Mercurial > repos > galaxyp > mqppep_preproc
annotate mqppep_preproc.xml @ 5:37203e501ea6 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit aa5f4a19e76ec636812865293b8ee9b196122121
author | galaxyp |
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date | Fri, 17 Feb 2023 22:38:08 +0000 |
parents | 2ccb9727516b |
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rev | line source |
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ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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1 <tool |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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2 id="mqppep_preproc" |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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3 name="MaxQuant Phosphopeptide Preprocessing" |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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4 version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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5 profile="21.05" |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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6 > |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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7 <description> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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8 Prep phosphoproteomic MaxQuant output for statistical anlaysis. |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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9 </description> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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10 <macros> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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11 <import>macros.xml</import> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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12 </macros> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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13 <edam_topics> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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14 <edam_topic>topic_0121</edam_topic><!-- Proteomics --> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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15 <edam_topic>topic_3520</edam_topic><!-- Proteomics experiment--> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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16 </edam_topics> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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17 <edam_operations> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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18 <edam_operation>operation_0338</edam_operation><!-- Sequence database search --> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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19 <edam_operation>operation_0361</edam_operation><!-- Sequence annotation --> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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20 <edam_operation>operation_3434</edam_operation><!-- Conversion --> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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21 <edam_operation>operation_3436</edam_operation><!-- Aggregation --> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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22 </edam_operations> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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23 <expand macro="requirements"/> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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24 <command detect_errors="exit_code"><![CDATA[ |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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25 echo '--- localization-filter step:' |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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26 && ( |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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27 Rscript '$__tool_directory__/MaxQuantProcessingScript.R' |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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28 -i '$phosphoSites' |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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29 #if $pst_py_selector == "y" |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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30 --enriched Y |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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31 #else |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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32 --enriched ST |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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33 #end if |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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34 --phosphoCol '$phosphocol_script' |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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35 --startCol '$startcol_script' |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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36 --intervalCol $intervalCol |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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37 --localProbCutoff $localProbCutoff |
5
37203e501ea6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit aa5f4a19e76ec636812865293b8ee9b196122121
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38 --collapse_func $merge_function |
0
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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39 -o '$phosphoPepIntensities' |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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40 --locProbCutoffGraph $locProbCutoffGraph |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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41 --enrichGraph $enrichGraph |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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42 --locProbCutoffGraph_svg $locProbCutoffGraph_svg |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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43 --enrichGraph_svg $enrichGraph_svg |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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44 --filtered_data $filteredData_tabular |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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45 --quant_data $quantData_tabular |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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46 ) && |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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47 echo '... end localization-filter.' |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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48 && ( |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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49 echo '--- kinase-mapping step:' |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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50 ) && ( |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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51 perl '$__tool_directory__/PhosphoPeptide_Upstream_Kinase_Mapping.pl' |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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52 -i '$phosphoPepIntensities' |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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53 -f '$protein_fasta' |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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54 -n '$networkin' |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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55 -m '$p_sty_motifs' |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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56 -p '$psp_kinase_substrate' |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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57 -r '$psp_regulatory_sites' |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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58 #if $pst_py_selector == "y" |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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59 -P y |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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60 #else |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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61 -P sty |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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62 #end if |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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63 -F $merge_function |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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64 -o '$mapped_phophopeptides' |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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65 -O '$melted_phophopeptide_map' |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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66 -D '$mqppep_output_sqlite' |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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67 -s '$species' |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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68 ) && |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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69 echo '... end kinase-mapping.' |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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70 && |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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71 echo '--- merge-and-filter step:' |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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72 && ( |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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73 python '$__tool_directory__/mqppep_mrgfltr.py' |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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74 --phosphopeptides='$mapped_phophopeptides' |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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75 --ppep_mapping_db='$mqppep_output_sqlite' |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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76 --species='$species' |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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77 --mrgfltr_tab='$preproc_tab' |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
