| Previous changeset 1:01f02c5ddff8 (2022-07-29) Next changeset 3:eb50e7eca3dc (2023-11-09) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6 |
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modified:
macros.xml metabat2.xml |
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removed:
test-data/process_log.txt |
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| diff -r 01f02c5ddff8 -r 708abf08a626 macros.xml --- a/macros.xml Fri Jul 29 12:38:24 2022 +0000 +++ b/macros.xml Tue Aug 02 09:40:59 2022 +0000 |
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| @@ -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> |
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| diff -r 01f02c5ddff8 -r 708abf08a626 metabat2.xml --- a/metabat2.xml Fri Jul 29 12:38:24 2022 +0000 +++ b/metabat2.xml Tue Aug 02 09:40:59 2022 +0000 |
| [ |
| b'@@ -7,34 +7,36 @@\n <command detect_errors="exit_code"><![CDATA[\n mkdir bins &&\n metabat2\n---inFile \'$inFile\'\n---outFile \'bins/bin\'\n-#if str($advanced.base_coverage_depth_cond.base_coverage_depth) == \'yes\':\n- #if $advanced.base_coverage_depth_cond.abdFile:\n- --abdFile \'$advanced.base_coverage_depth_cond.abdFile\'\n- #else if $advanced.base_coverage_depth_cond.cvExt:\n- --cvExt \'$advanced.base_coverage_depth_cond.cvExt\'\n+ --inFile \'$inFile\'\n+ --outFile \'bins/bin\'\n+#if str($advanced.base_coverage_depth_cond.base_coverage_depth) == \'yes\'\n+ #if $advanced.base_coverage_depth_cond.abdFile\n+ --abdFile \'$advanced.base_coverage_depth_cond.abdFile\'\n+ #else if $advanced.base_coverage_depth_cond.cvExt\n+ --cvExt \'$advanced.base_coverage_depth_cond.cvExt\'\n #end if\n #end if\n---minContig $advanced.minContig\n---maxP $advanced.maxP\n---minS $advanced.minS\n---maxEdges $advanced.maxEdges\n---pTNF $advanced.pTNF\n-$advanced.noAdd\n---minCV $advanced.minCV\n---minCVSum $advanced.minCVSum\n---minClsSize $advanced.minClsSize\n---numThreads \\${GALAXY_SLOTS:-4}\n-$advanced.onlyLabel\n-#if $advanced.saveCls:\n- $advanced.saveCls\n+ --minContig $advanced.minContig\n+ --maxP $advanced.maxP\n+ --minS $advanced.minS\n+ --maxEdges $advanced.maxEdges\n+ --pTNF $advanced.pTNF\n+ $advanced.noAdd\n+ --minCV $advanced.minCV\n+ --minCVSum $advanced.minCVSum\n+ --seed $advanced.seed\n+ --minClsSize $out.minClsSize\n+ --numThreads \\${GALAXY_SLOTS:-4}\n+ $out.onlyLabel\n+#if $out.saveCls\n+ $out.saveCls\n --noBinOut\n #end if\n-$advanced.unbinned\n---seed $advanced.seed\n-> process_log.txt\n-#if str($advanced.output_process_log) == \'yes\':\n+#if \'unbinned\' in $out.extra_outputs\n+ --unbinned\n+#end if\n+ > process_log.txt\n+#if \'log\' in $out.extra_outputs\n && mv process_log.txt \'$process_log\'\n #end if\n ]]></command>\n@@ -43,8 +45,8 @@\n <section name="advanced" title="Advanced options">\n <conditional name="base_coverage_depth_cond">\n <param name="base_coverage_depth" type="select" label="Use a base coverage depth file?">\n+ <option value="yes">Yes</option>\n <option value="no" selected="true">No</option>\n- <option value="yes">Yes</option>\n </param>\n <when value="no"/>\n <when value="yes">\n@@ -60,50 +62,160 @@\n <param argument="--noAdd" type="boolean" truevalue="--noAdd" falsevalue="" checked="false" label="Turn off additional binning for lost or small contigs?"/>\n <param argument="--minCV" type="float" value="1.0" label="Minimum mean coverage of a contig in each library for binning"/>\n <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"/>\n+ <param argument="--seed" type="integer" value="0" label="For exact reproducibility." help="Zero value will use random seed"/>\n+ </section>\n+ <section name="out" title="Output options">\n <param argument="--minClsSize" type="integer" value="200000" label="Minimum size of a bin as the output"/>\n <param argument="--onlyLabel" type="boolean" truevalue="--onlyLabel" falsevalue="" checked="false" label="Output only sequence labels as a list in a column without sequences?"