Mercurial > repos > galaxyp > pyprophet_export

annotate pyprophet_export.xml @ 2:102d940d365c 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 10:50:40 -0400
parents 2bc6bbf651b9
children 3cf580bf28e2
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2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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1 <tool id="pyprophet_export" name="PyProphet export" version="@VERSION@.0">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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2 <description>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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3 Export tabular files, optional swath2stats export
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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4 </description>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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5 <macros>
2bc6bbf651b9 "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>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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7 </macros>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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8 <expand macro="requirements">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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9 <requirement type="package" version="1.16.0">bioconductor-swath2stats</requirement>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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10 <requirement type="package" version="0.8.4">r-dplyr</requirement>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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11 <requirement type="package" version="1.12.8">r-data.table</requirement>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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12 <requirement type="package" version="2.3">r-gridextra</requirement>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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13 </expand>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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14 <command detect_errors="aggressive">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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15 <![CDATA[
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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16 ln -s '$input' ./input.osw &&
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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17 pyprophet export
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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18 --in=./input.osw
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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19 --format=$conditional_output.format
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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20
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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21 #if $conditional_output.format=='legacy_split':
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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22 $conditional_output.transition_quant
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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23 --max_transition_pep=$conditional_output.max_transition_pep
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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24 --ipf=$conditional_output.ipf
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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25 --ipf_max_peptidoform_pep=$conditional_output.ipf_max_peptidoform_pep
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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26 --max_rs_peakgroup_qvalue=$conditional_output.max_rs_peakgroup_qvalue
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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27 --max_global_peptide_qvalue=$conditional_output.max_global_peptide_qvalue
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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28 --max_global_protein_qvalue=$conditional_output.max_global_protein_qvalue
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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29
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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30 #elif $conditional_output.format=='legacy_merged':
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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31 $conditional_output.transition_quant
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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32 --max_transition_pep=$conditional_output.max_transition_pep
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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33 --ipf=$conditional_output.ipf
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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34 --ipf_max_peptidoform_pep=$conditional_output.ipf_max_peptidoform_pep
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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35 --max_rs_peakgroup_qvalue=$conditional_output.max_rs_peakgroup_qvalue
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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36 --max_global_peptide_qvalue=$conditional_output.max_global_peptide_qvalue
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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37 --max_global_protein_qvalue=$conditional_output.max_global_protein_qvalue
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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38
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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39 #elif $conditional_output.format=='matrix':
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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40 --ipf=$conditional_output.ipf
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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41 --ipf_max_peptidoform_pep=$conditional_output.ipf_max_peptidoform_pep
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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42 --max_rs_peakgroup_qvalue=$conditional_output.max_rs_peakgroup_qvalue
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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43 --max_global_peptide_qvalue=$conditional_output.max_global_peptide_qvalue
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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44 --max_global_protein_qvalue=$conditional_output.max_global_protein_qvalue
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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45 #end if
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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46 $peptide_error
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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47 $protein_error
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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48 --out=./output.tsv
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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49
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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50 #if $conditional_swath2stats.swath2stats=='yes_swath2stats':
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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51 && cat '${swath2stats}'
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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52 && Rscript '${swath2stats}'
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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53 #end if
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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54
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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55 #if $conditional_output.format=='score_plots':
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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56 && mv *score_plots.pdf '$score_plots'
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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57 #else:
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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58 && mv output.tsv '$export_file'
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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59 #end if
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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60
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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61
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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62 ]]>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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63 </command>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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64 <configfiles>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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65 <configfile name="swath2stats"><![CDATA[
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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66
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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67 #if $conditional_swath2stats.swath2stats=='yes_swath2stats':
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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68
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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69 library("SWATH2stats")
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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70 library("data.table")
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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71 library("dplyr")
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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72 library(gridExtra)
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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73
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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74 ########################### Input ##############################################
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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75
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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76 ## read in pyprophet export file
