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author | iuc |
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date | Sat, 05 Nov 2016 09:20:51 -0400 |
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children | 83b998fa34ea |
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<tool id="kobas_identify" name="KOBAS Identify" version="@WRAPPER_VERSION@"> <description>KEGG Orthology Based Annotation System</description> <macros> <import>kobas_macros.xml</import> </macros> <requirements> <requirement type="package" version="@KOBAS_VERSION@">kobas</requirement> </requirements> <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) 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> <inputs> <param format="tabular" type="data" label="Foreground" argument="--fgfile" 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: (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> <option value="b">BioCarta</option> <option value="R">Reactome</option> <option value="B">BioCyc</option> <option value="P">PANTHER</option> <option value="o">OMIM</option> <option value="k">KEGG Disease</option> <option value="f">FunDo</option> <option value="g">GAD</option> <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" 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 musculus, dme for Drosophila melanogaster, ath for Arabidopsis thaliana, sce for Saccharomyces cerevisiae and eco for Escherichia coli K-12 MG1655), default same species as annotate"> <option value="same" selected="True">Same species as annotate</option> <option value="file">Background file from KOBAS Annotate</option> <option value="species">Species abbreviation</option> </param> <when value="same"></when> <when value="file"> <param format="txt" name="bgfile" type="data" label="Background file"/> </when> <when value="species"> <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 thaliana, sce for Saccharomyces cerevisiae and eco for Escherichia coli K-12 MG1655"/> </when> </conditional> <param argument="--method" type="select" label="Statistical test method"> <option selected="True" value="h">Hpergeometric test / Fisher's exact test</option> <option value="b">Binomial test</option> <option value="c">Chi-square test</option> <option value="x">Frequency list</option> </param> <param type="select" argument="--fdr" 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"/> </inputs> <outputs> <data format="tabular" name="output"/> </outputs> <tests> <test> <param name="fgfile" value="kobas_annotate_output.txt"/> <param name="species" value="aaa"/> <param name="kobasdb" value="aaa.db"/> <param name="db" value="K"/> <conditional name="bg"> <param name="bgtype" value="same"/> </conditional> <output name="out_file1" file="kobas_identify_output.txt"/> </test> </tests> <help> @HELP_KOBAS_INFO@ **KOBAS Identify** Performs statistical tests to identify significantly enriched pathways and diseases. @HELP_KOBAS_URL@ </help> <expand macro="kobas_citations"/> </tool>