| Previous changeset 3:83b998fa34ea (2016-11-10) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kobas commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e" |
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modified:
kobas_annotate.xml kobas_identify.xml kobas_macros.xml repository_dependencies.xml |
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| diff -r 83b998fa34ea -r 20f1b45dea63 kobas_annotate.xml --- a/kobas_annotate.xml Thu Nov 10 16:21:41 2016 -0500 +++ b/kobas_annotate.xml Thu Nov 28 15:50:07 2019 -0500 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="kobas_annotate" name="KOBAS Annotate" version="@WRAPPER_VERSION@">\n+<tool id="kobas_annotate" name="KOBAS Annotate" version="@TOOL_VERSION@">\n <description>KEGG Orthology Based Annotation System</description>\n <macros>\n <import>kobas_macros.xml</import>\n@@ -10,78 +10,74 @@\n <exit_code range="0" level="warning" description="BiopythonDeprecationWarning"/>\n <exit_code range="1" level="fatal" description="Bad input settings or none of the entries was annotated successfully."/>\n </stdio>\n- <command>\n- <![CDATA[\n-\n- ## create the KOBAS directories\n- mkdir sqlite &&\n- mkdir seq_pep &&\n+ <command><![CDATA[\n+## create the KOBAS directories\n+mkdir sqlite &&\n+mkdir seq_pep &&\n \n- #if $blast_opts.choice == \'local\':\n- #set $blast_path = $blast_opts.localdb.fields.path\n- #else if $blast_opts.choice == \'fasta\':\n- makeblastdb\n- -in \'$blast_opts.fastadb\'\n- -dbtype \'prot\'\n- -out \'seq_pep/${species}.pep.fasta\' &&\n- #else:\n- #set $blast_path = $os.path.join($blast_opts.histdb.extra_files_path,\'blastdb\')\n- #end if\n+#if $blast_opts.choice == \'local\':\n+ #set $blast_path = $blast_opts.localdb.fields.path\n+#elif $blast_opts.choice == \'fasta\':\n+ makeblastdb\n+ -in \'$blast_opts.fastadb\'\n+ -dbtype \'prot\'\n+ -out \'seq_pep/${species}.pep.fasta\' &&\n+#else:\n+ #set $blast_path = $os.path.join($blast_opts.histdb.extra_files_path,\'blastdb\')\n+#end if\n \n- ## create the database symlinks to comply with how KOBAS wants them\n- ln -s \'$organismdb\' sqlite/organism.db &&\n- ln -s \'$kobasdb\' \'sqlite/${species}.db\' &&\n+## create the database symlinks to comply with how KOBAS wants them\n+ln -s \'$organismdb\' sqlite/organism.db &&\n+ln -s \'$kobasdb\' \'sqlite/${species}.db\' &&\n \n- #if $blast_opts.choice != \'fasta\':\n- ln -s \'${blast_path}.phr\' \'seq_pep/${species}.pep.fasta.phr\' &&\n- ln -s \'${blast_path}.pin\' \'seq_pep/${species}.pep.fasta.pin\' &&\n- ln -s \'${blast_path}.psq\' \'seq_pep/${species}.pep.fasta.psq\' && ls -l seq_pep/ &&\n- #end if\n+#if $blast_opts.choice != \'fasta\':\n+ ln -s \'${blast_path}.phr\' \'seq_pep/${species}.pep.fasta.phr\' &&\n+ ln -s \'${blast_path}.pin\' \'seq_pep/${species}.pep.fasta.pin\' &&\n+ ln -s \'${blast_path}.psq\' \'seq_pep/${species}.pep.fasta.psq\' && ls -l seq_pep/ &&\n+#end if\n \n- ## create the orthologe database symlinks to comply with how KOBAS wants them\n- #if $ortholog.only == \'YES\' and str($ortholog.species) != str($species):\n+## create the orthologe database symlinks to comply with how KOBAS wants them\n+#if $ortholog.only == \'YES\' and str($ortholog.species) != str($species):\n \n- #if $ortholog.blast_opts_ortholog.choice == \'local\':\n- #set $blast_path = $ortholog.blast_opts_ortholog.localdb.fields.path\n- #else if $ortholog.blast_opts_ortholog.choice == \'fasta\':\n- makeblastdb\n- -in \'$ortholog.blast_opts_ortholog.fastadb\'\n- -dbtype \'prot\'\n- -out \'seq_pep/${ortholog.species}.pep.fasta\' &&\n- #else:\n- #set $blast_path = $os.path.join($ortholog.blast_opts_ortholog.histdb.extra_files_path,\'blastdb\')\n- #end if\n+ #if $ortholog.blast_opts_ortholog.choice == \'local\':\n+ #set $blast_path = $ortholog.blast_opts_ortholog.localdb.fields.path\n+ #elif $ortholog.blast_opts_ortholog.choice == \'fasta\':\n+ makeblastdb\n+ -in \'$ortholog.blast_opts_ortholog.fastadb\'\n+ -dbtype \'prot\'\n+ -out \'seq_pep/${ortholog.species}.pep.fasta\' &&\n+ #else:\n+ #set $blast_path = $os.path.join($ortholog.blast_opts_ortholog.histdb.extra_files_path,\'blastdb\')\n+ #end if\n \n- ln -s \'$ortholog.kobasdb\' \'sqlite/${ortholog.species}.db\' &&\n+ ln -s \'$ortholog.kobasdb\' \'sqli'..b' ln -s \'${blast_path}.pin\' \'seq_pep/${ortholog.species}.pep.fasta.pin\' &&\n+ ln -s \'${blast_path}.psq\' \'seq_pep/${ortholog.species}.pep.fasta.psq\' &&\n+ #end if\n+#end if\n \n- kobas-annotate\n- -i \'$infile\'\n- -t \'$intype\'\n- -s \'$species\'\n- -e \'$evalue\'\n- -r $rank\n- -n "\\${GALAXY_SLOTS:-4}"\n- -c $coverage\n- #if $ortholog.only == \'YES\':\n- -z \'$ortholog.species\'\n- #end if\n- -y seq_pep\n- -q sqlite\n- -p blastp\n- -x blastx\n- -o \'$output\'\n-\n- ]]>\n- </command>\n+kobas-annotate\n+-i \'$infile\'\n+-t \'$intype\'\n+-s \'$species\'\n+-e \'$evalue\'\n+-r $rank\n+-n "\\${GALAXY_SLOTS:-4}"\n+-c $coverage\n+#if $ortholog.only == \'YES\':\n+ -z \'$ortholog.species\'\n+#end if\n+-y seq_pep\n+-q sqlite\n+-p blastp\n+-x blastx\n+-o \'$output\'\n+ ]]></command>\n <inputs>\n- <param format="fasta,tabular,txt" type="data" label="Input file" help="Input data file matching the input type." argument="--infile"/>\n+ <param argument="--infile" type="data" format="fasta,tabular,txt" label="Input file" help="Input data file matching the input type."/>\n <param type="select" label="Input type" argument="--intype" help="Input data type, default fasta:pro">\n <option value="fasta:pro">FASTA protein sequence</option>\n <option value="fasta:nuc">FASTA nucleotide sequence</option>\n@@ -99,12 +95,12 @@\n \n <expand macro="input_kobasdb"/>\n \n- <param format="sqlite" name="organismdb" type="data" label="Organism database" help="KOBAS organism database, available at http://kobas.cbi.pku.edu.cn/download.php"/>\n- <param type="text" argument="--evalue" value="1e-5" label="E-value" help="Expect threshold for BLAST, default 1e-5"/>\n- <param type="integer" argument="--rank" value="5" min="0" label="Rank cutoff" help="Rank cutoff for valid hits from BLAST result, default 5"/>\n- <param type="integer" argument="--coverage" value="0" min="0" label="Subject coverage cutoff" help="subject coverage cutoff for BLAST, default 0"/>\n+ <param name="organismdb" type="data" format="sqlite" label="Organism database" help="KOBAS organism database, available at http://kobas.cbi.pku.edu.cn/download.php"/>\n+ <param argument="--evalue" type="text" value="1e-5" label="E-value" help="Expect threshold for BLAST, default 1e-5"/>\n+ <param argument="--rank" type="integer" min="0" value="5" label="Rank cutoff" help="Rank cutoff for valid hits from BLAST result, default 5"/>\n+ <param argument="--coverage" type="integer" min="0" value="0" label="Subject coverage cutoff" help="subject coverage cutoff for BLAST, default 0"/>\n <conditional name="ortholog">\n- <param name="only" type="select" argument="--ortholog" label="Only use orthologs" help="Whether only use orthologs for cross-species annotation or not, default NO (if only use orthologs, please provide the species abbreviation of your input)">\n+ <param name="only" argument="--ortholog" type="select" label="Only use orthologs" help="Whether only use orthologs for cross-species annotation or not, default NO (if only use orthologs, please provide the species abbreviation of your input)">\n <option value="NO">No</option>\n <option value="YES">Yes</option>\n </param>\n@@ -118,7 +114,7 @@\n </conditional>\n </inputs>\n <outputs>\n- <data format="tabular" name="output"/>\n+ <data name="output" format="tabular"/>\n </outputs>\n \n <tests>\n@@ -132,7 +128,7 @@\n <param name="species" value="aaa"/>\n <param name="kobasdb" value="aaa.db"/>\n <param name="organismdb" value="organism.db"/>\n- <output name="out_file1" file="kobas_annotate_output.txt"/>\n+ <output name="output" file="kobas_annotate_output.txt"/>\n </test>\n </tests>\n \n' |
