Mercurial > repos > jjohnson > cistrome_beta
diff beta_macros.xml @ 2:9c5241259454 draft
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/cistrome_beta commit 76ad167e754d8254ee4e9c6d2047c84c5f2da55a-dirty
| author | jjohnson |
|---|---|
| date | Thu, 22 Mar 2018 08:33:55 -0400 |
| parents | 20453b656907 |
| children | 067573bac905 |
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--- a/beta_macros.xml Tue Sep 16 12:51:50 2014 -0500 +++ b/beta_macros.xml Thu Mar 22 08:33:55 2018 -0400 @@ -1,185 +1,187 @@ <macros> - <macro name="requirements"> - <requirements> - <requirement type="package" version="1.7.1">numpy</requirement> - <requirement type="package" version="2.15.0">R</requirement> - <requirement type="package" version="1.0.6">beta</requirement> - </requirements> - </macro> + <macro name="requirements"> + <requirements> + <requirement type="package" version="1.0.7">beta</requirement> + </requirements> + </macro> - <macro name="stdio"> - <stdio> - <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> - <exit_code range="1:" level="fatal" description="Error" /> - </stdio> - </macro> + <macro name="stdio"> + <stdio> + <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + </macro> - <macro name="common_params"> - <param format="bed" name="peakfile" type="data" label="BED file for Peaks"> - <validator type="unspecified_build" /> - </param> - <param name="output_dir" type="hidden" label="Name for the output files" value="BETA_OUTPUT"/> - <param name="name" type="hidden" label="Name for the output files" value="NA"/> - <param name="distance" type="integer" label="the distance from gene TSS within which peaks will be selected" value="100000"> - <validator type="in_range" max="20000000" min="0" message="The Relative distance is out of range, the parameter has to be between 0 to 20000000" /> - </param> - <param name="peaknumber" type="integer" label="Peaks considered to contribute to the genes" value="10000"> - <validator type="in_range" max="200000" min="100" message="The Relative distance is out of range, the parameter has to be between 100 to 10000" /> - </param> - </macro> + <macro name="common_params"> + <param format="bed" name="peakfile" type="data" label="BED file for Peaks"> + <validator type="unspecified_build" /> + </param> + <param name="output_dir" type="hidden" label="Name for the output files" value="BETA_OUTPUT"/> + <param name="name" type="hidden" label="Name for the output files" value="NA"/> + <param name="distance" type="integer" label="the distance from gene TSS within which peaks will be selected" value="100000"> + <validator type="in_range" max="20000000" min="0" message="The Relative distance is out of range, the parameter has to be between 0 to 20000000" /> + </param> + <param name="peaknumber" type="integer" label="Peaks considered to contribute to the genes" value="10000"> + <validator type="in_range" max="200000" min="100" message="The Relative distance is out of range, the parameter has to be between 100 to 10000" /> + </param> + </macro> - <macro name="boundary"> + <macro name="boundary"> <conditional name="boundary"> - <param name="boundaryLimit" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Use CTCF boundary to filter peaks around a gene"/> - <when value="no"/> - <when value="yes"> - <yield /> - </when> + <param name="boundaryLimit" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Use CTCF boundary to filter peaks around a gene"/> + <when value="no"/> + <when value="yes"> + <yield /> + </when> </conditional> - </macro> + </macro> - <macro name="genome_params"> - <conditional name="refGenome"> - <param name="genomeName" type="select" label="genome reference"> - <option value="hg19">hg19 (built-in)</option> - <option value="mm9">mm9 (built-in)</option> - <option value="other">other</option> - </param> - <when value="hg19"> - <expand macro="boundary" /> - </when> - <when value="mm9"> - <expand macro="boundary" /> - </when> - <when value="other"> - <param name="refseq" type="data" format="tabular" label="UCSC Refseq Genes (From UCSC Table Browser)" - help="Columns: name,chrom,strand,txStart,txEnd,name"/> - <expand macro="boundary"> - <param name="bl_bed" type="data" format="bed" label="BED format boundary file"/> - </expand> - </when> - </conditional> - </macro> + <macro name="genome_params"> + <conditional name="refGenome"> + <param name="genomeName" type="select" label="genome reference"> + <option value="hg19">hg19 (built-in)</option> + <option value="mm9">mm9 (built-in)</option> + <option value="other">other</option> + </param> + <when value="hg19"> + <expand macro="boundary" /> + </when> + <when value="mm9"> + <expand macro="boundary" /> + </when> + <when value="other"> + <param name="refseq" type="data" format="tabular" label="UCSC Refseq Genes (From UCSC Table Browser)" + help="Columns: name,chrom,strand,txStart,txEnd,name"/> + <expand