Mercurial > repos > galaxyp > pyprophet_score

annotate pyprophet_score.xml @ 2:8b30c8ffa687 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit d1c34e31a93761cf7cfd4068bcdb70495d4d90bb"
author galaxyp
date Tue, 14 Apr 2020 10:53:02 -0400
parents 00816d9855fc
children
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8b30c8ffa687 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit d1c34e31a93761cf7cfd4068bcdb70495d4d90bb"
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1 <tool id="pyprophet_score" name="PyProphet score" version="@VERSION@.2">
0
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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2 <description>
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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3 Error-rate estimation for MS1, MS2 and transition-level data
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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4 </description>
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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5 <macros>
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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6 <import>macros.xml</import>
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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7 </macros>
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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8 <expand macro="requirements"/>
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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9 <command detect_errors="aggressive">
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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10 <![CDATA[
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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11 pyprophet score
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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12 --in='$input'
2
8b30c8ffa687 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit d1c34e31a93761cf7cfd4068bcdb70495d4d90bb"
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13 --classifier=$conditional_classifier.classifier
8b30c8ffa687 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit d1c34e31a93761cf7cfd4068bcdb70495d4d90bb"
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14
0
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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15 #if str($conditional_classifier.classifier)=='XGBoost':
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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16 $conditional_classifier.xgb_autotune
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8b30c8ffa687 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit d1c34e31a93761cf7cfd4068bcdb70495d4d90bb"
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17 #end if
8b30c8ffa687 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit d1c34e31a93761cf7cfd4068bcdb70495d4d90bb"
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18 #if $apply_weights:
8b30c8ffa687 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit d1c34e31a93761cf7cfd4068bcdb70495d4d90bb"
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19 --apply_weights='$apply_weights'
0
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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20 #end if
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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21 --xeval_fraction=$xeval_fraction
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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22 --xeval_num_iter=$xeval_num_iter
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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23 --level=$level
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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24 --ss_initial_fdr=$ss_initial_fdr
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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25 --ss_iteration_fdr=$ss_iteration_fdr
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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26 --ss_num_iter=$ss_num_iter
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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27 --ss_main_score='$ss_main_score'
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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28 --group_id=$group_id
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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29 $parametric
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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30 $pfdr
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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31 --pi0_lambda=$pi0_lambda_start $pi0_lambda_end $pi0_lambda_steps
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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32
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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33 --pi0_method=$pi0_method
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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34 --pi0_smooth_df=$pi0_smooth_df
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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35 $pi0_smooth_log
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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36 $lfdr_truncate
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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37 $lfdr_monotone
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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38 --lfdr_transformation=$lfdr_transformation
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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39 --lfdr_adj=$lfdr_adj
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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40 --lfdr_eps=$lfdr_eps
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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41 --ipf_max_peakgroup_rank=$ipf_max_peakgroup_rank
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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42 --ipf_max_peakgroup_pep=$ipf_max_peakgroup_pep
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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43 $tric_chromprob
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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44 $test_mode
1
00816d9855fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit ededbd58827da5e8c14d1e2a6b2bab0f293a7482"
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45 --threads "\${GALAXY_SLOTS:-4}"
0
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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46 --out='./output.osw' && mv *_report.pdf report.pdf
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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47
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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48 ]]>
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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49 </command>
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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50 <inputs>
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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51 <param name="input" type="data" format="osw" label="Input file" help="This file needs to be in OSW format (--in)" />
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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52 <conditional name="conditional_classifier">
2
8b30c8ffa687 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit d1c34e31a93761cf7cfd4068bcdb70495d4d90bb"
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53 <param argument="--classifier" type="select" label="Either a 'LDA' or 'XGBoost' classifier is used for semi-supervised learning" >
0
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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54 <option value="LDA" selected="True" >LDA</option>
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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55 <option value="XGBoost">XGBoost</option>
