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Add fallback to Maxbin2 #8015

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87add53
Add fallback to Maxbin2
SantaMcCloud May 24, 2026
d89ac44
remove lint skipping and fix linting
SantaMcCloud May 24, 2026
efa8d9d
bump version
SantaMcCloud May 24, 2026
827cd41
revert commandline
SantaMcCloud May 28, 2026
d887504
add fallback logic
SantaMcCloud May 28, 2026
9db1e6f
add assert_stdout
SantaMcCloud May 28, 2026
b9f0c36
Merge branch 'update_maxbin' of https://github.com/SantaMcCloud/tools…
SantaMcCloud May 28, 2026
1b0da11
use tee to split stream
SantaMcCloud May 28, 2026
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1 change: 0 additions & 1 deletion tools/maxbin2/.lint_skip
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248 changes: 166 additions & 82 deletions tools/maxbin2/maxbin2.xml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
<tool id="maxbin2" name="MaxBin2" version="@MAXBIN_VERSION@+galaxy6">
<tool id="maxbin2" name="MaxBin2" version="@MAXBIN_VERSION@+galaxy7">
<description>clusters metagenomic contigs into bins</description>
<macros>
<token name="@MAXBIN_VERSION@">2.2.7</token>
Expand All @@ -24,82 +24,120 @@
</requirements>
<version_command><![CDATA[run_MaxBin.pl -version | head -n 1]]></version_command>
<command detect_errors="exit_code"><![CDATA[
## generate read or abundance files
#import re
#if $assembly.inputs.type == 'reads'
#if $assembly.type == 'individual'
## uncompress .gz reads files if necessary
#set $e = $assembly.inputs.reads
#set $identifier = re.sub('[^\w\-\\.]', '_', str($e.element_identifier))
#if $e.ext.endswith(".gz")
gunzip -c '$e' > '$identifier' &&
echo '$identifier' >> reads_list &&
#else
ln -s '$e' '$identifier' &&
echo '$identifier' >> reads_list &&
## generate read or abundance files
#import re
#if $assembly.inputs.type == 'reads'
#if $assembly.type == 'individual'
## uncompress .gz reads files if necessary
#set $e = $assembly.inputs.reads
#set $identifier = re.sub('[^\w\-\\.]', '_', str($e.element_identifier))
#if $e.ext.endswith(".gz")
gunzip -c '$e' > '$identifier' &&
echo '$identifier' >> reads_list &&
#else
ln -s '$e' '$identifier' &&
echo '$identifier' >> reads_list &&
#end if
#else
#for $i, $r in enumerate($assembly.inputs.reads)
#if $r
#set $identifier = re.sub('[^\w\-\\.]', '_', str($r.element_identifier))
#set $newid = $identifier + '_' + str($i)
#if $r.ext.endswith(".gz")
gunzip -c '$r' > '$newid' &&
echo '$newid' >> reads_list &&
#else
ln -s '$r' '$newid' &&
echo '$newid' >> reads_list &&
#end if
#end if
#end for
#end if
#else
#for $i, $r in enumerate($assembly.inputs.reads)
#if $r
#set $identifier = re.sub('[^\w\-\\.]', '_', str($r.element_identifier))
#set $newid = $identifier + '_' + str($i)
#if $r.ext.endswith(".gz")
gunzip -c '$r' > '$newid' &&
echo '$newid' >> reads_list &&
#else
ln -s '$r' '$newid' &&
echo '$newid' >> reads_list &&
#else if $assembly.inputs.type == 'abund'
#if $assembly.type == 'individual'
echo '$assembly.inputs.abund' >> abund_list &&
#else
#for $a in $assembly.inputs.abund
#if $a
echo '$a' >> abund_list &&
#end if
#end if
#end for
#end for
#end if
#end if
#else if $assembly.inputs.type == 'abund'
#if $assembly.type == 'individual'
echo '$assembly.inputs.abund' >> abund_list &&
#else
#for $a in $assembly.inputs.abund
#if $a
echo '$a' >> abund_list &&
#end if
#end for

## in case of reassembly the IBDA out and err is appended
## to differentiate this a header is added also befor the
## MaxBin2 outputs
#if $assembly.inputs.type == 'reads' and $assembly.inputs.reassembly != ""
echo "==== MaxBin2 stdout ====" &&
echo "==== MaxBin2 stderr ====" 1>&2 &&
#end if
#end if

