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annotate dialignr.xml @ 0:fbbbf8c145fc draft default tip

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
author galaxyp
date Wed, 30 Dec 2020 20:12:57 +0000
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fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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1 <tool id="dialignr" name="DIAlignR" version="@WRAPPER_VERSION@">
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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2 <description>for retention time alignment of targeted mass spectrometric data</description>
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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3 <macros>
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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4 <import>macros.xml</import>
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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5 </macros>
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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6 <requirements>
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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7 <requirement type="package" version="@TOOL_VERSION@">bioconductor-dialignr</requirement>
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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8 </requirements>
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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9 <command detect_errors="exit_code"><![CDATA[
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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10 #import re
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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11
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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12 mkdir -p ./data/mzml &&
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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13 mkdir -p ./data/osw &&
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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14
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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15 #for $mzml in $input_mzml_files:
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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16 #set $file_name_mzml = re.sub('[^\w\-_.]', '_', str($mzml.element_identifier))
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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17 echo '$file_name_mzml' >> ./runs.txt &&
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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18 ln -s '$mzml' './data/mzml/${file_name_mzml}.chrom.mzML' &&
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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19 #end for
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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20
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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21 #if $input_osw_file:
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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22 ln -s '$input_osw_file' './data/osw/merged.osw' &&
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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23 #end if
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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24
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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25 Rscript --vanilla '${__tool_directory__}/dialignr.R'
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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26 #if $input_osw_file:
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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27 --oswMerged 'TRUE'
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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28 #else:
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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29 --oswMerged 'FALSE'
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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30 #end if
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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31 --maxFdrQuery '${$adv_params.maxFdrQuery}'
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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32 --XICfilter '${$adv_params.XICfilter}'
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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33 --polyOrd '${adv_params.polyOrd}'
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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34 --kernelLen '${adv_params.kernelLen}'
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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35 --globalAlignment '${adv_params.globalAlignment}'
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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36 --globalAlignmentFdr '${adv_params.globalAlignmentFdr}'
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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37 --globalAlignmentSpan '${adv_params.globalAlignmentSpan}'
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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38 --RSEdistFactor '${adv_params.RSEdistFactor}'
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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39 --normalization '${adv_params.normalization}'
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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40 --simMeasure '${adv_params.simMeasure}'
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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41 --alignType '${adv_params.alignType}'
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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42 --goFactor '${adv_params.goFactor}'
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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43 --geFactor '${adv_params.geFactor}'
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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44 --cosAngleThresh '${adv_params.cosAngleThresh}'
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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45 --OverlapAlignment '${adv_params.OverlapAlignment}'
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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46 --dotProdThresh '${adv_params.dotProdThresh}'
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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47 --gapQuantile '${adv_params.gapQuantile}'
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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48 --hardConstrain '${adv_params.hardConstrain}'
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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49 --samples4gradient '${adv_params.samples4gradient}'
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50 --analyteFDR '${adv_params.analyteFDR}'
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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51 --unalignedFDR '${adv_params.unalignedFDR}'
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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52 --alignedFDR '${adv_params.alignedFDR}'
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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53 --baselineType '${adv_params.baselineType}'
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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54 --integrationType '${adv_params.integrationType}'
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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55 --fitEMG '${adv_params.fitEMG}'