macro="boundary"> + <param name="bl_bed" type="data" format="bed" label="BED format boundary file"/> + </expand> + </when> + </conditional> + </macro> - <macro name="refGenomeSourceConditional"> - <conditional name="refGenomeSource"> - <param name="genomeSource" type="select" label="Use a built in reference genome or own from your history" help="Genome Reference Fasta sequence"> - <option value="cached" selected="True">Use a built-in genome</option> - <option value="history">Use a genome from history</option> - </param> - <when value="cached"> - <param name="all_fasta_source" type="select" label="Source FASTA Sequence"> - <options from_data_table="all_fasta"/> - </param> - </when> - <when value="history"> - <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" /> - </when> <!-- history --> - </conditional> <!-- refGenomeSource --> - </macro> + <macro name="refGenomeSourceConditional"> + <conditional name="refGenomeSource"> + <param name="genomeSource" type="select" label="Use a built in reference genome or one from your history" help="Genome Reference Fasta sequence"> + <option value="cached" selected="True">Use a built-in genome</option> + <option value="history">Use a genome from history</option> + </param> + <when value="cached"> + <param name="all_fasta_source" type="select" label="Source FASTA Sequence"> + <options from_data_table="all_fasta"/> + </param> + </when> + <when value="history"> + <param name="ownFile" type="data" format="fasta" label="Select the reference genome" /> + </when> <!-- history --> + </conditional> <!-- refGenomeSource --> + </macro> - <macro name="extended_params"> - <param format="txt" name="exprefile" type="data" label="TEXT file for differential expression data"> - <validator type="unspecified_build" /> - </param> - <conditional name="expression"> - <param name="kind" type="select" label="Expression FIle Type" help="Preset columns for Cuffdiff, LIMMA, and BETA Specific Format"> - <option value="CUF">RNA-seq data with Cuffdiff default format</option> - <option value="LIM">MicroArray data with LIMMA default format</option> - <option value="BSF">BETA Specific Format</option> - <option value="O">Other tools processed data with BETA specific format</option> + <macro name="extended_params"> + <param format="txt" name="exprefile" type="data" label="TEXT file for differential expression data"> + <validator type="unspecified_build" /> </param> - <when value="CUF"> - <param name="expreinfo" type="text" value="2,10,13" label="Column number of the geneid, regulate status and statistics value"/> - </when> - <when value="LIM"> - <param name="expreinfo" type="text" value="2,5,7" label="Column number of the geneid, regulate status and statistics value"/> - </when> - <when value="BSF"> - <param name="expreinfo" type="text" value="1,2,3" label="Column number of the geneid, regulate status and statistics value"/> - </when> - <when value="O"> - <param name="expreinfo" type="text" value="" label="Column number of the geneid, regulate status and statistics value is required"> - <validator type="regex" message="Enter column numbers:geneid,test_stat,value">^\d+,\d+,\d+$</validator> + <conditional name="expression"> + <param name="kind" type="select" label="Expression FIle Type" help="Preset columns for Cuffdiff, LIMMA, and BETA Specific Format"> + <option value="CUF">RNA-seq data with Cuffdiff default format</option> + <option value="LIM">MicroArray data with LIMMA default format</option> + <option value="BSF">BETA Specific Format</option> + <option value="O">Other tools processed data with BETA specific format</option> </param> - </when> - </conditional> - <param name="gname2" type="select" label="TRUE if gene ID in expression file identified by official gene symbol"> - <option value="Refseq">Refseq</option> - <option value="Gene_Symbol">Gene Symbol</option> - </param> - <param name="diff_fdr" type="float" label="get the most significant expression differentially changed genes by this cutoff based on fdr or pvalue" value="1.0"> - <validator type="in_range" max="1.0" min="0" message="The Relative distance is out of range, the parameter has to be between 0 to 1.0" /> - </param> - <param name="diff_amount" type="float" label="get the most significant expression differentially changed genes by amount" value="0.5"> - <validator type="in_range" max="20000" min="0" message="The Relative distance is out of range, the parameter has to be between 0 to 20000" /> - </param> - <param name="method" type="select" label="method to do the TF/CR function prediction" optional="true"> - <option value="score">regulatory potential</option> - <option value="distance">distance to the nearest peak</option> - </param> - - </macro> + <when value="CUF"> + <param name="expreinfo" type="text" value="2,10,13" label="Column number of the geneid, regulate status and statistics