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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77 data_me <- data.frame(fread('output.tsv', sep='\t', header=TRUE))
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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78
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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79 ## read in study design template
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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80 study_design <- data.frame(fread('$conditional_swath2stats.study_design', sep='\t', header=TRUE))
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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81
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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82 ## merge both files on filename column
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
83 data.annotated <- sample_annotation(data_me, study_design, column.file = "filename")
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
84
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
85
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
86 ########################### QC plots and tabular files #########################
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
87
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
88 ## remove decoys when generating plots
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
89 data.annotated.nodecoy <- subset(data.annotated, decoy==FALSE)
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
90
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
91 pdf("summary.pdf", fonts = "Times", pointsize = 12)
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
92 plot(0,type='n',axes=FALSE,ann=FALSE)
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
93 title(main="Summarized plots and tables from pyprophet export file")
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
94
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
95 ## Look at Numbers of peptides and proteins per run
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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96 grid.table(count_analytes(data.annotated.nodecoy), rows= NULL)
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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97
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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98 ## Correlation of the intensities
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
99 correlation_int <- plot_correlation_between_samples(data.annotated.nodecoy, column.values = 'Intensity')
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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100
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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101 ## Plot the correlation of the delta_rt, which is the deviation of the retention time from the expected retention time
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
102 correlation_rt <- plot_correlation_between_samples(data.annotated.nodecoy, column.values = 'delta_rt')
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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103
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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104 ## Plot the variation of the signal across replicates
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
105 variation <- plot_variation(data.annotated.nodecoy)
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
106 plot(0,type='n',axes=FALSE,ann=FALSE)
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
107 grid.table(variation[[2]])
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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108
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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109 ## Plot the total variation versus variation within replicates
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
110 variation_total <- plot_variation_vs_total(data.annotated.nodecoy)
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
111
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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112 ## Calculate the summed signal per peptide and protein across samples
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
113 peptide_signal <- write_matrix_peptides(data.annotated.nodecoy)
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
114 protein_signal <- write_matrix_proteins(data.annotated.nodecoy)
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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115
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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116
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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117 #if str($conditional_swath2stats.conditional_fdr_replica.calc_fdr_replica) =="calc_fdr_replica_yes":
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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118
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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119 ## Estimate the overall FDR across runs using a target decoy strategy
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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120 fdr_target_decoy <- assess_fdr_overall(data.annotated, n.range = $conditional_swath2stats.conditional_fdr_replica.n_range, FFT = $conditional_swath2stats.conditional_fdr_replica.fft, output = 'Rconsole')
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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121 print(fdr_target_decoy)
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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122 dev.off()
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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123 #else
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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124 dev.off()
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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125 #end if
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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126
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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127 ############################# Filtering ########################################
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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128
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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129 data.filtered = data.annotated
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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130
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
131 #if str($conditional_swath2stats.conditional_fdr_replica.calc_fdr_replica) =="calc_fdr_replica_yes":
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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132
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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133 ## According to this FDR estimation one can filter the data with a higher mscore threshold to reach an overall protein FDR of 5%.
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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134 ## Check what m-score cut-off is requiered for Protein FDR of 5 %
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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135 cutoff_mscore = mscore4protfdr(data_me, FFT = $conditional_swath2stats.conditional_fdr_replica.fft, fdr_target = $conditional_swath2stats.conditional_fdr_replica.fdr_target)
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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136 print(cutoff_mscore)
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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137 ## Filter data for values that pass the 0.001 mscore criteria in at least two replicates of one condition
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
138 data.filtered <- filter_mscore_condition(data.filtered, cutoff_mscore, n.replica = $conditional_swath2stats.conditional_fdr_replica.n_replica)
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
139 #end if
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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140
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
141 #if str($conditional_swath2stats.conditional_max_pep.filter_max_pep) == "filter_max_pep_yes":
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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142 ## Select only the 10 peptides showing strongest signal per protein
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
143 data.filtered <- filter_on_max_peptides(data.filtered, n_peptides = $conditional_swath2stats.conditional_max_pep.n_peptides_max)
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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144 #end if
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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145
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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146
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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147 #if str($conditional_swath2stats.conditional_min_pep.filter_min_pep) == "filter_min_pep_yes":
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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148 ## Filter for proteins that are supported by at least two peptides
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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149 data.filtered <- filter_on_min_peptides(data.filtered, n_peptides = $conditional_swath2stats.conditional_min_pep.n_peptides_min)
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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150 #end if
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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151
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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152 ########################### Output ############################################
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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153 ## Convert the data into a transition-level format (one row per transition measured).
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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154 data.transition <- disaggregate(data.filtered)
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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155
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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156 ## Convert the data into the format required by MSstats.