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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56 --recalIntensity '${adv_params.recalIntensity}'
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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57 --fillMissing '${adv_params.fillMissing}'
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58 --smoothPeakArea '${adv_params.smoothPeakArea}'
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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59 &&
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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60
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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61 cat alignedTargetedRuns.csv | sed 's/,/\t/g' > alignedTargetedRuns.tsv
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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62 ]]></command>
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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63 <inputs>
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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64 <param name="input_mzml_files" type="data" format="mzml" multiple="true" label="MZML file(s)" help="Sample file(s) in .MZML format." />
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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65 <param name="input_osw_file" type="data" format="osw" optional="true" multiple="false" label="OSW file" help="Sample file in .OSW format." />
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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66 <section name="adv_params" title="Advanced parameters">
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67 <param name="maxFdrQuery" type="float" min="0" max="1" value="0.05" label="Maximum FDR query" help="Numeric value between 0 and 1. It is used to filter features from osw file which have SCORE_MS2.QVALUE less than itself." />
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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68 <param name="XICfilter" type="select">
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69 <option value="sgolay" selected="true">sgolay</option>
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70 <option value="boxcar">boxcar</option>
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71 <option value="gaussian">gaussian</option>
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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72 <option value="loess ">loess</option>
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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73 <option value="none">none</option>
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74 </param>
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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75 <param name="polyOrd" type="integer" min="0" value="4" label="Order of the polynomial to be fit in the kernel" />
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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76 <param name="kernelLen" type="integer" min="0" value="9" label="Number of data-points to consider in the kernel" />
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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77 <param name="globalAlignment" type="select" label="Global alignment">
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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78 <option value="loess" selected="true">loess</option>
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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79 <option value="linear">linear</option>
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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80 </param>
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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81 <param name="globalAlignmentFdr" type="float" min="0" max="1" value="0.01" label="Global alignment FDR" help="Numeric value between 0 and 1. Features should have m-score lower than this value for participation in LOESS fit." />
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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82 <param name="globalAlignmentSpan" type="float" min="0" max="1" value="0.1" label="Global alignment Span" help="Span value for LOESS fit. For targeted proteomics 0.1 could be used." />
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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83 <param name="RSEdistFactor" type="float" min="0" value="3.5" label="RSE distance" help="Defines how much distance in the unit of rse remains a noBeef zone." />
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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84 <param name="normalization" type="select" label="Normalization">
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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85 <option value="mean" selected="true">mean</option>
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galaxyp
parents:
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86 <option value="12">12</option>
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87 </param>
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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88 <param name="simMeasure" type="select" label="SIM measure">
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
galaxyp
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89 <option value="dotProduct">dotProduct</option>
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90 <option value="cosineAngle">cosineAngle</option>
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91 <option value="cosine2Angle">cosine2Angle</option>
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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92 <option value="dotProductMasked" selected="true">dotProductMasked</option>
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93 <option value="euclideanDist">euclideanDist</option>
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94 <option value="covariance">covariance</option>
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95 <option value="correlation">correlation</option>
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96 </param>
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97 <param name="alignType" type="select" label="Alignment method">
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98 <option value="global">global</option>
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99 <option value="local">local</option>
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100 <option value="hybrid" selected="true">hybrid</option>
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101 </param>
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102 <param name="goFactor" type="float" min="0" value="0.125" label="Gap penalty (first gap)" help="Penalty for introducing first gap in alignment. This value is multiplied by base gap-penalty." />
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103 <param name="geFactor" type="float" min="0" value="40" label="Gap penalty (subsequent gaps)" help="Penalty for introducing subsequent gaps in alignment. This value is multiplied by base gap-penalty." />
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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104 <param name="cosAngleThresh" type="float" min="0" value="0.3" label="cosAngleTresh" help="In SIM measure = dotProductMasked mode, angular similarity should be higher than cosAngleThresh otherwise similarity is forced to zero." />
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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105 <param name="OverlapAlignment" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Overlap alignment" help="An input for alignment with free end-gaps. No: Global alignment Yes: Overlap alignment" />
