Mercurial > repos > lecorguille > xcms_xcmsset

comparison abims_xcms_xcmsSet.xml @ 5:b9a87af62223 draft

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planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty
author lecorguille
date Wed, 06 Apr 2016 03:22:15 -0400
parents 4509e9dd03e4
children 60f6c208ca16
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4:4509e9dd03e4 5:b9a87af62223
2 2
3 <description>Filtration and Peak Identification using xcmsSet function from xcms R package to preprocess LC/MS data for relative quantification and statistical analysis </description> 3 <description>Filtration and Peak Identification using xcmsSet function from xcms R package to preprocess LC/MS data for relative quantification and statistical analysis </description>
4 4
5 <requirements> 5 <requirements>
6 <requirement type="package" version="3.1.2">R</requirement> 6 <requirement type="package" version="3.1.2">R</requirement>
7 <requirement type="binary">Rscript</requirement> 7 <requirement type="package" version="0.4_1">r-snow</requirement>
8 <requirement type="package" version="1.44.0">xcms</requirement> 8 <requirement type="package" version="1.44.0">bioconductor-xcms</requirement>
9 <requirement type="package" version="2.2.0">xcms_w4m_script</requirement> 9 <requirement type="package" version="1.1_4">r-batch</requirement>
10 </requirements> 10 </requirements>
11 11
12 <stdio> 12 <stdio>
13 <exit_code range="1:" level="fatal" /> 13 <exit_code range="1:" level="fatal" />
14 </stdio> 14 </stdio>
15 15
16 <command><![CDATA[ 16 <command><![CDATA[
17 xcms.r 17 $__tool_directory__/xcms.r
18 #if $inputs.input == "lib": 18 #if $inputs.input == "lib":
19 library $__app__.config.user_library_import_dir/$__user_email__/$inputs.library 19 library $__app__.config.user_library_import_dir/$__user_email__/$inputs.library
20 #elif $inputs.input == "zip_file": 20 #elif $inputs.input == "zip_file":
21 zipfile $inputs.zip_file 21 zipfile $inputs.zip_file
22 #end if 22 #end if
190 <data name="log" format="txt" label="xset.log.txt" /> 190 <data name="log" format="txt" label="xset.log.txt" />
191 </outputs> 191 </outputs>
192 192
193 <tests> 193 <tests>
194 <test> 194 <test>
195 <param name="inputs.input" value="zip_file" /> 195 <param name="inputs|input" value="zip_file" />
196 <param name="inputs.zip_file" value="sacuri.zip" /> 196 <param name="inputs|zip_file" value="sacuri.zip" ftype="zip" />
197 <param name="methods.method" value="matchedFilter" /> 197 <param name="methods|method" value="matchedFilter" />
198 <param name="methods.step" value="0.01" /> 198 <param name="methods|step" value="0.01" />
199 <param name="methods.fwhm" value="4" /> 199 <param name="methods|fwhm" value="4" />
200 <param name="methods.options_m.option" value="show" /> 200 <param name="methods|options_m|option" value="show" />
201 <param name="methods.options_m.max" value="50" /> 201 <param name="methods|options_m|max" value="50" />
202 <param name="methods.options_m.snthresh" value="1" /> 202 <param name="methods|options_m|snthresh" value="1" />
203 <param name="methods.options_m.steps" value="2" /> 203 <param name="methods|options_m|steps" value="2" />
204 <!--<output name="xsetRData" file="xset.RData" />--> 204 <!--<output name="xsetRData" file="xset.RData" />-->
205 <!--<output name="sampleMetadata" file="sampleMetadata.tsv" />--> 205 <!--<output name="sampleMetadata" file="sampleMetadata.tsv" />-->
206 <!--<output name="ticsRawPdf" file="xset.TICs_raw.pdf" />--> 206 <!--<output name="ticsRawPdf" file="xset.TICs_raw.pdf" />-->
207 <!--<output name="bpcsRawPdf" file="xset.BPCs_raw.pdf" />--> 207 <!--<output name="bpcsRawPdf" file="xset.BPCs_raw.pdf" />-->
208 <output name="log"> 208 <output name="log">