Mercurial > repos > alermine > nebula
comparison [APliBio]Nebula tools suite/Nebula/AnnotateGenes/annotateGenes_wrapper.xml @ 0:2ec3ba0e9e70 draft
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author | alermine |
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date | Thu, 25 Oct 2012 08:18:25 -0400 |
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-1:000000000000 | 0:2ec3ba0e9e70 |
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1 <tool id="annotateGenes" name="AnnotateGenes" version="1.0"> | |
2 <description>Annotation of genes with ChIP-Seq peaks</description> | |
3 <command interpreter="bash"> | |
4 #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 | |
5 </command> | |
6 <inputs> | |
7 | |
8 <param name="inputfile" type="data" label="ChIP peaks" value="ChIP peaks File" format="bed"/> | |
9 <conditional name="use_control"> | |
10 <param name="use_control_selector" type="select" label="Use control data"> | |
11 <option value="no" selected="true">No</option> | |
12 <option value="yes">Yes</option> | |
13 </param> | |
14 <when value="yes"> | |
15 <param name="controlfile" type="data" label="Control peaks" value="Control peaks File" format="bed"/> | |
16 <param name="bootstraps" type="select" label="Number of bootstrap iterations" help="Using bootstrap resampling from the control will significantly slow down the procedure"> | |
17 <option value="1" selected="true" >do not use bootstrap resampling</option> | |
18 <option value="10" >10</option> | |
19 <option value="100" >100</option> | |
20 </param> | |
21 </when> | |
22 </conditional> | |
23 | |
24 <param name="left" type="integer" label="Define Promoter is a region up to X bp upstream gene TSS" value="-2000"/> | |
25 <param name="right" type="integer" label="Define Immediate Downstream is a region up to X bp downstream gene TSS" value="2000"/> | |
26 <param name="EnhLeft" type="integer" label="Define Enhancer is a region up to X bp upstream gene TSS" value="-30000"/> | |
27 <param name="DownGene" type="integer" label="Define Gene Downstream is a region up to X bp downstream transcription end" value="5000"/> | |
28 | |
29 <conditional name="input_organism"> | |
30 <param name="input_organism_selector" type="select" label="Select organism"> | |
31 <option value="Human" selected="true">Homo sapiens</option> | |
32 <option value="Mouse">Mus musculus</option> | |
33 <option value="Zebrafish">Zebrafish (Danio rerio)</option> | |
34 <option value="XTropicalis">X.Tropicalis</option> | |
35 <option value="Bacteria/MycoTube">M. tuberculosis</option> | |
36 </param> | |
37 <when value="Human"> | |
38 <param name="version" type="select" label="Select genome vesion"> | |
39 <option value="hg19" selected="true">hg19</option> | |
40 <option value="hg18">hg18</option> | |
41 </param> | |
42 </when> | |
43 <when value="Mouse"> | |
44 <param name="version" type="select" label="Select genome vesion"> | |
45 <option value="mm8" >mm8</option> | |
46 <option value="mm9" selected="true">mm9</option> | |
47 <option value="mm10" >mm10</option> | |
48 </param> | |
49 </when> | |
50 <when value="Zebrafish"> | |
51 <param name="version" type="select" label="Select genome vesion"> | |
52 <option value="zv9" selected="true">zv9</option> | |
53 </param> | |
54 </when> | |
55 <when value="XTropicalis"> | |
56 <param name="version" type="select" label="Select genome vesion"> | |
57 <option value="xenTro2" >xenTro2</option> | |
58 <option value="xenTro3" selected="true">xenTro3</option> | |
59 </param> | |
60 </when> | |
61 <when value="Bacteria/MycoTube"> | |
62 <param name="version" type="select" label="Select genome vesion"> | |
63 <option value="H37Rv" selected="true">H37Rv</option> | |
64 </param> | |
65 </when> | |
66 </conditional> | |
67 | |
68 | |
69 | |
70 <conditional name="use_reg"> | |
71 <param name="use_reg_selector" type="select" label="Use transcriptomic data (up- and down- regulated genes)"> | |
72 <option value="no" selected="true">No</option> | |
73 <option value="yes">Yes</option> | |
74 </param> | |
75 <when value="yes"> | |
76 <param name="regfile" type="data" label="File with information about gene regulation" value="Regulation data" format="txt"/> | |
77 </when> | |
78 </conditional> | |
79 | |
80 <param name="if_PDF" type="boolean" label="Do you want to have a PDF image (default PNG)?" truevalue="1" falsevalue="0" checked="False"/> | |
81 </inputs> | |
82 <outputs> | |
83 <data name="outputPNG" format="png" label="Gene Stats (png)"> | |
84 <filter>(if_PDF == 0)</filter> | |
85 </data> | |
86 <data name="outputPDF" format="pdf" label="Gene Stats (pdf)"> | |
87 <filter>(if_PDF == True)</filter> | |
88 </data> | |
89 | |
90 <data name="stats" format="tabular" label="Annotated Genes (ChIP)"/> | |
91 <data name="log" format="tabular" label=".LOG for Annotated Genes"/> | |
92 <data name="statsControl" format="tabular" label="Annotated Genes (Control)"> | |
93 <filter>(use_control['use_control_selector'] == 'yes')</filter> | |
94 </data> | |
95 </outputs> | |
96 <help> | |
97 **What it does** | |
98 | |
99 This tool annotates peaks with genomic feature (promoter, enhancer, exon, intron, etc.) and creates a .png file with distribution | |
100 | |
101 </help> | |
102 </tool> |