Mercurial > repos > tomnl > track_rt_raw

annotate track_rt_raw.xml @ 13:c7dd031d02b9 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e6935a8c6a3da23f47a753ab5a8159fa9d165535
author tomnl
date Fri, 11 May 2018 05:57:56 -0400
parents a8d243fcf676
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1 <tool id="track_rt_raw" name="track_rt_raw" version="0.0.9">
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2 <description>Track the raw retention time in the peak slot of XCMSset objects.
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3 </description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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8 <expand macro="requirements">
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9 </expand>
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12 <stdio>
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13 <exit_code range="1:" />
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14 </stdio>
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15 <command interpreter="Rscript"><![CDATA[
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16 track_rt_raw.R
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17 --xset_path=$xset
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18 --out_dir=.
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19 #if $extract_peaks:
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20 --extract_peaks
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21 #end if
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23 ]]></command>
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24 <inputs>
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26 <param type="data" name="xset" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.fillpeaks,rdata"
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27 help="xcmsSet object saved as an RData file"/>
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29 <param name="extract_peaks" type="boolean" checked="false" label="Save peaks to a tsv file"
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30 />
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32 </inputs>
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33 <outputs>
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35 <data name="xset_with_rt_raw" format="rdata" label="xset.track_rt_raw.RData" from_work_dir="xset_rt_raw_tracked.RData"/>
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37 <data name="xset_extract_peaks" format="tsv" label="xset_peaks.tsv" from_work_dir="xset_peaks.tsv">
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38 <filter>extract_peaks is True</filter>
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39 </data>
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40 </outputs>
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41 <tests>
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42 <test>
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43 <param name="xset" value="LCMS_1_LCMS_2_LCMSMS_1_LCMSMS_2.xset.group.rdata"/>
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44 <param name="extract_peaks" value="True"/>
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45 <output name="xset_extract_peaks" value="xset_peaks.tsv"/>
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46 </test>
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47 </tests>
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50 <help><![CDATA[
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51 =============================================================
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52 Track raw retention time for XCMS set
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53 =============================================================
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54 -----------
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55 Description
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56 -----------
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57 Tool to store the original raw peak information on the xset@peaks slot. Note: This can only be done BEFORE the retention alignment has been performed.
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58
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60 -----------
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61 Outputs
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62 -----------
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64 * xset_with_rt_raw: xcmsSet object with raw retention of peaks saved on the xset@peaks slot
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68 ]]></help>
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69 <expand macro="citations" />
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70 </tool>