value"/> + </when> + <when value="LIM"> + <param name="expreinfo" type="text" value="2,5,7" label="Column number of the geneid, regulate status and statistics value"/> + </when> + <when value="BSF"> + <param name="expreinfo" type="text" value="1,2,3" label="Column number of the geneid, regulate status and statistics value"/> + </when> + <when value="O"> + <param name="expreinfo" type="text" value="" label="Column number of the geneid, regulate status and statistics value is required"> + <validator type="regex" message="Enter column numbers:geneid,test_stat,value">^\d+,\d+,\d+$</validator> + </param> + </when> + </conditional> + <param name="gname2" type="select" label="TRUE if gene ID in expression file identified by official gene symbol"> + <option value="Refseq">Refseq</option> + <option value="Gene_Symbol">Gene Symbol</option> + </param> + <param name="diff_fdr" type="float" label="get the most significant expression differentially changed genes by this cutoff based on fdr or pvalue" value="1.0"> + <validator type="in_range" max="1.0" min="0" message="The Relative distance is out of range, the parameter has to be between 0 to 1.0" /> + </param> + <param name="diff_amount" type="float" label="get the most significant expression differentially changed genes by amount" value="0.5"> + <validator type="in_range" max="20000" min="0" message="The Relative distance is out of range, the parameter has to be between 0 to 20000" /> + </param> + <param name="method" type="select" label="method to do the TF/CR function prediction" optional="true"> + <option value="score">regulatory potential</option> + <option value="distance">distance to the nearest peak</option> + </param> + </macro> - <template name="common_opts"> - -p "$peakfile" - -d $distance --pn $peaknumber -o $output_dir -n $name - </template> + <template name="common_opts"> + -p "$peakfile" + -d $distance --pn $peaknumber -o $output_dir -n $name + </template> - <template name="genome_opts"> -#if $refGenome.genomeName == 'hg19': - -g $refGenome.genomeName - ## -r \$BETA_LIB_PATH/BETA/references/hg19.refseq - #if $refGenome.boundary.boundaryLimit: - --bl - ## --bf \$BETA_LIB_PATH/BETA/references/hg19_CTCF_bound.bed - #end if -#elif $refGenome.genomeName == 'mm9': - -g $refGenome.genomeName - ## -r \$BETA_LIB_PATH/BETA/references/mm9.refseq - #if $refGenome.boundary.boundaryLimit: - --bl - ## --bf \$BETA_LIB_PATH/BETA/references/mm9_CTCF_bound.bed - #end if -#else - -r $refGenome.refseq - #if $refGenome.boundary.boundaryLimit: - --bl - --bf $refGenome.boundary.bl_bed - #end if -#end if - </template> - <template name="ref_genome_seq_opts"> -#if $refGenomeSource.genomeSource == 'cached': - --gs $refGenomeSource.all_fasta_source.fields.path -#else - --gs $refGenomeSource.ownFile -#end if - </template> + <template name="genome_opts"> + #if $refGenome.genomeName == 'hg19': + -g $refGenome.genomeName + ## -r \$BETA_LIB_PATH/BETA/references/hg19.refseq + #if $refGenome.boundary.boundaryLimit: + --bl + ## --bf \$BETA_LIB_PATH/BETA/references/hg19_CTCF_bound.bed + #end if + #elif $refGenome.genomeName == 'mm9': + -g $refGenome.genomeName + ## -r \$BETA_LIB_PATH/BETA/references/mm9.refseq + #if $refGenome.boundary.boundaryLimit: + --bl + ## --bf \$BETA_LIB_PATH/BETA/references/mm9_CTCF_bound.bed + #end if + #else + -r $refGenome.refseq + #if $refGenome.boundary.boundaryLimit: + --bl + --bf $refGenome.boundary.bl_bed + #end if + #end if + </template> + <template name="ref_genome_seq_opts"> + #if $refGenomeSource.genomeSource == 'cached': + --gs $refGenomeSource.all_fasta_source.fields.path + #else + --gs $refGenomeSource.ownFile + #end if + </template> - <template name="extended_opts"> - -e "$exprefile" - -k $expression.kind --info $expression.expreinfo --method $method - --da $diff_amount --df $diff_fdr -c 1 -#if $gname2 == "Gene_Symbol": - --gname2" -#end if - </template> + <template name="extended_opts"> + -e "$exprefile" + -k $expression.kind --info $expression.expreinfo --method $method + --da $diff_amount --df $diff_fdr -c 1 + #if $gname2 == "Gene_Symbol": + --gname2" + #end if + </template> - <token name="@EXTERNAL_DOCUMENTATION@"> + <token name="@EXTERNAL_DOCUMENTATION@"> For details about this application, please go to: - http://cistrome.org/BETA/index.html + http://cistrome.org/BETA/index.html - </token> - <token name="@CITATION_SECTION@">------ + </token> + <token name="@CITATION_SECTION@"> **Citation** For the underlying tool, please cite the following publication: Wang, S., Sun, H., Ma, J., Zang, C., Wang, C., Wang, J., Tang Q, Meyer CA, Zhang Y, Liu, X. S. (2013). Target analysis by integration of transcriptome and ChIP-seq data with BETA. Nature protocols, 8(12), 2502-2515. PMID: 24263090 - </token> + </token> + <xml name="citations"> + <citations> + <citation type="doi">10.1038/nprot.2013.150</citation> + </citations> + </xml> </macros>