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| diff -r 83b998fa34ea -r 20f1b45dea63 kobas_identify.xml --- a/kobas_identify.xml Thu Nov 10 16:21:41 2016 -0500 +++ b/kobas_identify.xml Thu Nov 28 15:50:07 2019 -0500 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="kobas_identify" name="KOBAS Identify" version="@WRAPPER_VERSION@"> +<tool id="kobas_identify" name="KOBAS Identify" version="@TOOL_VERSION@"> <description>KEGG Orthology Based Annotation System</description> <macros> <import>kobas_macros.xml</import> @@ -6,44 +6,41 @@ <expand macro="requirements"/> - <command> - <![CDATA[ - - mkdir sqlite && - mkdir seq_pep && + <command><![CDATA[ +mkdir sqlite && +mkdir seq_pep && - #if not isinstance( $db.value, list ): - #set $db_args = [ $db.value ] - #else: - #set $db_args = $db.value - #end if - #set $db_args = "/".join($db.value) +#if not isinstance( $db.value, list ): + #set $db_args = [ $db.value ] +#else: + #set $db_args = $db.value +#end if +#set $db_args = "/".join($db.value) - ln -s '$kobasdb' 'sqlite/${species}.db' && +ln -s '$kobasdb' 'sqlite/${species}.db' && - kobas-identify - -f '$fgfile' - #if $bg.bgtype == 'file': - -b '$bg.bgfile' - #elif $bg.bgtype == 'species': - -b '$bg.bgspecies' - #end if - -d '$db_args' - -m '$method' - -n '$fdr' - -c $cutoff - -q sqlite - -p blastp - -x blastx - -o '$output' - ]]> - </command> +kobas-identify +-f '$fgfile' +#if $bg.bgtype == 'file': + -b '$bg.bgfile' +#elif $bg.bgtype == 'species': + -b '$bg.bgspecies' +#end if +-d '$db_args' +-m '$method' +-n '$fdr' +-c $cutoff +-q sqlite +-p blastp +-x blastx +-o '$output' + ]]></command> <inputs> - <param format="tabular" type="data" label="Foreground" argument="--fgfile" help="Foreground file, the output of KOBAS Annotate"/> + <param argument="--fgfile" type="data" format="tabular" label="Foreground" help="Foreground file, the output of KOBAS Annotate"/> <expand macro="input_kobasdb"/> - <param type="select" label="Database" argument="--db" multiple="True" display="checkboxes" help="Select your desired databases: + <param type="select" label="Database" argument="--db" multiple="True" optional="false" display="checkboxes" help="Select your desired databases: (Note: the Corrected P-Values will be affected by the number of selected databases)"> <option value="K">KEGG Pathway</option> <option value="n">PID</option> @@ -58,15 +55,10 @@ <option value="N">NHGRI GWAS Catalog</option> <option value="G">Gene Ontology</option> <option value="S">Gene Ontology Slim (GOslim)</option> - <validator type="no_options" message="You must pick at least one database."/> </param> <conditional name="bg"> - <param - name="bgtype" - type="select" - argument="--bgfile" - label="Background" + <param name="bgtype" argument="--bgfile" type="select" label="Background" help="Optional background file, the output of annotate (3 or 4-letter file name is not allowed), or species abbreviation (for example: hsa for Homo sapiens, mmu for Mus @@ -80,13 +72,10 @@ </param> <when value="same"></when> <when value="file"> - <param format="txt" name="bgfile" type="data" label="Background file"/> + <param name="bgfile" type="data" format="txt" label="Background file"/> </when> <when value="species"> - <param - name="bgspecies" - type="text" - label="Species abbreviation" + <param name="bgspecies" type="text" label="Species abbreviation" help="For example: ko for KEGG Orthology, hsa for Homo sapiens, mmu for Mus musculus, dme for Drosophila melanogaster, ath for Arabidopsis @@ -102,18 +91,17 @@ <option value="x">Frequency list</option> </param> - <param type="select" argument="--fdr" label="FDR" help="False discovery rate (FDR) correction method"> + <param argument="--fdr" type="select" label="FDR" help="False discovery rate (FDR) correction method"> <option selected="True" value="BH">Benjamini and Hochberg</option> <option value="BY">Benjamini and Yekutieli</option> <option value="QVALUE">QVALUE</option> <option value="None">None</option> </param> - <param type="integer" min="0" argument="--cutoff" value="5" label="Cutoff" help="Terms with less than cutoff number of genes are not used for statistical tests, default 5"/> - + <param argument="--cutoff" type="integer" min="0" value="5" label="Cutoff" help="Terms with less than cutoff number of genes are not used for statistical tests, default 5"/> </inputs> <outputs> - <data format="tabular" name="output"/> + <data name="output" format="tabular"/> </outputs> <tests> @@ -125,7 +113,7 @@ <conditional name="bg"> <param name="bgtype" value="same"/> </conditional> - <output name="out_file1" file="kobas_identify_output.txt"/> + <output name="output" file="kobas_identify_output.txt"/> </test> </tests> |