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
157 MSstats.input <- convert4MSstats(data.transition)
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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158
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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159 ### Transitions which were found at different RT / multiple scans are combined by summarizing the Intensities
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
160 Test = MSstats.input %>% group_by(ProteinName, PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge, IsotopeLabelType, BioReplicate, Condition, Run) %>% summarise(Intensity = sum(Intensity))
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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161
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
162 Test = Test[, c("ProteinName", "PeptideSequence", "PrecursorCharge", "FragmentIon", "ProductCharge", "IsotopeLabelType", "Intensity", "BioReplicate", "Condition", "Run")]
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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163
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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diff changeset
164 write.table(Test, file="$msstats_input", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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165 write.table(peptide_signal, file="$peptide_signal", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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166 write.table(protein_signal, file="$protein_signal", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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167
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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168 #end if
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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169
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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170 ]]></configfile>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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171 </configfiles>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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172 <inputs>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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173 <param name="input" type="data" format="osw" label="Input file" help="This file needs to be in OSW format (--in)" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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174 <conditional name="conditional_output">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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175 <param argument="format" type="select" label="Export format, either matrix, legacy_split, legacy_merged (mProphet/PyProphet) or score_plots format" >
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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176 <option value="legacy_split" selected="True">legaxy_split</option>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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177 <option value="legacy_merged">legacy_merged</option>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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178 <option value="matrix">matrix</option>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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179 <option value="score_plots">score_plots</option>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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180 </param>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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181 <when value="legacy_split">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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182
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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183 <param name="transition_quant" type="boolean" truevalue="--transition_quantification" falsevalue="--no-transition_quantification" checked="True" label="Report aggregated transition-level quantification" help="(--transition_quantification / --no-transition_quantification)" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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184 <param argument="max_transition_pep" type="float" value="0.7" label="Maximum PEP to retain scored transitions for quantification (requires transition-level scoring)" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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185 <param argument="ipf" type="select" display="radio" label="Should IPF results be reported if present? 'peptidoform': Report results on peptidoform-level, 'augmented': Augment OpenSWATH results with IPF scores, 'disable': Ignore IPF results" >
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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186 <option value="peptidoform" selected="True" >peptidoform </option>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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187 <option value="augmented">augmented</option>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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188 <option value="disable">disable</option>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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189 </param>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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diff changeset
190 <param argument="ipf_max_peptidoform_pep" type="float" value="0.4" label="IPF: Filter results to maximum run-specific peptidoform-level PEP" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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191 <param argument="max_rs_peakgroup_qvalue" type="float" value="0.05" label="Filter results to maximum run-specific peak group-level q-value" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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192 <param argument="max_global_peptide_qvalue" type="float" value="0.01" label="Filter results to maximum global peptide-level q-value" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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193 <param argument="max_global_protein_qvalue" type="float" value="0.01" label="ilter results to maximum global protein-level q-value" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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194 </when>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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195 <when value="legacy_merged">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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196
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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197 <param name="transition_quant" type="boolean" truevalue="--transition_quantification" falsevalue="--no-transition_quantification" checked="True" label="Report aggregated transition-level quantification" help="(--transition_quantification / --no-transition_quantification)" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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198 <param argument="max_transition_pep" type="float" value="0.7" label="Maximum PEP to retain scored transitions for quantification (requires transition-level scoring)" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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199 <param argument="ipf" type="select" display="radio" label="Should IPF results be reported if present? 'peptidoform': Report results on peptidoform-level, 'augmented': Augment OpenSWATH results with IPF scores, 'disable': Ignore IPF results" >
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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200 <option value="peptidoform" selected="True">peptidoform </option>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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201 <option value="augmented">augmented</option>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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202 <option value="disable">disable</option>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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203 </param>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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204 <param argument="ipf_max_peptidoform_pep" type="float" value="0.4" label="IPF: Filter results to maximum run-specific peptidoform-level PEP" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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205 <param argument="max_rs_peakgroup_qvalue" type="float" value="0.05" label="Filter results to maximum run-specific peak group-level q-value" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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206 <param argument="max_global_peptide_qvalue" type="float" value="0.01" label="Filter results to maximum global peptide-level q-value" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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207 <param argument="max_global_protein_qvalue" type="float" value="0.01" label="ilter results to maximum global protein-level q-value" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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208 </when>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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209 <when value="matrix">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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210
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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211 <param argument="ipf" type="select" display="radio" label="Should IPF results be reported if present? 'peptidoform': Report results on peptidoform-level, 'augmented': Augment OpenSWATH results with IPF scores, 'disable': Ignore IPF results" >