/>\n <param argument="--saveCls" type="boolean" truevalue="--saveCls" falsevalue="" checked="false" label="Save cluster memberships as a matrix format?"/>\n- <param argument="--unbinned" type="boolean" truevalue="--unbinned" falsevalue="" checked="false" label="Output fasta file containing unbinned contigs?"/>\n- <param argument="--seed" type="integer" value="0" label="For exact reproducibility." help="Zero value will use random seed"/>\n- <param name="output_process_log" type="select" label="Output process log file?">\n- <option va'..b'="fasta">\n+ <assert_contents>\n+ <has_text text=">NC_045512.2"/>\n+ <has_text text=">MW130872.1"/>\n+ </assert_contents>\n+ </output>\n+ <output name="process_log" ftype="txt">\n+ <assert_contents>\n+ <has_text text="MetaBAT"/>\n+ <has_text text="2 bins (897090 bases in total) formed"/>\n+ </assert_contents>\n+ </output>\n </test>\n- <test expect_num_outputs="2">\n+ <test expect_num_outputs="1">\n+ <param name="inFile" value="input0.fasta.gz" ftype="fasta.gz"/>\n+ <section name="advanced">\n+ <conditional name="base_coverage_depth_cond">\n+ <param name="base_coverage_depth" value="yes"/>\n+ <param name="abdFile" value="input_depth1.tabular" ftype="tabular"/>\n+ </conditional>\n+ <param name="seed" value="345678"/>\n+ </section>\n+ <section name="out">\n+ <param name="onlyLabel" value="false"/>\n+ <param name="saveCls" value="false"/>\n+ <param name="extra_outputs" value=""/>\n+ </section>\n+ <output_collection name="bins" type="list" count="0"/>\n+ </test>\n+ <test expect_num_outputs="1">\n <param name="inFile" value="input0.fasta.gz" ftype="fasta.gz"/>\n- <param name="base_coverage_depth" value="yes"/>\n- <param name="abdFile" value="input_depth1.tabular" ftype="tabular"/>\n- <param name="seed" value="345678"/>\n- <param name="output_process_log" value="yes"/>\n- <output_collection name="bin_files" type="list" count="0"/>\n- <output name="process_log" file="process_log.txt" ftype="txt"/>\n+ <section name="advanced">\n+ <conditional name="base_coverage_depth_cond">\n+ <param name="base_coverage_depth" value="no"/>\n+ </conditional>\n+ <param name="seed" value="345678"/>\n+ </section>\n+ <section name="out">\n+ <param name="onlyLabel" value="false"/>\n+ <param name="saveCls" value="true"/>\n+ <param name="extra_outputs" value=""/>\n+ </section>\n+ <output name="bin_saveCls" ftype="tabular">\n+ <assert_contents>\n+ <has_text text="NC_045512.2"/>\n+ <has_text text="MT810119.1"/>\n+ <has_text text="MW130860.1"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test expect_num_outputs="1">\n+ <param name="inFile" value="input0.fasta.gz" ftype="fasta.gz"/>\n+ <section name="advanced">\n+ <conditional name="base_coverage_depth_cond">\n+ <param name="base_coverage_depth" value="no"/>\n+ </conditional>\n+ <param name="seed" value="345678"/>\n+ </section>\n+ <section name="out">\n+ <param name="onlyLabel" value="true"/>\n+ <param name="saveCls" value="false"/>\n+ <param name="extra_outputs" value=""/>\n+ </section>\n+ <output_collection name="bin_onlyLabel" type="list" count="2">\n+ <element name="1" ftype="tabular">\n+ <assert_contents>\n+ <has_text text="MW127518.1"/>\n+ <has_text text="MW127521.1"/>\n+ </assert_contents>\n+ </element>\n+ <element name="2" ftype="tabular">\n+ <assert_contents>\n+ <has_text text="MT810119.1"/>\n+ <has_text text="MW130866.1"/>\n+ </assert_contents>\n+ </element>\n+ </output_collection>\n </test>\n </tests>\n <help><![CDATA[\n' |
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| diff -r 01f02c5ddff8 -r 708abf08a626 test-data/process_log.txt --- a/test-data/process_log.txt Fri Jul 29 12:38:24 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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. |