Mercurial > repos > tomnl > flag_remove_peaks

comparison flag-remove-peaks.xml @ 12:cb8dce9812ff draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
author tomnl
date Thu, 14 Jun 2018 09:19:47 -0400
parents e00a33906b3e
children ac2e4562b70a
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11:e00a33906b3e 12:cb8dce9812ff
1 <tool id="flag_remove_peaks" name="flag_remove_peaks" version="0.1.6"> 1 <tool id="flag_remove_peaks" name="flag_remove_peaks" version="0.1.6">
2 <requirements>
3 <requirement type="package" >r-optparse</requirement>
4 <requirement type="package" version="1.7.2" >bioconductor-mspurity</requirement>
5 <requirement type="package" version="0.2.5" >r-xcmswrapper</requirement>
6 </requirements>
7 <description>Tool to flag and remove XCMS grouped peaks from the xcmsSet object based on various thresholds 2 <description>Tool to flag and remove XCMS grouped peaks from the xcmsSet object based on various thresholds
8 (e.g. RSD of intensity and retention time). 3 (e.g. RSD of intensity and retention time).
9 </description> 4 </description>
5
6 <macros>
7 <import>macros.xml</import>
8 </macros>
9
10 <expand macro="requirements" />
10 11
11 <stdio> 12 <stdio>
12 <exit_code range="1:" /> 13 <exit_code range="1:" />
13 </stdio> 14 </stdio>
14 <command interpreter="Rscript"><![CDATA[ 15 <command interpreter="Rscript"><![CDATA[
15 flag-remove-peaks.R 16 flag-remove-peaks.R
16 --xset_path=$xset_path 17 --xset_path=$xset_path
18 --out_dir=.
17 19
18 #if $sample_flag.sample_flag=='update' 20 #if $sample_flag.sample_flag=='update'
19 --rsd_i_sample=$sample_flag.rsd_i_sample 21 --rsd_i_sample=$sample_flag.rsd_i_sample
20 --minfrac_sample=$sample_flag.minfrac_sample 22 --minfrac_sample=$sample_flag.minfrac_sample
21 --ithres_sample=$sample_flag.ithres_sample 23 --ithres_sample=$sample_flag.ithres_sample
46 #if $choose_samp.choose_samp=='yes' 48 #if $choose_samp.choose_samp=='yes'
47 --samplelist=$choose_samp.samplelist 49 --samplelist=$choose_samp.samplelist
48 #end if 50 #end if
49 ]]></command> 51 ]]></command>
50 <inputs> 52 <inputs>
51 <param type="data" name="xset_path" 53 <param type="data" name="xset_path" format='rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata'
52 help="The path to the xcmsSet object saved as an RData file"/> 54 help="The path to the xcmsSet object saved as an RData file"/>
53 <conditional name="sample_flag"> 55 <conditional name="sample_flag">
54 <param name="sample_flag" type="select" label="Change biological sample flag parameters?"> 56 <param name="sample_flag" type="select" label="Change biological sample flag parameters?">
55 <option value="update" >Update biological sample flag parameters</option> 57 <option value="update" >Update biological sample flag parameters</option>
56 <option value="" selected="true">Use default biological sample flag parameters</option> 58 <option value="" selected="true">Use default biological sample flag parameters</option>
151 153
152 </when> 154 </when>
153 </conditional> 155 </conditional>
154 </inputs> 156 </inputs>
155 <outputs> 157 <outputs>
156 <data name="peaklist_filtered" format="tabular" label="peaklist_filtered" 158 <data name="peaklist_filtered" format="tsv" label="${tool.name} on ${on_string}: peaklist_filtered (tsv)"
157 from_work_dir="peaklist_filtered.txt" visible="true"/> 159 from_work_dir="peaklist_filtered.tsv" />
158 <data name="removed_peaks" format="tabular" label="removed_peaks" 160 <data name="removed_peaks" format="tsv" label="${tool.name} on ${on_string}: removed_peaks (tsv)"
159 from_work_dir="removed_peaks.txt" visible="true"/> 161 from_work_dir="removed_peaks.tsv" />
160 <data name="xset_filtered" format="rdata" label="xset_filtered" 162 <data name="xset_filtered" format="rdata" label="xset_filtered"
161 from_work_dir="xset_filtered.RData" visible="true"/> 163 from_work_dir="xset_filtered.RData"/>
162 </outputs> 164 </outputs>
163 <tests> 165 <tests>
164 <test> 166 <test>
167 <param name="blank_flag.blank_flag" value="update" />
168 <param name="xset_path" value="xset_flag_filter_input.RData"/>
169
165 <param name="blank_flag.blank_flag" value="update" /> 170 <param name="blank_flag.blank_flag" value="update" />
166 <conditional name="blank_flag"> 171 <conditional name="blank_flag">
167 <param name="blank_flag" value="update"/> 172 <param name="blank_flag" value="update"/>
168 <param name="blank_class" value="KO" /> 173 <param name="blank_class" value="KO" />
169 </conditional> 174 </conditional>
170 <conditional name="peak_removal"> 175 <conditional name="peak_removal">
171 <param name="peak_removal" value="remove"/> 176 <param name="peak_removal" value="remove"/>
172 </conditional> 177 </conditional>
173 <param name="xset_path" value="xset.RData" type="rdata" /> 178 <output name="peaklist_filtered" file="peaklist_filtered.tsv"/>
174 <output name="peaklist_filtered" type="tabular" file="peaklist_filtered.tabular"> 179
175 </output> 180
176 <output name="removed_peaks" type="tabular" file="removed_peaks.tabular">
177 </output>
178 181
179 182
180 </test> 183 </test>
181 </tests> 184 </tests>
182 <help><![CDATA[ 185 <help><![CDATA[
270 still being flagged. If so the process will be repeated untill the xcmsSet object only contains peaks that match 273 still being flagged. If so the process will be repeated untill the xcmsSet object only contains peaks that match
271 the peak criteria. 274 the peak criteria.
272 275
273 The output file is an xcmsSet.RData file. 276 The output file is an xcmsSet.RData file.
274 ]]></help> 277 ]]></help>
278
279 <expand macro="citations" />
275 </tool> 280 </tool>