra_output and "pre_reclustering_bins" in extra_output</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/output_prerecluster_bins"/>
         </collection>
         <collection name="output_after_recluster_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins after reclustering">
-            <filter>mode["select"]!="multi" and extra_output and "pre_reclustering_bins" in extra_output</filter>
+            <filter>mode['select']!="multi" and extra_output and "pre_reclustering_bins" in extra_output</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/output_recluster_bins"/>
         </collection>
         <collection name="output_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins">
-            <filter>mode["select"]!="multi" and not "pre_reclustering_bins" in extra_output</filter>
+            <filter>mode['select']!="multi" and not "pre_reclustering_bins" in extra_output</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/output_bins"/>
         </collection>
         <collection name="multi_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins before reclustering (multi_bins)">
-            <filter>mode["select"]=="multi"</filter>
+            <filter>mode['select']=="multi"</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/bins"/>
         </collection>
         <data name="single_data" format="csv" from_work_dir="output/data.csv" label="${tool.name} on ${on_string}: Training data">
-            <filter>(mode["select"]=="single" or mode["select"]=="co") and extra_output and "data" in extra_output</filter>
+            <filter>(mode['select']=="single" or mode['select']=="co") and extra_output and "data" in extra_output</filter>
         </data>
         <data name="single_data_split" format="csv" from_work_dir="output/data_split.csv" label="${tool.name} on ${on_string}: Split training data">
-            <filter>(mode["select"]=="single" or mode["select"]=="co") and extra_output and "data" in extra_output</filter>
+            <filter>(mode['select']=="single" or mode['select']=="co") and extra_output and "data" in extra_output</filter>
         </data>
         <collection name="multi_data" type="list" label="${tool.name} on ${on_string}: Training data per sample">
-            <filter>mode["select"]=="multi" and extra_output and "data" in extra_output</filter>
+            <filter>mode['select']=="multi" and extra_output and "data" in extra_output</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
         </collection>
         <collection name="multi_data_split" type="list" label="${tool.name} on ${on_string}: Split training data per sample">
-            <filter>mode["select"]=="multi" and extra_output and "data" in extra_output</filter>
+            <filter>mode['select']=="multi" and extra_output and "data" in extra_output</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.*)\/data_split.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>
         </collection>
-        <expand macro="generate_sequence_features_extra_outputs"/>
+        <expand macro="generate_sequence_features_extra_outputs_main"/>
     </outputs>
     <tests>
         <test expect_num_outputs="5">
             <conditional name="mode">
                 <param name="select" value="single"/>
-                <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
+                <param name="input_fasta" ftype="fasta.gz" value="input_single.fasta.gz"/>
                 <param name="input_bam" ftype="bam" value="input_single.bam"/>
                 <conditional name="ref">
                     <param name="select" value="taxonomy"/>
@@ -166,7 +198,6 @@
                 <param name="minfasta_kbs" value="200"/>
             </section>
             <param name="extra_output" value="data,coverage,contigs"/>
-            <output_collection name="output_bins" count="0"/>
             <output name="single_data" ftype="csv">
                 <assert_contents>
                     <has_text text="g1k_0"/>
@@ -194,7 +225,7 @@
         <test expect_num_outputs="5">
             <conditional name="mode">
                 <param name="select" value="single"/>
-                <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
+                <param name="input_fasta" ftype="fasta.bz2" value="input_single.fasta.bz2"/>
                 <param name="input_bam" ftype="bam" value="input_single.bam"/>
                 <conditional name="ref">
                     <param name="select" value="ml"/>
@@ -217,7 +248,6 @@
                 <param name="minfasta_kbs" value="200"/>
             </section>
             <param name="extra_output" value="data,coverage,contigs"/>
-            <output_collection name="output_bins" count="0"/>
             <output name="single_data" ftype="csv">
                 <assert_contents>
                     <has_text text="g1k_0"/>
@@ -246,7 +276,10 @@
             <conditional name="mode">