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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56 </param>
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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57 <when value="LDA"/>
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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58 <when value="XGBoost">
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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59 <param name="xgb_autotune" type="boolean" truevalue="--xgb_autotune" falsevalue="--no-xgb_autotune" label="XGBoost: Autotune hyperparameters" help="(--xgb_autotune / --no-xgb_autotune)"/>
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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60 </when>
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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61 </conditional>
2
8b30c8ffa687 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit d1c34e31a93761cf7cfd4068bcdb70495d4d90bb"
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62 <param argument="apply_weights" type="data" format="osw" optional="True" label="Apply PyProphet score weights file (osw format) instead of semi-supervised learning." />
0
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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63 <param argument="--level" type="select" display="radio" label="The data level selected for scoring. 'ms1ms2' integrates both MS1- and MS2-level scores and can be used instead of 'ms2'-level results" >
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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64 <option value="ms1" >MS1</option>
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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65 <option value="ms2" >MS2</option>
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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66 <option value="ms1ms2" selected="True" >MS1MS2</option>
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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67 <option value="transition">transition</option>
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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68 </param>
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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69 <param argument="--xeval_fraction" type="float" value="0.5" label="Data fraction used for cross-validation of semi-supervised learning step" />
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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70 <param argument="--xeval_num_iter" type="integer" value="10" label="Number of iterations for cross-validation of semi-supervised learning step" />
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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71 <param argument="--ss_initial_fdr" type="float" value="0.15" label="Initial FDR cutoff for best scoring targets" />
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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72 <param argument="--ss_iteration_fdr" type="float" value="0.05" label="Iteration FDR cutoff for best scoring targets" />
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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73 <param argument="--ss_num_iter" type="integer" value="10" label="Number of iterations for semi-supervised learning step" />
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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74 <param argument="--ss_main_score" type="text" value="var_xcorr_shape" label="Main score to start semi-supervised-learning" />
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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75 <param argument="--group_id" type="text" value="group_id" label="Group identifier for calculation of statistics" />
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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76 <param name="parametric" type="boolean" truevalue="--parametric" falsevalue="--no-parametric" label="Do parametric estimation of p-values" help="(--parametric / --no-parametric)"/>
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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77 <param name="pfdr" type="boolean" truevalue="--pfdr" falsevalue="--no-pfdr" label="Compute positive false discovery rate (pFDR) instead of FDR" help="(--pfdr / --no-pfdr)"/>
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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78 <param name="pi0_lambda_start" type="float" value="0.1" label="Use non-parametric estimation of p-values. Start value" help="(--pi0_lambda)"/>
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79 <param name="pi0_lambda_end" type="float" value="0.5" label="Use non-parametric estimation of p-values. End value" help="(--pi0_lambda)"/>
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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80 <param name="pi0_lambda_steps" type="float" value="0.05" label="Use non-parametric estimation of p-values. Steps value" help="(--pi0_lambda)"/>
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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81 <param argument="--pi0_method" type="select" display="radio" label="Either 'smoother' or 'bootstrap'; the method for automatically choosing tuning parameter in the estimation of pi_0, the proportion of true null hypotheses" >
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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82 <option value="bootstrap" selected="True" >bootstrap</option>
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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83 <option value="smoother">smoother</option>
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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84 </param>
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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85 <param argument="pi0_smooth_df" type="integer" value="3" label="Number of degrees-of-freedom to use when estimating pi_0 with a smoother" />
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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86 <param name="pi0_smooth_log" type="boolean" truevalue="--pi0_smooth_log_pi0" falsevalue="--no-pi0_smooth_log_pi0" label="If True and pi0_method = 'smoother', pi0 will be estimated by applying a smoother to a scatterplot of log(pi0) estimates against the tuning parameter lambda" help="(--pi0_smooth_log_pi0 / --no-pi0_smooth_log_pi0)"/>
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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87 <param name="lfdr_truncate" type="boolean" checked="True" truevalue="--lfdr_truncate" falsevalue="--no-lfdr_truncate" label="If True, local FDR values >1 are set to 1" help="(--lfdr_truncate / --no-lfdr_truncate)"/>
1
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88 <param name="lfdr_monotone" type="boolean" checked="True" truevalue="--lfdr_monotone" falsevalue="--no-lfdr_monotone" label="If True, local FDR values are non-decreasing with increasing p-values" help="(--lfdr_monotone / --no-lfdr_monotone)"/>
0
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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89 <param argument="--lfdr_transformation" type="select" display="radio" label="Either a 'probit' or 'logit' transformation is applied to the p-values so that a local FDR estimate can be formed that does not involve edge effects of the [0,1] interval in which the p-values lie" >
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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90 <option value="probit" selected="True" >probit</option>
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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91 <option value="logit">logit</option>
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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92 </param>
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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93 <param argument="--lfdr_adj" type="float" value="1.5" label="Numeric value that is applied as a multiple of the smoothing bandwidth used in the density estimation" />
