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Update Binette #6716

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merged 3 commits into from
Feb 8, 2025
Merged

Update Binette #6716

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d61f03a
change binette wrappe to work in a workflow
SantaMcCloud Feb 3, 2025
35f274a
Update binette.xml
SantaMcCloud Feb 3, 2025
f605637
revert changes
SantaMcCloud Feb 6, 2025
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34 changes: 26 additions & 8 deletions tools/binette/binette.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
<description>Binning refinement tool</description>
<macros>
<token name="@TOOL_VERSION@">1.0.5</token>
<token name="@VERSION_SUFFIX@">0</token>
<token name="@VERSION_SUFFIX@">1</token>
<token name="@PROFILE@">24.1</token>
</macros>
<requirements>
Expand All @@ -12,8 +12,8 @@
<![CDATA[
mkdir -p 'input' 'output' &&

#for $i, $file in enumerate($contig2bin_tables):
ln -s '$file' 'input/bin_table_${i}.tsv' &&
#for $i, $file in enumerate($contig2bin):
ln -s '$file.contig2bin_tables' 'input/bin_table_${i}.tsv' &&
#end for

ln -s '$contigs' 'input_contigs.fasta' &&
Expand Down Expand Up @@ -44,8 +44,10 @@
]]>
</command>
<inputs>
<param argument="--contig2bin_tables" type="data" multiple="true" min="2" format="tabular" label="Input contig table"
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<repeat name="contig2bin" title="Contig tables" min="2">
<param argument="--contig2bin_tables" type="data" format="tabular" label="Input contig table"
help="Input at least 2 different contig tables. Look into the help section at the bottom for more information!"/>
</repeat>
<param argument="--contigs" type="data" format="fasta,fasta.gz" label="Input contig file"/>
<param argument="--proteins" type="data" format="fasta,fasta.gz" optional="true" label="Input FASTA file in Prodigal format (>contigID_geneID)"
help="If this file is provided all predicted genes contained in this file will be skipped. A example for this format is in the help section"/>
Expand All @@ -63,7 +65,7 @@
help="When a CheckM2 diamond database should be used download and input it here."/>
</when>
<when value="cached">
<param name="datamanager" type="select" label="Select reference genome" help="Checkm2 Diamond database">
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<param name="datamanager" type="select" label="Select Diamond DB" help="Checkm2 Diamond database">
<options from_data_table="checkm2">
<filter type="sort_by" column="2"/>
</options>
Expand All @@ -83,7 +85,15 @@
</outputs>
<tests>
<test expect_num_outputs="3">
<param name="contig2bin_tables" ftype="tabular" value="A.binning,B.binning,C.binning"/>
<repeat name="contig2bin">
<param name="contig2bin_tables" ftype="tabular" value="A.binning"/>
</repeat>
<repeat name="contig2bin">
<param name="contig2bin_tables" ftype="tabular" value="C.binning"/>
</repeat>
<repeat name="contig2bin">
<param name="contig2bin_tables" ftype="tabular" value="B.binning"/>
</repeat>
<param name="contigs" value="all_contig.fasta.gz" ftype="fasta.gz"/>
<param name="min_completeness" value="5"/>
<param name="contamination_weight" value="0"/>
Expand All @@ -101,7 +111,15 @@
<output_collection name="bins" count="4"/>
</test>
<test expect_num_outputs="3">
<param name="contig2bin_tables" ftype="tabular" value="A.binning,B.binning,C.binning"/>
<repeat name="contig2bin">
<param name="contig2bin_tables" ftype="tabular" value="A.binning"/>
</repeat>
<repeat name="contig2bin">
<param name="contig2bin_tables" ftype="tabular" value="C.binning"/>
</repeat>
<repeat name="contig2bin">
<param name="contig2bin_tables" ftype="tabular" value="B.binning"/>
</repeat>
<param name="contigs" value="all_contig.fasta.gz" ftype="fasta.gz"/>
<param name="min_completeness" value="40"/>
<param name="contamination_weight" value="2"/>
Expand Down Expand Up @@ -185,4 +203,4 @@
<citations>
<citation type="doi">10.21105/joss.06782</citation>
</citations>
</tool>
</tool>