                 <param name="select" value="co"/>
                 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
-                <param name="input_bam" ftype="bam" value="input_coassembly_sorted1.bam,input_coassembly_sorted2.bam,input_coassembly_sorted3.bam,input_coassembly_sorted4.bam,input_coassembly_sorted5.bam"/>
+                <conditional name="align_select">
+                    <param name="align_select" value="bam"/>
+                    <param name="input_bam" ftype="bam" value="input_coassembly_sorted1.bam,input_coassembly_sorted2.bam,input_coassembly_sorted3.bam,input_coassembly_sorted4.bam,input_coassembly_sorted5.bam"/>
+                </conditional>
                 <conditional name="ref">
                     <param name="select" value="ml"/>
                 </conditional>
@@ -267,8 +300,7 @@
                 <param name="minfasta_kbs" value="200"/>
             </section>
             <param name="extra_output" value="coverage"/>
-            <output_collection name="output_bins" count="0"/>
-            <output_collection name="co_cov" count="5">
+            <output_collection name="co_cov_bam" count="5">
                 <element name="0" ftype="csv">
                     <assert_contents>
                         <has_text text="g1k_0"/>
@@ -288,7 +320,7 @@
                     </assert_contents>
                 </element>
             </output_collection>
-            <output_collection name="co_split_cov" count="5">
+            <output_collection name="co_split_cov_bam" count="5">
                 <element name="0" ftype="csv">
                     <assert_contents>
                         <has_text text="g1k_0_1"/>
@@ -313,7 +345,10 @@
             <conditional name="mode">
                 <param name="select" value="co"/>
                 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
-                <param name="input_bam" ftype="bam" value="input_coassembly_sorted1.bam,input_coassembly_sorted2.bam,input_coassembly_sorted3.bam,input_coassembly_sorted4.bam,input_coassembly_sorted5.bam"/>
+                <conditional name="align_select">
+                    <param name="align_select" value="bam"/>
+                    <param name="input_bam" ftype="bam" value="input_coassembly_sorted1.bam,input_coassembly_sorted2.bam,input_coassembly_sorted3.bam,input_coassembly_sorted4.bam,input_coassembly_sorted5.bam"/>
+                </conditional>
                 <conditional name="ref">
                     <param name="select" value="taxonomy"/>
                     <param name="taxonomy_annotation_table" value="taxonomy.tsv"/>
@@ -335,8 +370,7 @@
                 <param name="minfasta_kbs" value="200"/>
             </section>
             <param name="extra_output" value="coverage"/>
-            <output_collection name="output_bins" count="0"/>
-            <output_collection name="co_cov" count="5">
+            <output_collection name="co_cov_bam" count="5">
                 <element name="0" ftype="csv">
                     <assert_contents>
                         <has_text text="g1k_0"/>
@@ -356,7 +390,7 @@
                     </assert_contents>
                 </element>
             </output_collection>
-            <output_collection name="co_split_cov" count="5">
+            <output_collection name="co_split_cov_bam" count="5">
                 <element name="0" ftype="csv">
                     <assert_contents>
                         <has_text text="g1k_0_1"/>
@@ -381,7 +415,10 @@
             <conditional name="mode">
                 <param name="select" value="co"/>
                 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
-                <param name="input_bam" ftype="bam" value="input_coassembly_sorted1.bam,input_coassembly_sorted2.bam,input_coassembly_sorted3.bam,input_coassembly_sorted4.bam,input_coassembly_sorted5.bam"/>
+                <conditional name="align_select">
+                    <param name="align_select" value="bam"/>
+                    <param name="input_bam" ftype="bam" value="input_coassembly_sorted1.bam,input_coassembly_sorted2.bam,input_coassembly_sorted3.bam,input_coassembly_sorted4.bam,input_coassembly_sorted5.bam"/>
+                </conditional>
                 <conditional name="ref">
                     <param name="select" value="taxonomy"/>
                     <param name="taxonomy_annotation_table" value="taxonomy.tsv"/>
@@ -391,8 +428,11 @@
                 <param name="method" value="ratio"/>
                 <param name="ratio" value="0.05"/>
             </conditional>
-            <param name="orf_finder" value="fraggenescan"/>
+            <param name="orf_finder" value="fast-naive"/>
             <param name="random_seed" value="0"/>
+            <section name="annot">
+                <param name="ml_threshold" value="0"/>
+            </section>
             <section name="training">