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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212 <option value="peptidoform" selected="True">peptidoform </option>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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213 <option value="augmented">augmented</option>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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214 <option value="disable">disable</option>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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215 </param>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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216 <param argument="ipf_max_peptidoform_pep" type="float" value="0.4" label="IPF: Filter results to maximum run-specific peptidoform-level PEP" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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diff changeset
217 <param argument="max_rs_peakgroup_qvalue" type="float" value="0.05" label="Filter results to maximum run-specific peak group-level q-value" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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218 <param argument="max_global_peptide_qvalue" type="float" value="0.01" label="Filter results to maximum global peptide-level q-value" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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219 <param argument="max_global_protein_qvalue" type="float" value="0.01" label="ilter results to maximum global protein-level q-value" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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220 </when>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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221 <when value="score_plots"/>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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222 </conditional>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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223 <param name="peptide_error" type="boolean" truevalue="--peptide" falsevalue="--no-peptide" checked="True" label="Append peptide-level error-rate estimates if available" help="(--peptide / --no-peptide)" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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224 <param name="protein_error" type="boolean" truevalue="--protein" falsevalue="--no-protein" checked="True" label="Append protein-level error-rate estimates if available" help="(--protein / --no-protein)" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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225 <conditional name="conditional_swath2stats">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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226 <param name="swath2stats" type="select" label="Use swath2stats to export file for statsics" >
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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227 <option value="yes_swath2stats" selected="True">yes</option>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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228 <option value="no_swath2stats">no</option>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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229 </param>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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230 <when value="yes_swath2stats">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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231 <param name="study_design" type="data" format="tabular" label="Study design tabular file" help="Needs to have columns with Filename, Condition, BioReplicate, Run" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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232 <conditional name="conditional_fdr_replica">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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233 <param name="calc_fdr_replica" type="select" label="Filter for fdr and number of replicates" >
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
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234 <option value="calc_fdr_replica_yes" selected="True">Yes</option>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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235 <option value="calc_fdr_replica_no">No</option>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
236 </param>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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237 <when value="calc_fdr_replica_yes">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
238 <param name="fft" type="float" value="0.5" label="FFT. Ratio of false positives to true negatives, q-values from pyProphet stats output" help="As an approximation, the q-values of multiple runs are averaged and supplied as argument FFT. Numeric from 0 to 1."/>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
239 <param name="n_range" type="float" value="10" label="Option to set the number of magnitude for which the m_score threshold is decreased" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
240 <param name="fdr_target" type="float" value="0.05" label="FDR target." help="An m_score cutoff achieving and FDR smaller fdr_target will be selected. Calculated as FDR = decoys*FFT/targets" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
241 <param name="n_replica" type="integer" value="2" label="Number Replicates." help="Number of measurements within at least one condition that have to pass the mscore threshold for this transition." />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
242 </when>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
243 <when value="calc_fdr_replica_no"/>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
244 </conditional>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
245 <conditional name="conditional_max_pep">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
246 <param name="filter_max_pep" type="select" label="Filter for a maximum number of peptides per protein" >
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
247 <option value="filter_max_pep_yes" selected="True">Yes</option>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
248 <option value="filter_max_pep_no">No</option>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
249 </param>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
250 <when value="filter_max_pep_yes">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
251 <param name="n_peptides_max" type="integer" value="10" label="Maximum number of peptides per protein." help="Maximum number of highest intense peptides to filter the data on." />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
252 </when>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
253 <when value="filter_max_pep_no"/>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
254 </conditional>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
255 <conditional name="conditional_min_pep">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
256 <param name="filter_min_pep" type="select" label="Filter for a proteins that are supported by a minimum number of peptides" >
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
257 <option value="filter_min_pep_yes" selected="True">Yes</option>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
258 <option value="filter_min_pep_no">No</option>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
259 </param>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
260 <when value="filter_min_pep_yes">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
261 <param name="n_peptides_min" type="integer" value="2" label="Minimum number of peptides per protein" help="Number of minimal number of peptide IDs associated with a protein ID in order to be kept in the dataset." />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
262 </when>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
263 <when value="filter_min_pep_no"/>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
264 </conditional>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
265 </when>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
266 <when value="no_swath2stats"/>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
267 </conditional>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
268 </inputs>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
269 <outputs>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
270 <data name="export_file" format="tabular" label="${tool.name} on ${on_string}: export.tabular" >
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
271 <filter>conditional_output['format'] != 'score_plots'</filter>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
272 </data>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
273 <data name="score_plots" format="pdf" label="${tool.name} on ${on_string}: score_plots.pdf" >
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
274 <filter>conditional_output['format'] == 'score_plots'</filter>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
275 </data>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
276 <data name="summary" format="pdf" from_work_dir="summary.pdf" label = "${tool.name} on ${on_string}: summary.pdf">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
277 <filter>conditional_swath2stats['swath2stats'] == 'yes_swath2stats'</filter>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
278 </data>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
279 <data name="peptide_signal" format="tabular" label="${tool.name} on ${on_string}: peptide_signal.tabular" from_work_dir="peptide_signal.tabular" >
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
280 <filter>conditional_swath2stats['swath2stats'] == 'yes_swath2stats'</filter>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
281 </data>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
