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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="ProteinQuantifier" name="ProteinQuantifier" version="1.12.0">
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3 <description>Compute peptide and protein abundances</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">ProteinQuantifier</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="stdio"/>
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9 <expand macro="requirements"/>
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10 <command>ProteinQuantifier
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11
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12 -in ${param_in}
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13 -protxml ${param_protxml}
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14 -out ${param_out}
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15 -peptide_out ${param_peptide_out}
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16 -mzTab_out ${param_mzTab_out}
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17 -top ${param_top}
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18 -average ${param_average}
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19 ${param_include_all}
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20 ${param_filter_charge}
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21 ${param_ratios}
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22 ${param_ratiosSILAC}
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23 -threads \${GALAXY_SLOTS:-24}
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24 ${param_normalize}
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25 ${param_fix_peptides}
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26 -format:separator ${param_separator}
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27 -format:quoting ${param_quoting}
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28 -format:replacement ${param_replacement}
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29 </command>
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30 <inputs>
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31 <param name="param_in" type="data" format="featureXML,consensusXML,idXML" optional="False" label="Input file" help="(-in)"/>
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32 <param name="param_protxml" type="data" format="idXML" optional="True" label="ProteinProphet results (protXML converted to idXML) for the identification runs that were used to annotate the input.#br#Information about indistinguishable proteins will be used for protein quantification." help="(-protxml)"/>
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33 <param name="param_top" type="integer" min="0" optional="True" value="3" label="Calculate protein abundance from this number of proteotypic peptides (most abundant first; '0' for all)" help="(-top)"/>
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34 <param name="param_average" type="select" optional="True" value="median" label="Averaging method used to compute protein abundances from peptide abundances" help="(-average)">
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35 <option value="median">median</option>
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36 <option value="mean">mean</option>
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37 <option value="sum">sum</option>
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38 </param>
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39 <param name="param_include_all" type="boolean" truevalue="-include_all true" falsevalue="-include_all false" checked="false" optional="True" label="Include results for proteins with fewer proteotypic peptides than indicated by 'top' (no effect if 'top' is 0 or 1)" help="(-include_all)"/>
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40 <param name="param_filter_charge" type="boolean" truevalue="-filter_charge true" falsevalue="-filter_charge false" checked="false" optional="True" label="Distinguish between charge states of a peptide. For peptides, abundances will be reported separately for each charge;#br#for proteins, abundances will be computed based only on the most prevalent charge of each peptide.#br#By default, abundances are summed over all charge states." help="(-filter_charge)"/>
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41 <param name="param_ratios" type="boolean" truevalue="-ratios true" falsevalue="-ratios false" checked="false" optional="True" label="Add the log2 ratios of the abundance values to the output. Format: log_2(x_0/x_0) <sep> log_2(x_1/x_0) <sep> log_2(x_2/x_0) ..." help="(-ratios)"/>
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42 <param name="param_ratiosSILAC" type="boolean" truevalue="-ratiosSILAC true" falsevalue="-ratiosSILAC false" checked="false" optional="True" label="Add the log2 ratios for a triple SILAC experiment to the output. Only applicable to consensus maps of exactly three sub-maps. Format: log_2(heavy/light) <sep> log_2(heavy/middle) <sep> log_2(middle/light)" help="(-ratiosSILAC)"/>
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43 <param name="param_normalize" type="boolean" truevalue="-consensus:normalize true" falsevalue="-consensus:normalize false" checked="false" optional="True" label="Scale peptide abundances so that medians of all samples are equal" help="(-normalize)"/>
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44 <param name="param_fix_peptides" type="boolean" truevalue="-consensus:fix_peptides true" falsevalue="-consensus:fix_peptides false" checked="false" optional="True" label="Use the same peptides for protein quantification across all samples.#br#With 'top 0', all peptides that occur in every sample are considered.#br#Otherwise ('top N'), the N peptides that occur in the most samples (independently of each other) are selected,#br#breaking ties by total abundance (there is no guarantee that the best co-ocurring peptides are chosen!)." help="(-fix_peptides)"/>
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45 <param name="param_separator" type="text" size="20" label="Character(s) used to separate fields; by default, the 'tab' character is used" help="(-separator)"/>
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46 <param name="param_quoting" type="select" optional="True" value="double" label="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes,#br#'escape' for quoting with backslash-escaping of embedded quotes" help="(-quoting)">
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47 <option value="none">none</option>
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48 <option value="double">double</option>
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49 <option value="escape">escape</option>
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50 </param>
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51 <param name="param_replacement" type="text" size="20" value="_" label="If 'quoting' is 'none', used to replace occurrences of the separator in strings before writing" help="(-replacement)"/>
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52 </inputs>
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53 <outputs>
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54 <data name="param_out" label="Output file for protein abundances" format="tabular"/>
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55 <data name="param_peptide_out" label="Output file for peptide abundances" format="tabular"/>
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56 <data name="param_mzTab_out" label="Export to mzTab.#br#Either 'out', 'peptide_out', or 'mzTab_out' are required. They can be used together." format="tabular"/>
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57 </outputs>
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58 <help>**What it does**
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59
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60 Compute peptide and protein abundances
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61
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62
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63 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ProteinQuantifier.html
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64
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65 @REFERENCES@
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66 </help>
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67 </tool>
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