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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94 <param argument="--lfdr_eps" type="float" value="1e-08" label="Numeric value that is threshold for the tails of the empirical p-value distribution" />
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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95 <param argument="--ipf_max_peakgroup_rank" type="integer" value="1" label="Assess transitions only for candidate peak groups until maximum peak group rank" />
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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96 <param argument="--ipf_max_peakgroup_pep" type="float" value="0.7" label="Assess transitions only for candidate peak groups until maximum posterior error probability" />
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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97 <param argument="--ipf_max_transition_isotope_overlap" type="float" value="0.5" label="Maximum isotope overlap to consider transitions in IPF" />
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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98 <param argument="--ipf_min_transition_sn" type="float" value="0" label="Minimum log signal-to-noise level to consider transitions in IPF. Set -1 to disable this filter" />
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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99 <param name="tric_chromprob" type="boolean" truevalue="--tric_chromprob" falsevalue="--no-tric_chromprob" label="Whether chromatogram probabilities for TRIC should be computed" help="( --tric_chromprob / --no-tric_chromprob)"/>
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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100 <param name="test_mode" type="boolean" truevalue="--test" falsevalue="--no-test" label="Run in test mode with fixed seed" />
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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101 </inputs>
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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102 <outputs>
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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103 <data name="output" format="osw" label="${tool.name} on ${on_string}: score.osw" from_work_dir="output.osw"/>
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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104 <data name="score_report" format="pdf" label="${tool.name} on ${on_string}: report.pdf" from_work_dir="report.pdf" />
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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105 </outputs>
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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106 <tests>
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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107 <test>
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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108 <param name="input" value="merged.osw" ftype="osw"/>
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109 <param name="level" value="ms2"/>
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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110 <param name="xeval_num_iter" value="2" />
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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111 <param name="ss_num_iter" value="2" />
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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112 <param name="pi0_lambda_start" value="0.1" />
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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113 <param name="pi0_lambda_end" value="0.3" />
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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114 <param name="pi0_lambda_steps" value="0.01" />
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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115 <param name="test_mode" value="True" />
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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116 <output name="output" file="score.osw" compare="sim_size" />
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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117 <output name="score_report" file="score_report.pdf" compare="sim_size" />
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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118 </test>
1
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119 <test>
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120 <param name="input" value="merged.osw" ftype="osw"/>
2
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121 <param name="apply_weights" value="score.osw" ftype="osw"/>
1
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122 <param name="level" value="ms2"/>
00816d9855fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit ededbd58827da5e8c14d1e2a6b2bab0f293a7482"
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123 <param name="xeval_num_iter" value="2" />
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124 <param name="ss_num_iter" value="2" />
00816d9855fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit ededbd58827da5e8c14d1e2a6b2bab0f293a7482"
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125 <param name="pi0_lambda_start" value="0.1" />
00816d9855fc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit ededbd58827da5e8c14d1e2a6b2bab0f293a7482"
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126 <param name="pi0_lambda_end" value="0.3" />
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127 <param name="pi0_lambda_steps" value="0.01" />
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128 <param name="test_mode" value="True" />
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129 <output name="output" file="score2.osw" compare="sim_size" />
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130 <output name="score_report" file="score_report2.pdf" compare="sim_size" />
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131 </test>
0
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132 </tests>
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133 <help>
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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134 <![CDATA[
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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135 **What it does**
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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136
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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137 PyProphet: Semi-supervised learning and scoring of OpenSWATH results.
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138
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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139 Conduct semi-supervised learning and error-rate estimation for MS1, MS2 and transition-level data.
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140
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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141 PyProphet is a Python re-implementation of the mProphet algorithm (Reiter 2010 Nature Methods) optimized for SWATH-MS data acquired by data-independent acquisition (DIA). The algorithm was originally published in (Telemann 2014 Bioinformatics) and has since been extended to support new data types and analysis modes (Rosenberger 2017, Nature biotechnology and Nature methods).
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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142
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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143 For more information, visit @link@
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144
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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145 ]]>
8b11789d8b95 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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146 </help>
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147 <expand macro="citations"/>
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148 </tool>
2
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149