## in case of reassembly the IBDA out and err is appended
## to differentiate this a header is added also befor the
## MaxBin2 outputs
#if $assembly.inputs.type == 'reads' and $assembly.inputs.reassembly != ""
echo "==== MaxBin2 stdout ====" &&
echo "==== MaxBin2 stderr ====" 1>&2 &&
#end if
(run_MaxBin.pl
-contig '$contig'
-out out
#if $assembly.inputs.type == 'reads':
-reads_list reads_list
$assembly.inputs.reassembly
#else if $assembly.inputs.type == 'abund':
-abund_list abund_list
#end if
-min_contig_length $adv.min_contig_length
-max_iteration $adv.max_iteration
-prob_threshold $adv.prob_threshold
$output.plotmarker
-markerset $output.markerset
-thread \${GALAXY_SLOTS:-1}
> maxbin.stdout 2> maxbin.stderr
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||
(
if grep -qi "cannot be binned" maxbin.stdout maxbin.stderr; then

echo "MaxBin2 could not bin dataset. Creating empty fallback outputs." ;
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touch out.summary ;
touch out.noclass ;
touch out.tooshort ;
touch out.001.fasta ;
touch out.log ;
touch out.marker ;
touch out.abund1 ;

#if $output.plotmarker
printf "%s\n" "%PDF-1.4" "%%EOF" > out.marker.pdf ;
#end if

mkdir empty_markers ;
tar -czf out.marker_of_each_bin.tar.gz empty_markers ;

#if $assembly.inputs.type == 'reads'
#if $assembly.inputs.reassembly != ""
mkdir -p out.reassem ;
touch out.reassem/out.001.fasta ;
touch out.reassem/out.reads.001 ;
touch out.reassem/out.reads.noclass ;
touch out.reassem/N50.txt ;
#end if
#end if

run_MaxBin.pl
-contig '$contig'
-out out
#if $assembly.inputs.type == 'reads':
-reads_list reads_list
$assembly.inputs.reassembly
#else if $assembly.inputs.type == 'abund':
-abund_list abund_list
#end if
-min_contig_length $adv.min_contig_length
-max_iteration $adv.max_iteration
-prob_threshold $adv.prob_threshold
$output.plotmarker
-markerset $output.markerset
-thread \${GALAXY_SLOTS:-1}
gzip -cd out.marker_of_each_bin.tar.gz | tar -xf - ;
exit 0 ;

&& gzip -cd out.marker_of_each_bin.tar.gz | tar -xf -
fi
))
&& cat maxbin.stdout
&& cat maxbin.stderr >&2
&& gzip -cd out.marker_of_each_bin.tar.gz | tar -xf -

