diff metabat2.xml @ 0:76bc4efa1aeb draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/metabat2.xml	Fri Jan 28 12:21:05 2022 +0000
@@ -0,0 +1,131 @@
+<tool id="metabat2" name="MetaBAT2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>metagenome binning</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+mkdir bins &&
+metabat2
+--inFile '$inFile'
+--outFile 'bins/bin'
+#if str($advanced.base_coverage_depth_cond.base_coverage_depth) == 'yes':
+    #if $advanced.base_coverage_depth_cond.abdFile:
+        --abdFile '$advanced.base_coverage_depth_cond.abdFile'
+    #else if $advanced.base_coverage_depth_cond.cvExt:
+        --cvExt '$advanced.base_coverage_depth_cond.cvExt'
+    #end if
+#end if
+--minContig $advanced.minContig
+--maxP $advanced.maxP
+--minS $advanced.minS
+--maxEdges $advanced.maxEdges
+--pTNF $advanced.pTNF
+$advanced.noAdd
+--minCV $advanced.minCV
+--minCVSum $advanced.minCVSum
+--minClsSize $advanced.minClsSize
+--numThreads \${GALAXY_SLOTS:-4}
+$advanced.onlyLabel
+#if $advanced.saveCls:
+    $advanced.saveCls
+    --noBinOut
+#end if
+$advanced.unbinned
+--seed $advanced.seed
+> process_log.txt
+#if str($advanced.output_process_log) == 'yes':
+    && mv process_log.txt '$process_log'
+#end if
+    ]]></command>
+    <inputs>
+        <param argument="--inFile" type="data" format="fasta,fasta.gz" label="Fasta file containing contigs"/>
+        <section name="advanced" title="Advanced options">
+            <conditional name="base_coverage_depth_cond">
+                <param name="base_coverage_depth" type="select" label="Use a base coverage depth file?">
+                    <option value="no" selected="true">No</option>
+                    <option value="yes">Yes</option>
+                </param>
+                <when value="no"/>
+                <when value="yes">
+                    <param argument="--abdFile" type="data" format="tabular" optional="True" label="Tabular depth matrix file having mean and variance of base coverage depth" help="Generated by the Calculate contig depths for MetaBAT2 tool"/>
+                    <param argument="--cvExt" type="data" format="tabular" optional="True" label="Base coverage depth file without variance" help="Generated by a tool - not the Calculate contig depths for MetaBAT2 tool"/>
+                </when>
+            </conditional>
+            <param argument="--minContig" type="integer" min="1500" value="1500" label="Minimum size of a contig for binning"/>
+            <param argument="--maxP" type="integer" min="1" max="100" value="95" label="Percentage of good contigs considered for binning decided by connection among contigs" help="The greater, the more sensitive"/>
+            <param argument="--minS" type="integer" min="1" max="99" value="60" label="Minimum score of an edge for binning" help="The greater, the more specific"/>
+            <param argument="--maxEdges" type="integer" value="200" label="Maximum number of edges per node" help="The greater, the more sensitive"/>
+            <param argument="--pTNF" type="integer" value="0" label="TNF probability cutoff for building TNF graph" help="Use it to skip the preparation step (0:auto)"/>
+            <param argument="--noAdd" type="boolean" truevalue="--noAdd" falsevalue="" checked="false" label="Turn off additional binning for lost or small contigs?"/>
+            <param argument="--minCV" type="float" value="1.0" label="Minimum mean coverage of a contig in each library for binning"/>
+            <param argument="--minCVSum" type="float" value="1.0" label="Minimum total effective mean coverage of a contig for binning" help="Sum of depth over minCV"/>
+            <param argument="--minClsSize" type="integer" value="200000" label="Minimum size of a bin as the output"/>
+            <param argument="--onlyLabel" type="boolean" truevalue="--onlyLabel" falsevalue="" checked="false" label="Output only sequence labels as a list in a column without sequences?"/>
+            <param argument="--saveCls" type="boolean" truevalue="--saveCls" falsevalue="" checked="false" label="Save cluster memberships as a matrix format?"/>
+            <param argument="--unbinned" type="boolean" truevalue="--unbinned" falsevalue="" checked="false" label="Output fasta file containing unbinned contigs?"/>
+            <param argument="--seed" type="integer" value="0" label="For exact reproducibility." help="Zero value will use random seed"/>
+            <param name="output_process_log" type="select" label="Output process log file?">
+                <option value="no" selected="true">No</option>
+                <option value="yes">Yes</option>
+            </param>
+        </section>
+    </inputs>
+    <outputs>
+        <collection name="bin_files" type="list" label="${tool.name} on ${on_string}: (bins)">
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)\.fa" format="fasta" directory="bins"/>
+        </collection>
+        <data name="process_log" format="txt" label="${tool.name} on ${on_string} (process log)">
+            <filter>advanced['output_process_log'] == 'yes'</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="inFile" value="input0.fasta.gz" ftype="fasta.gz"/>
+            <param name="seed" value="345678"/>
+            <output_collection name="bin_files" type="list" count="2">
+                <element name="bin.1" ftype="fasta">
+                    <assert_contents>
+                        <has_size value="334554"/>
+                    </assert_contents>
+                </element>
+                <element name="bin.2" ftype="fasta">
+                    <assert_contents>
+                        <has_size value="577866"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>
+        <test expect_num_outputs="2">
+            <param name="inFile" value="input0.fasta.gz" ftype="fasta.gz"/>
+            <param name="base_coverage_depth" value="yes"/>
+            <param name="abdFile" value="input_depth1.tabular" ftype="tabular"/>
+            <param name="seed" value="345678"/>
+            <param name="output_process_log" value="yes"/>
+            <output_collection name="bin_files" type="list" count="0"/>
+            <output name="process_log" file="process_log.txt" ftype="txt"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binning
+software that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency.  The
+tool accepts a fast file containing contigs and produces a collection (i.e., bins) of fasta files.
+        
+MetaBAT2 includes optionizations to MetaBAT.  It requires virtually no parameter optimization. Default parameter
+values are more reliable to use in most cases since MetaBAT2 adapts to the given data to find the best parameter.
+Some parameter settings are still available for advanced users, helping to manage some exceptional cases by changing
+the amount of data used for the analysis.
+
+**More information**
+
+https://bitbucket.org/berkeleylab/metabat/src/master/
+
+**Options**
+
+ * **Use base coverage depth file** - optionally select a base coverage depth file that was either generated by the Calculate contig depths for MetaBAT2 tool or another 3rd party tool.
+ 
+    ]]></help>
+    <expand macro="citations"/>
+</tool>