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| diff -r 83b998fa34ea -r 20f1b45dea63 kobas_macros.xml --- a/kobas_macros.xml Thu Nov 10 16:21:41 2016 -0500 +++ b/kobas_macros.xml Thu Nov 28 15:50:07 2019 -0500 |
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| @@ -1,23 +1,21 @@ <macros> - <token name="@WRAPPER_VERSION@">0.4</token> - <token name="@KOBAS_VERSION@">2.1.1</token> + <token name="@TOOL_VERSION@">2.1.1</token> <xml name="requirements"> <requirements> - <requirement type="package" version="@KOBAS_VERSION@">kobas</requirement> + <requirement type="package" version="@TOOL_VERSION@">kobas</requirement> + <!-- kobas 2.1.1 is not compatible with Biopython >=1.73 due to https://github.com/biopython/biopython/issues/1952 --> + <requirement type="package" version="1.72">biopython</requirement> + <!-- Help conda resolving the enviroment, hopefully this can be removed for next update --> + <requirement type="package" version="3.4">r-base</requirement> </requirements> </xml> <xml name="input_kobasdb"> - <param - name="species" - type="text" - label="Species abbreviation" - argument="--species" - help="For example: ko for KEGG - Orthology, hsa for Homo sapiens, mmu for Mus musculus, - dme for Drosophila melanogaster, ath for Arabidopsis - thaliana, sce for Saccharomyces cerevisiae and eco for - Escherichia coli K-12 MG1655"/> - <param format="sqlite" name="kobasdb" type="data" label="KOBAS database" help="KOBAS species database, available for multiple species at http://kobas.cbi.pku.edu.cn/download.php"/> + <param argument="--species" type="text" label="Species abbreviation" + help="For example: ko for KEGG Orthology, hsa for Homo sapiens, mmu + for Mus musculus, dme for Drosophila melanogaster, ath for + Arabidopsis thaliana, sce for Saccharomyces cerevisiae and eco + for Escherichia coli K-12 MG1655"/> + <param name="kobasdb" type="data" format="sqlite" label="KOBAS database" help="KOBAS species database, available for multiple species at http://kobas.cbi.pku.edu.cn/download.php"/> </xml> <xml name="blastdb_selector"> <param name="choice" type="select" label="BLAST Protein database"> @@ -26,26 +24,16 @@ <option value="local" selected="True">Locally installed BLAST database</option> </param> <when value="fasta"> - <param name="fastadb" format="fasta" type="data" label="FASTA File for BLAST DB" help="FASTA file which will be used to create a BLAST database with makeblastdb."/> - <param name="histdb" type="hidden" value=""/> - <param name="fasta" type="hidden" value=""/> + <param name="fastadb" type="data" format="fasta" label="FASTA File for BLAST DB" help="FASTA file which will be used to create a BLAST database with makeblastdb."/> </when> <when value="histdb"> - <param name="localdb" type="hidden" value=""/> - <param name="fastadb" type="hidden" value=""/> - <param - name="histdb" - type="data" - format="blastdbp" - label="Protein BLAST database" + <param name="histdb" type="data" format="blastdbp" label="Protein BLAST database" help="The protein BlAST database used by KOBAS. FASTA files to create BLAST databases with makeblastdb can be found for multiple species at http://kobas.cbi.pku.edu.cn/download.php"/> </when> <when value="local"> <param name="localdb" type="select" label="Protein BLAST database"> <options from_data_table="blastdb_p"/> </param> - <param name="histdb" type="hidden" value=""/> - <param name="fastadb" type="hidden" value=""/> </when> </xml> <xml name="kobas_citations"> |
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| diff -r 83b998fa34ea -r 20f1b45dea63 repository_dependencies.xml --- a/repository_dependencies.xml Thu Nov 10 16:21:41 2016 -0500 +++ b/repository_dependencies.xml Thu Nov 28 15:50:07 2019 -0500 |
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| @@ -1,4 +1,4 @@ -<?xml version="1.0"?> +<?xml version="1.0" ?> <repositories description="This requires the BLAST datatype definitions (e.g. the BLAST XML format)."> - <repository changeset_revision="01b38f20197e" name="blast_datatypes" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> -</repositories> + <repository changeset_revision="01b38f20197e" name="blast_datatypes" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu"/> +</repositories> \ No newline at end of file |