## redirect the idba out and err file content to stdout and err
## since this is also wanted in case the error case ';' is used here to
## separate commands
#if $assembly.inputs.type == 'reads' and $assembly.inputs.reassembly != ""
; echo "==== IDBA stdout ===="
&& if [[ -f out.idba.out ]]; then cat out.idba.out; fi
&& echo "==== IDBA stderr ====" 1>&2
&& if [[ -f out.idba.err ]]; then cat out.idba.err 1>&2; fi
#end if
## redirect the idba out and err file content to stdout and err
## since this is also wanted in case the error case ';' is used here to
## separate commands
#if $assembly.inputs.type == 'reads' and $assembly.inputs.reassembly != ""
; echo "==== IDBA stdout ===="
&& if [[ -f out.idba.out ]]; then cat out.idba.out; fi
&& echo "==== IDBA stderr ====" 1>&2
&& if [[ -f out.idba.err ]]; then cat out.idba.err 1>&2; fi
#end if
]]></command>
<inputs>
<expand macro="contig"/>
Expand Down Expand Up @@ -200,7 +238,7 @@ run_MaxBin.pl
<param name="type" value="reads"/>
<param name="reads" value="interleavedPE_unmapped_Sample3_small.fasta" ftype="fasta"/>
<param name="output_abundances" value="false"/>
<param name="reassembly" value=""/>
<param name="reassembly" value="false"/>
</conditional>
</conditional>
<section name="adv">
Expand All @@ -209,7 +247,7 @@ run_MaxBin.pl
<param name="prob_threshold" value="0.5"/>
</section>
<section name="output">
<param name="plotmarker" value=""/>
<param name="plotmarker" value="false"/>
<param name="marker" value="false"/>
<param name="markers" value="false" />
<param name="log" value="false"/>
Expand All @@ -232,7 +270,7 @@ run_MaxBin.pl
<param name="type" value="reads"/>
<param name="reads" value="interleavedPE_unmapped_Sample3_small.fasta,interleavedPE_unmapped_Sample3_small.fasta" ftype="fasta"/>
<param name="output_abundances" value="true"/>
<param name="reassembly" value=""/>
<param name="reassembly" value="false"/>
</conditional>
</conditional>
<section name="adv">
Expand Down Expand Up @@ -289,7 +327,7 @@ run_MaxBin.pl
<param name="prob_threshold" value="0.95"/>
</section>
<section name="output">
<param name="plotmarker" value="-plotmarker"/>
<param name="plotmarker" value="true"/>
<param name="marker" value="false"/>
<param name="markers" value="false" />
<param name="log" value="false"/>
Expand All @@ -313,7 +351,7 @@ run_MaxBin.pl
<param name="type" value="reads"/>
<param name="reads" value="interleavedPE_unmapped_Sample3_small.fasta" ftype="fasta"/>
<param name="output_abundances" value="false"/>
<param name="reassembly" value="-reassembly"/>
<param name="reassembly" value="true"/>
</conditional>
</conditional>
<section name="adv">
Expand All @@ -322,7 +360,7 @@ run_MaxBin.pl
<param name="prob_threshold" value="0.5"/>
</section>
<section name="output">
<param name="plotmarker" value=""/>
<param name="plotmarker" value="false"/>
<param name="marker" value="false"/>
<param name="markers" value="false" />
<param name="log" value="false"/>
Expand Down Expand Up @@ -371,7 +409,7 @@ run_MaxBin.pl
<param name="type" value="reads"/>
<param name="reads" value="test4_reads.fastqsanger" ftype="fastqsanger"/>
<param name="output_abundances" value="false"/>
<param name="reassembly" value=""/>
<param name="reassembly" value="false"/>
</conditional>
</conditional>
<section name="adv">
Expand All @@ -380,7 +418,7 @@ run_MaxBin.pl
<param name="prob_threshold" value="0.5"/>
</section>
<section name="output">
<param name="plotmarker" value=""/>
<param name="plotmarker" value="false"/>
<param name="marker" value="false"/>
<param name="markers" value="false" />
<param name="log" value="false"/>
Expand All @@ -403,7 +441,7 @@ run_MaxBin.pl
<param name="type" value="reads"/>
<param name="reads" value="test4_reads 2.fastqsanger" ftype="fastqsanger"/>
<param name="output_abundances" value="false"/>
<param name="reassembly" value=""/>
<param name="reassembly" value="false"/>
</conditional>
</conditional>
<section name="adv">
Expand All @@ -412,7 +450,7 @@ run_MaxBin.pl
<param name="prob_threshold" value="0.5"/>
</section>
<section name="output">
<param name="plotmarker" value=""/>
<param name="plotmarker" value="false"/>
<param name="marker" value="false"/>
<param name="markers" value="false" />
<param name="log" value="false"/>
Expand All @@ -435,7 +473,7 @@ run_MaxBin.pl
<param name="type" value="reads"/>
<param name="reads" value="test4_reads.fastqsanger.gz" ftype="fastqsanger.gz"/>
<param name="output_abundances" value="false"/>
<param name="reassembly" value=""/>
<param name="reassembly" value="false"/>
</conditional>
</conditional>
<section name="adv">
Expand All @@ -444,7 +482,7 @@ run_MaxBin.pl
<param name="prob_threshold" value="0.5"/>
</section>
<section name="output">
<param name="plotmarker" value=""/>
<param name="plotmarker" value="false"/>
<param name="marker" value="false"/>
<param name="markers" value="false" />
<param name="log" value="false"/>
Expand All @@ -467,7 +505,7 @@ run_MaxBin.pl
<param name="type" value="reads"/>
<param name="reads" value="test4_reads.fastqsanger.gz,test4_reads.fastqsanger.gz" ftype="fasta"/>
<param name="output_abundances" value="true"/>
<param name="reassembly" value=""/>
<param name="reassembly" value="false"/>
</conditional>
</conditional>
<section name="adv">
Expand Down Expand Up @@ -517,6 +555,52 @@ run_MaxBin.pl
</element>
</output_collection>
</test>
<test expect_num_outputs="4">
<param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" />
<conditional name="assembly">
<param name="type" value="individual"/>
<conditional name="inputs">
<param name="type" value="reads"/>
<param name="reads" value="interleavedPE_unmapped_Sample3_small.fasta" ftype="fasta"/>
<param name="output_abundances" value="false"/>
<param name="reassembly" value="false"/>
</conditional>
</conditional>
<section name="adv">
<param name="min_contig_length" value="10000"/>
<param name="max_iteration" value="50"/>
<param name="prob_threshold" value="0.5"/>
</section>
<section name="output">
<param name="plotmarker" value="false"/>
<param name="marker" value="false"/>
<param name="markers" value="false" />
<param name="log" value="false"/>
<param name="markerset" value="107"/>
</section>
<output_collection name="bins" type="list" count="1">
<element name="001" ftype="fasta">
<assert_contents>
<has_size value="0"/>
</assert_contents>
</element>
</output_collection>
<output name="summary" ftype="tabular">
<assert_contents>
<has_size value="0"/>
</assert_contents>
</output>
<output name="noclass" ftype="fasta">
<assert_contents>
<has_size value="0"/>
</assert_contents>
</output>
<output name="toshort" ftype="fasta">
<assert_contents>
<has_size value="704488"/>
</assert_contents>
</output>
</test>
</tests>
<help><![CDATA[
MaxBin is a software that clusters metagenomic contigs into different bins,
Expand Down
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