| Next changeset 1:75cb9dfa2a43 (2016-01-04) |
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Commit message:
Uploaded |
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added:
annotateGenes_wrapper.xml |
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| diff -r 000000000000 -r 21c035ec4d66 annotateGenes_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/annotateGenes_wrapper.xml Mon Jan 04 11:38:24 2016 -0500 |
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| b'@@ -0,0 +1,146 @@\n+<!--annotateGenes - developed by Jocelyn Brayet <jocelyn.brayet@curie.fr>\n+Copyright (C) 2015 Institut Curie\n+\n+This program is free software: you can redistribute it and/or modify\n+it under the terms of the GNU General Public License as published by\n+the Free Software Foundation, either version 3 of the License, or\n+(at your option) any later version.\n+\n+This program is distributed in the hope that it will be useful,\n+but WITHOUT ANY WARRANTY; without even the implied warranty of\n+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n+GNU General Public License for more details.\n+\n+You should have received a copy of the GNU General Public License\n+along with this program. If not, see <http://www.gnu.org/licenses/>.-->\n+<tool id="annotateGenes" name="Annotation of genes with ChIP-seq peaks (transcription factors)" version="1.0">\n+ <description>Caclulates statistics for promoters, enhancers, introns/exons, etc.</description>\n+ <requirements>\n+ <container type="docker">institutcuriengsintegration/annotategenes:1.0</container>\n+ </requirements>\n+ <command interpreter="bash">\n+#if str( $if_PDF ) == \'0\' and $use_reg.use_reg_selector == "no" and $use_control.use_control_selector == "no" #annotateGenes_wrapper.sh -f $inputfile -y $log -l $left -o $outputPNG -r $right -d $DownGene -h $EnhLeft -u $stats -v $input_organism.version -p 0 #elif str( $if_PDF ) == \'0\' and $use_reg.use_reg_selector == "no" and $use_control.use_control_selector == "yes" # annotateGenes_wrapper.sh -f $inputfile -y $log -c $controlfile -b $use_control.bootstraps -x $statsControl -o $outputPNG -l $left -r $right -d $DownGene -h $EnhLeft -u $stats -v $input_organism.version -p 0 #elif str( $if_PDF ) == \'0\' and $use_reg.use_reg_selector == "yes" and $use_control.use_control_selector == "no" # annotateGenes_wrapper.sh -y $log -f $inputfile -e $regfile -l $left -o $outputPNG -r $right -d $DownGene -h $EnhLeft -u $stats -v $input_organism.version -p 0 #elif str( $if_PDF ) == \'0\' and $use_reg.use_reg_selector == "yes" and $use_control.use_control_selector == "yes" # annotateGenes_wrapper.sh -f $inputfile -c $controlfile -b $use_control.bootstraps -x $statsControl -l $left -y $log -o $outputPNG -r $right -d $DownGene -h $EnhLeft -u $stats -v $input_organism.version -e $regfile -p 0 #elif str( $if_PDF ) == \'1\' and $use_reg.use_reg_selector == "no" and $use_control.use_control_selector == "no" #annotateGenes_wrapper.sh -f $inputfile -y $log -l $left -o $outputPDF -r $right -d $DownGene -h $EnhLeft -u $stats -v $input_organism.version -p 1 #elif str( $if_PDF ) == \'1\' and $use_reg.use_reg_selector == "no" and $use_control.use_control_selector == "yes" # annotateGenes_wrapper.sh -f $inputfile -y $log -c $controlfile -b $use_control.bootstraps -x $statsControl -o $outputPDF -l $left -r $right -d $DownGene -h $EnhLeft -u $stats -v $input_organism.version -p 1 #elif str( $if_PDF ) == \'1\' and $use_reg.use_reg_selector == "yes" and $use_control.use_control_selector == "no" # annotateGenes_wrapper.sh -y $log -f $inputfile -e $regfile -l $left -o $outputPDF -r $right -d $DownGene -h $EnhLeft -u $stats -v $input_organism.version -p 1 #elif str( $if_PDF ) == \'1\' and $use_reg.use_reg_selector == "yes" and $use_control.use_control_selector == "yes" # annotateGenes_wrapper.sh -f $inputfile -c $controlfile -b $use_control.bootstraps -x $statsControl -l $left -y $log -o $outputPDF -r $right -d $DownGene -h $EnhLeft -u $stats -v $input_organism.version -e $regfile -p 1 #end if\n+ </command>\n+ <inputs>\n+ \n+ <param name="inputfile" type="data" label="ChIP