                 <param name="epoches" value="20"/>
                 <param name="batch_size" value="2048"/>
@@ -403,8 +443,7 @@
                 <param name="minfasta_kbs" value="200"/>
             </section>
             <param name="extra_output" value="coverage"/>
-            <output_collection name="output_bins" count="0"/>
-            <output_collection name="co_cov" count="5">
+            <output_collection name="co_cov_bam" count="5">
                 <element name="0" ftype="csv">
                     <assert_contents>
                         <has_text text="g1k_0"/>
@@ -424,7 +463,7 @@
                     </assert_contents>
                 </element>
             </output_collection>
-            <output_collection name="co_split_cov" count="5">
+            <output_collection name="co_split_cov_bam" count="5">
                 <element name="0" ftype="csv">
                     <assert_contents>
                         <has_text text="g1k_0_1"/>
@@ -459,8 +498,11 @@
                 <param name="method" value="ratio"/>
                 <param name="ratio" value="0.05"/>
             </conditional>
-            <param name="orf_finder" value="fraggenescan"/>
+            <param name="orf_finder" value="fast-naive"/>
             <param name="random_seed" value="0"/>
+            <section name="annot">
+                <param name="ml_threshold" value="0"/>
+            </section>
             <section name="training">
                 <param name="epoches" value="20"/>
                 <param name="batch_size" value="2048"/>
@@ -470,13 +512,6 @@
                 <param name="max_edges" value="200"/>
                 <param name="minfasta_kbs" value="200"/>
             </section>
-            <output_collection name="output_bins" count="1">
-                <element name="SemiBin_30" ftype="fasta">
-                    <assert_contents>
-                        <has_text text=">g3k_0"/>
-                    </assert_contents>
-                </element>
-            </output_collection>
         </test>
         <test expect_num_outputs="2">
             <conditional name="mode">
@@ -492,8 +527,11 @@
                 <param name="method" value="ratio"/>
                 <param name="ratio" value="0.05"/>
             </conditional>
-            <param name="orf_finder" value="fraggenescan"/>
+            <param name="orf_finder" value="fast-naive"/>
             <param name="random_seed" value="0"/>
+            <section name="annot">
+                <param name="ml_threshold" value="0"/>
+            </section>
             <section name="training">
                 <param name="epoches" value="20"/>
                 <param name="batch_size" value="2048"/>
@@ -504,7 +542,7 @@
                 <param name="minfasta_kbs" value="200"/>
             </section>
             <param name="extra_output" value="pre_reclustering_bins"/>
-            <output_collection name="output_pre_recluster_bins" count="3">
+            <output_collection name="output_pre_recluster_bins">
                 <element name="SemiBin_0" ftype="fasta">
                     <assert_contents>    
                         <has_text text="g1k_0"/>
@@ -536,7 +574,10 @@
                     <param name="select" value="concatenated"/>
                     <param name="input_fasta" ftype="fasta" value="input_multi.fasta.gz"/>
                 </conditional>
-                <param name="input_bam" ftype="bam" value="input_multi_sorted1.bam,input_multi_sorted2.bam,input_multi_sorted3.bam,input_multi_sorted4.bam,input_multi_sorted5.bam,input_multi_sorted6.bam,input_multi_sorted7.bam,input_multi_sorted8.bam,input_multi_sorted9.bam,input_multi_sorted10.bam"/>
+                <conditional name="align_select">
+                    <param name="align_select" value="bam"/>
+                    <param name="input_bam" ftype="bam" value="input_multi_sorted1.bam,input_multi_sorted2.bam,input_multi_sorted3.bam,input_multi_sorted4.bam,input_multi_sorted5.bam,input_multi_sorted6.bam,input_multi_sorted7.bam,input_multi_sorted8.bam,input_multi_sorted9.bam,input_multi_sorted10.bam"/>
+                </conditional>
                 <conditional name="ref">
                     <param name="select" value="taxonomy"/>
                     <param name="taxonomy_annotation_table" value="taxonomy.tsv,taxonomy_2.tsv,taxonomy_3.tsv,taxonomy_4.tsv,taxonomy_5.tsv,taxonomy_6.tsv,taxonomy_7.tsv,taxonomy_8.tsv,taxonomy_9.tsv,taxonomy_10.tsv"/>
@@ -546,7 +587,7 @@
                 <param name="method" value="ratio"/>
                 <param name="ratio" value="0.05"/>
             </conditional>
-            <param name="orf_finder" value="fraggenescan"/>
+            <param name="orf_finder" value="fast-naive"/>
             <param name="random_seed" value="0"/>
             <section name="training">
                 <param name="epoches" value="20"/>
