Mercurial > repos > iuc > semibin_bin
changeset 2:dbf5571a8140 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 13abac83068b126399ec415141007a48c2efaa84
| author | iuc |
|---|---|
| date | Fri, 10 Nov 2023 20:49:03 +0000 |
| parents | 4d561bdc2c31 |
| children | |
| files | bin.xml macros.xml |
| diffstat | 2 files changed, 52 insertions(+), 44 deletions(-) [+] |
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--- a/bin.xml Mon Mar 27 08:24:46 2023 +0000 +++ b/bin.xml Fri Nov 10 20:49:03 2023 +0000 @@ -11,7 +11,7 @@ <command detect_errors="exit_code"><![CDATA[ #import re @FASTA_FILES@ -SemiBin bin +SemiBin2 bin --input-fasta 'contigs.fasta' --data '$data' #if $mod.select == 'history' @@ -22,10 +22,13 @@ --output 'output' --threads \${GALAXY_SLOTS:-1} --minfasta-kbs $minfasta_kbs - $no_recluster +#if $mode.select == 'single' or $mode_fasta.mode_select == 'co' + $write_pre_reclustering_bins +#end if --max-node $max_node --max-edges $max_edges --random-seed $random_seed + --compression none @MIN_LEN@ --orf-finder '$orf_finder' ]]></command> @@ -50,20 +53,20 @@ <expand macro="max-node"/> <expand macro="max-edges"/> <expand macro="minfasta-kbs"/> - <expand macro="no-recluster"/> + <expand macro="write_pre_reclustering_bins"/> </inputs> <outputs> - <collection name="output_recluster_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins after reclustering"> - <filter>not no_recluster</filter> - <discover_datasets pattern=".*?\.(?P<designation>.*).fa" format="fasta" directory="output/output_recluster_bins" /> + <collection name="output_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins after reclustering"> + <filter>not write_pre_reclustering_bins</filter> + <discover_datasets pattern="(?P<designation>.*).fa" format="fasta" directory="output/output_bins" /> </collection> - <collection name="output_prerecluster_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins before reclustering"> - <filter>not no_recluster</filter> - <discover_datasets pattern=".*?\.(?P<designation>.*).fa" format="fasta" directory="output/output_prerecluster_bins" /> + <collection name="output_recluster_bins" type="list" label="${tool.name} on ${on_string}: Reclustered bins?"> + <filter>write_pre_reclustering_bins</filter> + <discover_datasets pattern="(?P<designation>.*).fa" format="fasta" directory="output/output_recluster_bins" /> </collection> - <collection name="output_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins without reeclustering"> - <filter>no_recluster</filter> - <discover_datasets pattern=".*?\.(?P<designation>.*).fa" format="fasta" directory="output/output_bins" /> + <collection name="output_prerecluster_bins" type="list" label="${tool.name} on ${on_string}: Pre reclustered bins"> + <filter>write_pre_reclustering_bins</filter> + <discover_datasets pattern="(?P<designation>.*).fa" format="fasta" directory="output/output_prerecluster_bins" /> </collection> </outputs> <tests> @@ -86,22 +89,21 @@ <param name="max_node" value="1"/> <param name="max_edges" value="200"/> <param name="minfasta_kbs" value="200"/> - <param name="no_recluster" value="false"/> - <output_collection name="output_recluster_bins" count="0"/> + <param name="write_pre_reclustering_bins" value="true"/> <output_collection name="output_prerecluster_bins" count="3"> - <element name="0" ftype="fasta"> + <element name="SemiBin_0" ftype="fasta"> <assert_contents> <has_text text=">g1k_0"/> <has_text text=">g4k_9"/> </assert_contents> </element> - <element name="1" ftype="fasta"> + <element name="SemiBin_1" ftype="fasta"> <assert_contents> <has_text text=">g2k_0"/> <has_text text=">g2k_9"/> </assert_contents> </element> - <element name="2" ftype="fasta"> + <element name="SemiBin_2" ftype="fasta"> <assert_contents> <has_text text=">g3k_0"/> <has_text text=">g3k_9"/> @@ -128,27 +130,30 @@ <param name="max_node" value="1"/> <param