Mercurial > repos > iuc > metabat2
changeset 2:708abf08a626 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
| author | iuc |
|---|---|
| date | Tue, 02 Aug 2022 09:40:59 +0000 |
| parents | 01f02c5ddff8 |
| children | eb50e7eca3dc |
| files | macros.xml metabat2.xml test-data/process_log.txt |
| diffstat | 3 files changed, 159 insertions(+), 50 deletions(-) [+] |
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--- a/macros.xml Fri Jul 29 12:38:24 2022 +0000 +++ b/macros.xml Tue Aug 02 09:40:59 2022 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">2.15</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">2</token> <token name="@PROFILE@">21.01</token> <xml name="requirements"> <requirements>
--- a/metabat2.xml Fri Jul 29 12:38:24 2022 +0000 +++ b/metabat2.xml Tue Aug 02 09:40:59 2022 +0000 @@ -7,34 +7,36 @@ <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' + --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 + --minContig $advanced.minContig + --maxP $advanced.maxP + --minS $advanced.minS + --maxEdges $advanced.maxEdges + --pTNF $advanced.pTNF + $advanced.noAdd + --minCV $advanced.minCV + --minCVSum $advanced.minCVSum + --seed $advanced.seed + --minClsSize $out.minClsSize + --numThreads \${GALAXY_SLOTS:-4} + $out.onlyLabel +#if $out.saveCls + $out.saveCls --noBinOut #end if -$advanced.unbinned ---seed $advanced.seed -> process_log.txt -#if str($advanced.output_process_log) == 'yes': +#if 'unbinned' in $out.extra_outputs + --unbinned +#end if + > process_log.txt +#if 'log' in $out.extra_outputs && mv process_log.txt '$process_log' #end if ]]></command> @@ -43,8 +45,8 @@ <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="yes">Yes</option> <option value="no" selected="true">No</option> - <option value="yes">Yes</option> </param> <when value="no"/> <when value="yes"> @@ -60,50 +62,160 @@ <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="--seed" type="integer" value="0" label="For exact reproducibility." help="Zero value will use random seed"/> + </section> + <section name="out" title="Output options"> <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 name="extra_outputs" type="select" multiple="true" optional="true" label="Extra outputs"> + <option value="lowDepth">Fasta file containing low depth bins (if no matrix format and label selected)</option> + <option value="tooShort">Fasta file containing too short bins (if no matrix format and label selected)</option> + <option value="unbinned">Fasta file containing unbinned contigs (if no matrix format and label selected)</option> + <option value="log">Process log file</option> </param> </section> </inputs> <outputs> - <collection name="bin_files" type="list" label="${tool.name} on ${on_string}: (bins)"> - <discover_datasets pattern="(?P<designation>.*)\.fa" format="fasta" directory="bins"/> + <collection name="bins" type="list" label="${tool.name} on ${on_string}: Bins"> + <filter>not out['saveCls'] and not out['onlyLabel']</filter> + <discover_datasets pattern="bin\.(?P<designation>\d*)\.fa" format="fasta" directory="bins"/> + </collection> + <data name="bin_saveCls" format="tabular" from_work_dir="bins/bin" label="${tool.name} on ${on_string}: Bins"> + <filter>out['saveCls'] and not out['onlyLabel']</filter> + </data> + <collection name="bin_onlyLabel" type="list" label="${tool.name} on ${on_string}: Bins"> + <filter>not out['saveCls'] and out['onlyLabel']</filter> + <discover_datasets pattern="bin\.(?P<designation>\d*)" format="tabular" directory="bins"/> </collection> - <data name="process_log" format="txt" label="${tool.name} on ${on_string} (process log)"> - <filter>advanced['output_process_log'] == 'yes'</filter> + <data name="lowDepth" format="fasta" from_work_dir="bins/bin.lowDepth.fa" label="${tool.name} on ${on_string}: Low depth bins"> + <filter>not out['saveCls'] and not out['onlyLabel'] and 'lowDepth' in out['extra_outputs']</filter> + </data> + <data name="tooShort" format="fasta" from_work_dir="bins/bin.tooShort.fa" label="${tool.name} on ${on_string}: Too short bins"> + <filter>not out['saveCls'] and not out['onlyLabel'] and 'tooShort' in out['extra_outputs']</filter> + </data> + <data name="unbinned" format="fasta" from_work_dir="bins/bin.unbinned.fa" label="${tool.name} on ${on_string}: Unbinned sequences"> + <filter>not out['saveCls'] and not out['onlyLabel'] and 'unbinned' in out['extra_outputs']</filter> + </data> + <data name="process_log" format="txt" label="${tool.name} on ${on_string}: Process log"> + <filter>'log' in out['extra_outputs']</filter> </data> </outputs> <tests> - <test expect_num_outputs="1"> + <test expect_num_outputs="5"> <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"> + <section name="advanced"> + <conditional name="base_coverage_depth_cond"> + <param name="base_coverage_depth" value="no"/> + </conditional> + <param name="seed" value="345678"/> + </section> + <section name="out"> + <param name="extra_outputs" value="lowDepth,tooShort,unbinned,log"/> + </section> + <output_collection name="bins" type="list" count="2"> + <element name="1" ftype="fasta"> <assert_contents> <has_size value="334554"/> + <has_text text=">MW127517.1"/> + <has_text text=">MW127521.1"/> </assert_contents> </element> - <element name="bin.2" ftype="fasta"> + <element name="2" ftype="fasta"> <assert_contents> <has_size value="577866"/> + <has_text text=">MT810119.1"/> + <has_text text=">MW130866.1"/> </assert_contents> </element> </output_collection> + <output name="lowDepth" ftype="fasta"> + <assert_contents> + <has_text text=""/> + </assert_contents> + </output> + <output name="tooShort" ftype="fasta"> + <assert_contents> + <has_text text=""/> + </assert_contents> + </output> + <output name="unbinned" ftype="fasta"> + <assert_contents> + <has_text text=">NC_045512.2"/> + <has_text text=">MW130872.1"/> + </assert_contents> + </output> + <output name="process_log" ftype="txt"> + <assert_contents> + <has_text text="MetaBAT"/> + <has_text text="2 bins (897090 bases in total) formed"/> + </assert_contents> + </output> </test> - <test expect_num_outputs="2"> + <test expect_num_outputs="1"> + <param name="inFile" value="input0.fasta.gz" ftype="fasta.gz"/> + <section name="advanced"> + <conditional name="base_coverage_depth_cond"> + <param name="base_coverage_depth" value="yes"/> + <param name="abdFile" value="input_depth1.tabular" ftype="tabular"/> + </conditional> + <param name="seed" value="345678"/> + </section> + <section name="out"> + <param name="onlyLabel" value="false"/> + <param name="saveCls" value="false"/> + <param name="extra_outputs" value=""/> + </section> + <output_collection name="bins" type="list" count="0"/> + </test> + <test expect_num_outputs="1"> <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"/> + <section name="advanced"> + <conditional name="base_coverage_depth_cond"> + <param name="base_coverage_depth" value="no"/> + </conditional> + <param name="seed" value="345678"/> + </section> + <section name="out"> + <param name="onlyLabel" value="false"/> + <param name="saveCls" value="true"/> + <param name="extra_outputs" value=""/> + </section> + <output name="bin_saveCls" ftype="tabular"> + <assert_contents> + <has_text text="NC_045512.2"/> + <has_text text="MT810119.1"/> + <has_text text="MW130860.1"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <param name="inFile" value="input0.fasta.gz" ftype="fasta.gz"/> + <section name="advanced"> + <conditional name="base_coverage_depth_cond"> + <param name="base_coverage_depth" value="no"/> + </conditional> + <param name="seed" value="345678"/> + </section> + <section name="out"> + <param name="onlyLabel" value="true"/> + <param name="saveCls" value="false"/> + <param name="extra_outputs" value=""/> + </section> + <output_collection name="bin_onlyLabel" type="list" count="2"> + <element name="1" ftype="tabular"> + <assert_contents> + <has_text text="MW127518.1"/> + <has_text text="MW127521.1"/> + </assert_contents> + </element> + <element name="2" ftype="tabular"> + <assert_contents> + <has_text text="MT810119.1"/> + <has_text text="MW130866.1"/> + </assert_contents> + </element> + </output_collection> </test> </tests> <help><![CDATA[
--- a/test-data/process_log.txt Fri Jul 29 12:38:24 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -MetaBAT 2 (2.15 (Bioconda)) using minContig 1500, minCV 1.0, minCVSum 1.0, maxP 95%, minS 60, maxEdges 200 and minClsSize 200000. with random seed=345678 -No edges were formed by TNF. -0 bins (0 bases in total) formed.