282 <data name="protein_signal" format="tabular" label="${tool.name} on ${on_string}: protein_signal.tabular" from_work_dir="protein_signal.tabular" >
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
283 <filter>conditional_swath2stats['swath2stats'] == 'yes_swath2stats'</filter>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
284 </data>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
285 <data name="msstats_input" format="tabular" label="${tool.name} on ${on_string}: msstats_input.tabular" from_work_dir="msstats_input.tabular" >
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
286 <filter>conditional_swath2stats['swath2stats'] == 'yes_swath2stats'</filter>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
287 </data>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
288 </outputs>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
289 <tests>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
290 <test expect_num_outputs="1">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
291 <param name="input" value="protein2.osw" ftype="osw" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
292 <param name="format" value="legacy_merged" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
293 <param name="max_global_peptide_qvalue" value="0.2" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
294 <conditional name="conditional_swath2stats">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
295 <param name="swath2stats" value="no_swath2stats"/>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
296 </conditional>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
297 <output name="export_file" file="output.tabular" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
298 </test>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
299 <test expect_num_outputs="1">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
300 <param name="input" value="protein2.osw" ftype="osw" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
301 <param name="format" value="score_plots" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
302 <conditional name="conditional_swath2stats">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
303 <param name="swath2stats" value="no_swath2stats"/>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
304 </conditional>
2
102d940d365c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit d1c34e31a93761cf7cfd4068bcdb70495d4d90bb"
galaxyp
parents: 0
diff changeset
305 <output name="score_plots" file="score_plots.pdf" compare="sim_size" />
0
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
306 </test>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
307 <test expect_failure="true">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
308 <param name="input" value="protein2.osw" ftype="osw" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
309 <param name="format" value="legacy_merged" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
310 <conditional name="conditional_swath2stats">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
311 <param name="study_design" value="study_design.tabular" ftype="tabular" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
312 <conditional name="conditional_fdr_replica">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
313 <param name="calc_fdr_replica" value="calc_fdr_replica_no"/>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
314 </conditional>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
315 <conditional name="conditional_max_pep">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
316 <param name="filter_max_pep" value="filter_max_pep_no" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
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317 </conditional>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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318 <conditional name="conditional_min_pep">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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319 <param name="filter_min_pep" value="filter_min_pep_no" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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320 </conditional>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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321 </conditional>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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322 <assert_stderr>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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323 <has_text text="replacement has 1 row, data has 0" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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324 </assert_stderr>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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325 </test>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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326 </tests>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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327 <help>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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328 <![CDATA[
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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329 **What it does**
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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330
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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331 PyProphet: Semi-supervised learning and scoring of OpenSWATH results.
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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332
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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333 Export tabular (tsv) tables.
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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334
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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335 Optional SWATH2stats output. SWATH2stats is intended to transform SWATH data from the OpenSWATH software into a format readable by other statistics packages while performing filtering, annotation and FDR estimation.
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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336
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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337 **Study desing file for SWATH2stats**
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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338
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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339 - Tabular file with columns that are named: Filename, Condition, BioReplicate, Run.
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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340 - The Filename should be part or the same as the original filenames used in OpenSWATH workflow
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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341 - The Condition should be a
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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342 - The BioReplicate is corresponds to the biological replicate
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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343 - The Run is the number of the run in which the sample was measured
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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344
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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345 ::
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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346
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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347 Filename Condition BioReplicate Run
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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348 healthy1.mzml healthy 1 1
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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349 healthy2.mzml healthy 2 2
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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350 diseased1.mzml diseased 3 3
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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351 ...
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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352 ...
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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353
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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354
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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355 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).
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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356
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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357 For more information, visit @link@
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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358
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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359 ]]>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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360 </help>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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361 <expand macro="citations">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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362 <citation type="doi">10.1371/journal.pone.0153160</citation>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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363 </expand>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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364 </tool>