name="max_edges" value="200"/> <param name="minfasta_kbs" value="200"/> - <param name="no_recluster" value="true"/> - <output_collection name="output_bins" count="3"> - <element name="0" ftype="fasta"> - <assert_contents> - <has_text text=">g1k_0"/> - <has_text text=">g4k_9"/> - </assert_contents> - </element> - <element name="1" ftype="fasta"> - <assert_contents> - <has_text text=">g2k_0"/> - <has_text text=">g2k_9"/> - </assert_contents> - </element> - <element name="2" ftype="fasta"> - <assert_contents> - <has_text text=">g3k_0"/> - <has_text text=">g3k_9"/> - </assert_contents> - </element> - </output_collection> + <param name="write_pre_reclustering_bins" value="false"/> + <output_collection name="output_bins" count="0"/> + </test> + <test expect_num_outputs="2"> + <conditional name="mode"> + <param name="select" value="single"/> + <param name="input_fasta" ftype="fasta" value="input_single.fasta"/> + </conditional> + <param name="data" ftype="csv" value="data.csv"/> + <conditional name="mod"> + <param name="select" value="history"/> + <param name="model" ftype="h5" value="model.h5"/> + </conditional> + <conditional name="min_len"> + <param name="method" value="min-len"/> + <param name="min_len" value="0" /> + </conditional> + <param name="orf_finder" value="prodigal"/> + <param name="random-seed" value="0"/> + <param name="max_node" value="1"/> + <param name="max_edges" value="200"/> + <param name="minfasta_kbs" value="200"/> + <param name="write_pre_reclustering_bins" value="true"/> + <output_collection name="output_prerecluster_bins" count="3"/> </test> </tests> <help><![CDATA[
--- a/macros.xml Mon Mar 27 08:24:46 2023 +0000 +++ b/macros.xml Fri Nov 10 20:49:03 2023 +0000 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">1.5.1</token> + <token name="@TOOL_VERSION@">2.0.2</token> <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">21.01</token> <xml name="biotools"> @@ -15,7 +15,7 @@ </requirements> </xml> <xml name="version"> - <version_command>SemiBin -v</version_command> + <version_command>SemiBin2 -v</version_command> </xml> <xml name="mode_fasta_bam"> <conditional name="mode"> @@ -109,10 +109,11 @@ #end if #end for #set $separator = ':' -SemiBin concatenate_fasta +SemiBin2 concatenate_fasta --input-fasta *.fasta --output 'output' --separator '$separator' + --compression none -m $mode.multi_fasta.min_len && ln -s 'output/concatenated.fa' 'contigs.fasta' && @@ -222,7 +223,8 @@ </xml> <xml name="orf-finder"> <param argument="--orf-finder" type="select" label="ORF finder used to estimate the number of bins"> - <option value="prodigal" selected="true">Prodigal</option> + <option value="fast-naive" selected="true">Fast-Naive</option> + <option value="prodigal">Prodigal</option> <option value="fraggenescan">Fraggenescan</option> </param> </xml> @@ -251,8 +253,8 @@ <xml name="minfasta-kbs"> <param argument="--minfasta-kbs" type="integer" min="0" value="200" label="Miminimum bin size in Kbps"/> </xml> - <xml name="no-recluster"> - <param argument="--no-recluster" type="boolean" truevalue="--no-recluster" falsevalue="" checked="false" label="Do not recluster bins?"/> + <xml name="write_pre_reclustering_bins"> + <param argument="--write-pre-reclustering-bins" type="boolean" truevalue="--write-pre-reclustering-bins" falsevalue="" checked="false" label="Return also the pre reclustered bins?"/> </xml> <xml name="data"> <param argument="--data" type="data" format="csv" label="Train data"/> @@ -310,6 +312,7 @@ <filter>mode["select"]=="multi" and extra_output and "contigs" in extra_output</filter> <discover_datasets pattern="(?P<designation>.*).fa" format="fasta" directory="output/samples/" /> </collection> + </xml> <xml name="train_output"> <data name="model" format="h5" from_work_dir="output/model.h5" label="${tool.name} on ${on_string}: Semi-supervised deep learning model" />