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comparison loadandplot.xml @ 74:2bb6b44093ba draft

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Uploaded 20170619
author fabio
date Mon, 19 Jun 2017 12:08:59 -0400
parents a3bfaf944f73
children 7dcc25a1a062
comparison
equal deleted inserted replaced
73:156b29da2f0b 74:2bb6b44093ba
2 <description>Smooth and Plot</description> 2 <description>Smooth and Plot</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <stdio> 7
8 <exit_code range="255" level="fatal" description="Missing IWTomics package. Please be sure to have it installed before using this tool." /> 8 <command detect_errors="exit_code">
9 <exit_code range="10" level="fatal" description="An error has occurred reading the header file for regions. Please try again." />
10 <exit_code range="11" level="fatal" description="Not all region files are present in the first column of header file for regions." />
11 <exit_code range="20" level="fatal" description="An error has occurred reading the header file for features. Please try again." />
12 <exit_code range="21" level="fatal" description="Not all feature files are present in the first column of header file for features." />
13 <exit_code range="30" level="fatal" description="An error has occurred reading the data. Please try again." />
14 <exit_code range="31" level="fatal" description="Not enough columns in input file." />
15 <exit_code range="32" level="fatal" description="Duplicated regions in region file." />
16 <exit_code range="33" level="fatal" description="Duplicated windows in feature file." />
17 <exit_code range="34" level="fatal" description="Overlapping windows in feature file." />
18 <exit_code range="35" level="fatal" description="Windows in feature files do not cover all regions in region files." />
19 <exit_code range="36" level="fatal" description="All windows in a feature file must have the same size." />
20 <exit_code range="40" level="fatal" description="An error has occurred smoothing the data. Please try again." />
21 <regex match="Error" source="both" level="fatal" description="An error has occurred. Please try again." />
22 </stdio>
23
24 <command>
25 <![CDATA[ 9 <![CDATA[
26 Rscript '$__tool_directory__/loadandplot.R' outrdata='${outrdata}' outregions='${outregions}' outfeatures='${outfeatures}' outpdf='${outpdf}' 10 Rscript '$__tool_directory__/loadandplot.R' outrdata='${outrdata}' outregions='${outregions}' outfeatures='${outfeatures}' outpdf='${outpdf}'
27 11
28 #set region_paths = '|'.join( [ str( $r ) for $r in $regions ] ) 12 #set region_paths = '|'.join( [ str( $r ) for $r in $regions ] )
29 regionspaths='${region_paths}' 13 regionspaths='${region_paths}'
84 #if $probs != "": 68 #if $probs != "":
85 probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})' 69 probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})'
86 #else: 70 #else:
87 probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2})' 71 probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2})'
88 #end if 72 #end if
89 #end if 73 #end if
90
91 >& /dev/null
92 ]]> 74 ]]>
93 <!--
94 to print the stack add the following line at the end of the command and enable the corresponding entry in output
95 2> "${stackerr}"
96 -->
97 </command> 75 </command>
98 76
99 <inputs> 77 <inputs>
100 <!-- regions --> 78 <!-- regions -->
101 <param format="tabular" name="regions" type="data" label="Select region files" multiple="true" help="" /> 79 <param format="tabular" name="regions" type="data" label="Select region files" multiple="true" help="" />
223 </conditional> 201 </conditional>
224 </section> 202 </section>
225 </inputs> 203 </inputs>
226 204
227 <outputs> 205 <outputs>
228 <!--<data format="txt" name="stackerr" label="iwtomics.loadandplot.stackerr.txt" from_work_dir="iwtomics.loadandplot.stackerr.txt" />-->
229 <data format="rdata" name="outrdata" label="${tool.name} on ${on_string}: IWTomicsData Object" from_work_dir="iwtomics.loadandplot.RData" /> 206 <data format="rdata" name="outrdata" label="${tool.name} on ${on_string}: IWTomicsData Object" from_work_dir="iwtomics.loadandplot.RData" />
230 <data format="tabular" name="outregions" label="${tool.name} on ${on_string}: Region Dataset IDs" from_work_dir="iwtomics.loadandplot.regions.txt" /> 207 <data format="tabular" name="outregions" label="${tool.name} on ${on_string}: Region Dataset IDs" from_work_dir="iwtomics.loadandplot.regions.txt" />
231 <data format="tabular" name="outfeatures" label="${tool.name} on ${on_string}: Feature IDs" from_work_dir="iwtomics.loadandplot.features.txt" /> 208 <data format="tabular" name="outfeatures" label="${tool.name} on ${on_string}: Feature IDs" from_work_dir="iwtomics.loadandplot.features.txt" />
232 <data format="pdf" name="outpdf" label="${tool.name} on ${on_string}: Plotted Data" from_work_dir="iwtomics.loadandplot.pdf" /> 209 <data format="pdf" name="outpdf" label="${tool.name} on ${on_string}: Plotted Data" from_work_dir="iwtomics.loadandplot.pdf" />
233 </outputs> 210 </outputs>