@@ -573,29 +614,29 @@
                     </assert_contents>
                 </element>
             </output_collection>
-            <output_collection name="multi_cov" count="10">
+            <output_collection name="multi_cov_bam" count="10">
                 <element name="8" ftype="csv">
                     <assert_contents>
                         <has_text text="S1:g1k_5,"/>
                     </assert_contents>
                 </element>
             </output_collection>
-            <output_collection name="multi_cov_sample" count="10">
+            <output_collection name="multi_cov_sample_bam" count="10">
                 <element name="S8" ftype="csv">
                     <assert_contents>
                         <has_text text="g1k_3"/>
                     </assert_contents>
                 </element>
             </output_collection>
-            <output_collection name="multi_split_cov" count="10">
+            <output_collection name="multi_split_cov_bam" count="10">
                 <element name="8" ftype="csv">
                     <assert_contents>
                         <has_text text="S1:g1k_5_1,0."/>
                     </assert_contents>
                 </element>
             </output_collection>
-            <output_collection name="multi_split_cov_sample" count="10">
-                <element name="S8" ftype="csv">
+            <output_collection name="multi_split_cov_sample_bam" count="10">
+                <element name="8" ftype="csv">
                     <assert_contents>
                         <has_text text="g1k_3_1"/>
                     </assert_contents>
@@ -609,8 +650,116 @@
                 </element>
             </output_collection>
         </test>
+        <test expect_num_outputs="6">
+            <conditional name="mode">
+                <param name="select" value="co"/>
+                <param name="input_fasta" ftype="fasta" value="input_multi.fasta.gz"/>
+                <conditional name="align_select">
+                    <param name="align_select" value="txt"/>
+                    <param name="abundance" ftype="txt" value="strobealign_1.txt,strobealign_2.txt,strobealign_3.txt,strobealign_4.txt,strobealign_5.txt"/>
+                </conditional>
+                <conditional name="ref">
+                    <param name="select" value="taxonomy"/>
+                    <param name="taxonomy_annotation_table" value="taxonomy.tsv"/>
+                </conditional>
+            </conditional>
+            <conditional name="min_len">
+                <param name="method" value="ratio"/>
+                <param name="ratio" value="0.05"/>
+            </conditional>
+            <param name="orf_finder" value="fast-naive"/>
+            <param name="random_seed" value="0"/>
+            <section name="annot">
+                <param name="ml_threshold" value="0"/>
+            </section>
+            <section name="training">
+                <param name="epoches" value="20"/>
+                <param name="batch_size" value="2048"/>
+            </section>
+            <section name="bin">
+                <param name="max_node" value="0.15"/>
+                <param name="max_edges" value="20"/>
+                <param name="minfasta_kbs" value="20"/>
+            </section>
+            <param name="extra_output" value="data,coverage,contigs,pre_reclustering_bins"/>
+        </test> 
+        <test expect_num_outputs="6">
+            <conditional name="mode">
+                <param name="select" value="multi"/>
+                <conditional name="multi_fasta">
+                    <param name="select" value="concatenated"/>
+                    <param name="input_fasta" ftype="fasta" value="input_multi.fasta.gz"/>
+                </conditional>
+                <conditional name="align_select">
+                    <param name="align_select" value="txt"/>
+                    <param name="abundance" ftype="txt" value="strobealign_1.txt,strobealign_2.txt,strobealign_3.txt,strobealign_4.txt,strobealign_5.txt"/>
+                </conditional>
+                <conditional name="ref">
+                    <param name="select" value="taxonomy"/>
+                    <param name="taxonomy_annotation_table" value="taxonomy.tsv,taxonomy_2.tsv,taxonomy_3.tsv,taxonomy_4.tsv,taxonomy_5.tsv,taxonomy_6.tsv,taxonomy_7.tsv,taxonomy_8.tsv,taxonomy_9.tsv,taxonomy_10.tsv"/>
+                </conditional>
+            </conditional>
+            <conditional name="min_len">
+                <param name="method" value="ratio"/>
+                <param name="ratio" value="0.05"/>
+            </conditional>
+            <param name="orf_finder" value="fast-naive"/>
+            <param name="random_seed" value="0"/>
+            <section name="annot">
+                <param name="ml_threshold" value="0"/>
+            </section>
+            <section name="training">