peaks" value="ChIP peaks File" format="bed"/>\n+ <conditional name="use_control">\n+ <param name="use_control_selector" type="select" label="Use control data">\n+ <option value="no" selected="true">No</option>\n+ <option value="yes">Yes</option>\n+ </param>\n+ <when value="yes">\n+ <param name="controlfile" type="data" label="Control peaks" value="Control peaks File'..b' value="5000"/>\n+ \n+<conditional name="input_organism">\n+ <param name="input_organism_selector" type="select" label="Select organism">\n+ <option value="Human" selected="true">Homo sapiens</option>\n+ <option value="Mouse">Mus musculus</option>\n+\t<option value="Rat">Rattus norvegicus</option> \n+\t<option value="Cow">Cow</option> \n+ <option value="Zebrafish">Zebrafish (Danio rerio)</option> \n+ <option value="XTropicalis">X.Tropicalis</option> \n+ <option value="Bacteria/MycoTube">M. tuberculosis</option> \n+\t<option value="Celegans">C. elegans</option> \n+\t<option value="Drosophila">D. melanogaster</option> \n+ </param>\n+ <when value="Human">\n+ <param name="version" type="select" label="Select genome vesion">\n+ <option value="hg38">hg38</option>\n+ <option value="hg19" selected="true">hg19</option>\n+ <option value="hg18">hg18</option>\n+ </param>\n+ </when>\n+ <when value="Mouse">\n+ <param name="version" type="select" label="Select genome vesion">\n+ <option value="mm8" >mm8</option>\n+ <option value="mm9" selected="true">mm9</option>\n+ <option value="mm10" >mm10</option>\n+ </param>\n+ </when>\n+ <when value="Rat">\n+ <param name="version" type="select" label="Select genome vesion">\n+ <option value="rn5">rn5</option> \n+ </param>\n+ </when>\n+ <when value="Cow">\n+ <param name="version" type="select" label="Select genome vesion">\n+ <option value="bosTau7">bosTau7</option> \n+ </param>\n+ </when>\n+ <when value="Zebrafish">\n+ <param name="version" type="select" label="Select genome vesion">\n+ <option value="zv9" selected="true">zv9</option>\n+ </param>\n+ </when>\n+ <when value="XTropicalis">\n+ <param name="version" type="select" label="Select genome vesion">\n+ <option value="xenTro2" >xenTro2</option>\n+ <option value="xenTro3" selected="true">xenTro3</option>\n+ </param>\n+ </when>\n+ <when value="Bacteria/MycoTube">\n+ <param name="version" type="select" label="Select genome vesion">\n+ <option value="H37Rv" selected="true">H37Rv</option>\n+ </param>\n+ </when>\n+ <when value="Celegans">\n+ <param name="version" type="select" label="Select genome vesion">\n+ <option value="ce10" selected="true">ce10</option>\n+ </param>\n+ </when>\n+ <when value="Drosophila">\n+ <param name="version" type="select" label="Select genome vesion">\n+ <option value="dm6" selected="true">dm6</option>\n+ </param>\n+ </when>\n+</conditional>\n+\n+\n+\n+<conditional name="use_reg">\n+ <param name="use_reg_selector" type="select" label="Use transcriptomic data (up- and down- regulated genes)">\n+ <option value="no" selected="true">No</option>\n+ <option value="yes">Yes</option>\n+ </param>\n+ <when value="yes">\n+ <param name="regfile" type="data" label="File with information about gene regulation" value="Regulation data" format="txt"/>\n+ </when> \n+ </conditional>\n+\n+ <param name="if_PDF" type="boolean" label="Do you want to have a PDF image (default PNG)?" truevalue="1" falsevalue="0" checked="False"/>\n+\n+ </inputs>\n+ <outputs>\n+ <data name="outputPNG" format="png" label="Gene Stats (png)">\n+ <filter>(if_PDF == 0)</filter>\n+ </data>\n+ <data name="outputPDF" format="pdf" label="Gene Stats (pdf)">\n+ <filter>(if_PDF == True)</filter>\n+ </data>\n+\n+ <data name="stats" format="tabular" label="Annotated Genes (ChIP)"/> \n+ <data name="log" format="tabular" label=".LOG for Annotated Genes"/> \n+ <data name="statsControl" format="tabular" label="Annotated Genes (Control)">\n+ <filter>(use_control[\'use_control_selector\'] == \'yes\')</filter>\n+ </data>\n+ </outputs>\n+ <help>\n+**What it does**\n+\n+This tool annotates peaks with genomic feature (promoter, enhancer, exon, intron, etc.) and creates a .png file with distribution\n+\n+ </help>\n+</tool>\n' |