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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106 <param name="dotProdThresh" type="float" min="0" value="0.96" label="dotProdThresh" help="In SIM measure = dotProductMasked mode, values in similarity matrix higher than dotProdThresh quantile are checked for angular similarity." />
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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107 <param name="gapQuantile" type="float" min="0" max="1" value="0.5" label="Gap quantile" help="Must be between 0 and 1. This is used to calculate base gap-penalty from similarity distribution." />
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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108 <param name="hardConstrain" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Hard constrain" help="No: Indices farther from noBeef distance are filled with distance from linear fit line." />
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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109 <param name="samples4gradient" type="float" min="0" value="100" label="Samples for gradient" help="Modulates penalization of masked indices." />
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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110 <param name="analyteFDR" type="float" min="0" max="1" value="0.01" label="Analyte FDR" help="Defines the upper limit of FDR on a precursor to be considered for multipeptide." />
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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111 <param name="unalignedFDR" type="float" min="0" max="1" value="0.01" label="Unaligned FDR" help="Must be between 0 and maxFdrQuery. Features below unalignedFDR are considered for quantification even without the RT alignment." />
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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112 <param name="alignedFDR" type="float" min="0" max="1" value="0.05" label="Aligned FDR" help="Must be between unalignedFDR and 1. Features below alignedFDRare considered for quantification after the alignment." />
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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113 <param name="baselineType" type="select" label="Baseline method" help="Method to estimate the background of a peak contained in XICs.">
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114 <option value="base_to_base" selected="true">base to base</option>
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115 <option value="vertical_division_min">vertical division min</option>
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116 <option value="vertical_division_max">vertical division max</option>
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117 </param>
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118 <param name="integrationType" type="select" label="Integration method" help="Method to compute the area of a peak contained in XICs.">
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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119 <option value="intensity_sum" selected="true">intensity sum</option>
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120 <option value="trapezoid">trapezoid</option>
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121 <option value="simpson">simpson</option>
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122 </param>
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123 <param name="fitEMG" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Fit EMG" help="Enable/disable exponentially modified gaussian peak model fitting." />
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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124 <param name="recalIntensity" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Recal intensity" help="Recalculate intensity for all analytes." />
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125 <param name="fillMissing" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Fill missing" help="Calculate intensity for analytes for which features are not found." />
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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126 <param name="smoothPeakArea" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Smooth peak area" help="No: Raw chromatograms will be used for quantification. Yes: Smoothed chromatograms will be used for quantification." />
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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127 </section>
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128 </inputs>
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129 <outputs>
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130 <data name="out_aligned_targeted_runs" format="tabular" label="${tool.name} on ${on_string}: alignedTargetedRuns.tsv" from_work_dir="alignedTargetedRuns.tsv" />
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131 </outputs>
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132 <tests>
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133 <test>
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134 <param name="input_mzml_files" ftype="mzml" value="hroest_K120809_Strep0_PlasmaBiolRepl2_R04_SW_filt,hroest_K120809_Strep10_PlasmaBiolRepl2_R04_SW_filt" />
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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135 <param name="input_osw_file" ftype="osw" value="merged.osw" />
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136 <output name="out_aligned_targeted_runs" file="alignedTargetedRuns.tsv" />
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137 </test>
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138 <test>
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139 <param name="input_mzml_files" ftype="mzml" value="hroest_K120809_Strep0_PlasmaBiolRepl2_R04_SW_filt,hroest_K120809_Strep10_PlasmaBiolRepl2_R04_SW_filt" />
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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140 <param name="input_osw_file" ftype="osw" value="merged.osw" />
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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141 <param name="adv_params|maxFdrQuery" value="0.001" />
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142 <output name="out_aligned_targeted_runs" file="alignedTargetedRuns_fdr.tsv" />
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143 </test>
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144 </tests>
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145 <help><![CDATA[
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146 DIAlignR
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147 =============
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148
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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149 DIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks.
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
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150
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151 For more information see the DIAlignR documentation_.
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152
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153 .. _documentation: https://github.com/shubham1637/DIAlignR
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154
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155 ]]></help>
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156 <citations>
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
galaxyp
parents:
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157 <citation type="doi">10.1074/mcp.TIR118.001132</citation>
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
galaxyp
parents:
diff changeset
158 </citations>
fbbbf8c145fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr commit 8dd046346db8261c462e2f3f5b4ff7f2433348df"
galaxyp
parents:
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159 </tool>