+                <param name="epoches" value="20"/>
+                <param name="batch_size" value="2048"/>
+            </section>
+            <section name="bin">
+                <param name="max_node" value="0.15"/>
+                <param name="max_edges" value="30"/>
+                <param name="minfasta_kbs" value="30"/>
+            </section>
+            <param name="extra_output" value="data,coverage,contigs"/>
+            <output_collection name="multi_bins" count="10"/>
+            <output_collection name="multi_data" count="10">
+                <element name="S8" ftype="csv">
+                    <assert_contents>
+                        <has_text text="g1k_0,"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <output_collection name="multi_data_split" count="10">
+                <element name="S8" ftype="csv">
+                    <assert_contents>
+                        <has_text text="g1k_0_1,"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <output_collection name="multi_cov_txt" count="10">
+                <element name="S8" ftype="csv">
+                    <assert_contents>
+                        <has_text text="g1k_5,"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <output_collection name="multi_split_cov_txt" count="10">
+                <element name="S8" ftype="csv">
+                    <assert_contents>
+                        <has_text text="g1k_5_1,1."/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <output_collection name="multi_contigs" count="10">
+                <element name="S8" ftype="fasta">
+                    <assert_contents>
+                        <has_text text=">g1k_0"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>        
     </tests>
     <help><![CDATA[
+**Please note that there is a known issue with Semibin2 where results may be inconsistent across runs on different, despite a set seed. This may cause issues with reproducibility.**
+For more information, see this [issue]{https://github.com/BigDataBiology/SemiBin/issues/186} on their repository: https://github.com/BigDataBiology/SemiBin/issues/186
+
 @HELP_HEADER@
 
 Inputs
diff -r 9de6b5e570df -r 8673617e7e09 test-data/input_multi_sorted10_naming.bam
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diff -r 9de6b5e570df -r 8673617e7e09 test-data/input_multi_sorted1_naming.bam
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diff -r 9de6b5e570df -r 8673617e7e09 test-data/input_multi_sorted2_naming.bam
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diff -r 9de6b5e570df -r 8673617e7e09 test-data/input_multi_sorted3_naming.bam
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diff -r 9de6b5e570df -r 8673617e7e09 test-data/input_multi_sorted4_naming.bam
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diff -r 9de6b5e570df -r 8673617e7e09 test-data/input_multi_sorted5_naming.bam
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diff -r 9de6b5e570df -r 8673617e7e09 test-data/input_multi_sorted6_naming.bam
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diff -r 9de6b5e570df -r 8673617e7e09 test-data/input_multi_sorted7_naming.bam
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diff -r 9de6b5e570df -r 8673617e7e09 test-data/input_multi_sorted8_naming.bam
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diff -r 9de6b5e570df -r 8673617e7e09 test-data/input_multi_sorted9_naming.bam
Binary file test-data/input_multi_sorted9_naming.bam has changed
diff -r 9de6b5e570df -r 8673617e7e09 test-data/input_single.fasta.bz2
Binary file test-data/input_single.fasta.bz2 has changed
diff -r 9de6b5e570df -r 8673617e7e09 test-data/input_single.fasta.gz
Binary file test-data/input_single.fasta.gz has changed
diff -r 9de6b5e570df -r 8673617e7e09 test-data/strobealign_1.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/strobealign_1.txt	Tue Oct 28 08:15:27 2025 +0000
@@ -0,0 +1,400 @@
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diff -r 9de6b5e570df -r 8673617e7e09 test-data/strobealign_2.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/strobealign_2.txt	Tue Oct 28 08:15:27 2025 +0000
@@ -0,0 +1,400 @@
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diff -r 9de6b5e570df -r 8673617e7e09 test-data/strobealign_3.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/strobealign_3.txt	Tue Oct 28 08:15:27 2025 +0000
@@ -0,0 +1,400 @@
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diff -r 9de6b5e570df -r 8673617e7e09 test-data/strobealign_4.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/strobealign_4.txt	Tue Oct 28 08:15:27 2025 +0000
@@ -0,0 +1,400 @@
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diff -r 9de6b5e570df -r 8673617e7e09 test-data/strobealign_5.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/strobealign_5.txt	Tue Oct 28 08:15:27 2025 +0000
@@ -0,0 +1,400 @@
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