78 --mrgfltr_csv='$preproc_csv' |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
79 --mrgfltr_sqlite='$preproc_sqlite' |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
80 ) |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
81 && echo '... end merge-and-filter.' |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
82 ]]></command> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
83 <configfiles> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
84 <configfile name="phosphocol_script">$phosphoCol |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
85 </configfile> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
86 <configfile name="startcol_script">$startCol |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
87 </configfile> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
88 </configfiles> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
89 <inputs> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
90 <param name="phosphoSites" type="data" format="tabular" |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
91 label="Phospho (STY)Sites.txt" |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
92 help="Tabular 'Phospho (STY)Sites.txt' produced by MaxQuant" |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
93 /> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
94 <param name="phosphoCol" type="text" |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
95 label="pattern for column 'Number of Phospho (STY)'" |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
96 help="PERL-compatible regular expression matching header of column having number of 'Phospho (STY)'" |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
97 value="^Number of Phospho [(]STY[)]$"> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
98 <sanitizer> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
99 <valid initial="string.printable"> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
100 <remove value="'"/> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
101 </valid> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
102 </sanitizer> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
103 </param> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
104 <param name="startCol" type="text" |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
105 label="pattern for first column of intensity values" |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
106 help="PERL-compatible regular expression matching column header having first sample intensity" |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
107 value="^Intensity[^_]"> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
108 <sanitizer> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
109 <valid initial="string.printable"> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
110 <remove value="'"/> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
111 </valid> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
112 </sanitizer> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
113 </param> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
114 <param name="intervalCol" type="integer" value="1" min="1" |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
115 label="Interval between the intensity column of samples" |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
116 help="E.g., 1 if subsequent column is next sample; 2 if next sample is two columns away, etc."/> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
117 <param name="pst_py_selector" type="select" |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
118 label="Phosphopeptide enrichment type" |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
119 help="Were samples enriched for pS and pT, or were they enriched for pY instead?" |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
120 > |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
121 <option value="st" selected="true">pST</option> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
122 <option value="y">pY</option> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
123 </param> |
5
37203e501ea6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit aa5f4a19e76ec636812865293b8ee9b196122121
galaxyp
parents:
1
diff
changeset
|
124 <param name="merge_function" type="select" |
0
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
125 label="Intensity merge function" |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
126 help="When a peptide is multiply phosphorylated, how should intensities be merged? [default: sum]" |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
127 > |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
128 <option value="sum" selected="true">sum</option> |
5
37203e501ea6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit aa5f4a19e76ec636812865293b8ee9b196122121
galaxyp
parents:
1
diff
changeset
|
129 <option value="average">average</option> |
0
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
130 </param> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
131 <param name="localProbCutoff" type="float" value="0.75" min="0" max="1.0" |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
132 label="Localization Probability Cutoff" |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
133 help="See help below for an explanation." |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
134 /> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
135 <param name="protein_fasta" type="data" format="fasta" label="UniProtKB/SwissProt FASTA database" |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
136 help="Sequence database; supply the same FASTA file as you supplied to by MaxQuant" |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
137 /> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
138 <param name="networkin" type="data" format="tabular" label="NetworKIN file" |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
139 help="NetworKIN file; see help section below"/> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
140 <param name="p_sty_motifs" type="data" format="tabular" label="pSTY_Motifs file" |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
141 help="pS/pT/pY phosphorylation site motifs; see help section below"/> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
142 <param name="psp_kinase_substrate" type="data" format="tabular" label="PSP_Kinase_Substrate_Dataset" |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
143 help="'Kinase-substrate dataset'; see help section below"/> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
144 <param name="psp_regulatory_sites" type="data" format="tabular" label="PSP_Regulatory_sites" |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
145 help="'Regulatory sites'; see help section below"/> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
146 <param name="species" |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
147 type="text" |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
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|
148 value = "human" |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
149 label="filter to limit PhosphoSitePlus records to indicated species" |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
150 help="(field may be empty) [default: human]. If you supply this parameter, use the species indentifier seen as a suffix in UniProtKB" |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
151 /> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
152 </inputs> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
153 <outputs> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
154 <!-- localization filter --> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
155 <data name="phosphoPepIntensities" format="tabular" label="${phosphoSites.name}.ppep_intensities" /> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
156 <data name="enrichGraph" format="pdf" label="${phosphoSites.name}.enrichment.pdf" /> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
157 <data name="locProbCutoffGraph" format="pdf" label="${phosphoSites.name}.locProbCutoff.pdf" /> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
158 <data name="enrichGraph_svg" format="svg" label="${phosphoSites.name}.enrichment.svg" /> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
159 <data name="locProbCutoffGraph_svg" format="svg" label="${phosphoSites.name}.locProbCutoff.svg" /> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
160 <data name="filteredData_tabular" format="tabular" label="${phosphoSites.name}.filteredData" /> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
161 <data name="quantData_tabular" format="tabular" label="${phosphoSites.name}.quantData" /> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
162 <!-- upstream kinase mapping --> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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163 <data name="mapped_phophopeptides" format="tabular" label="${phosphoSites.name}.ppep_intensities.ppep_map"/> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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changeset
|
164 <data name="melted_phophopeptide_map" format="tabular" label="${phosphoSites.name}.ppep_intensities.melted"/> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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165 <data name="mqppep_output_sqlite" format="sqlite" label="${phosphoSites.name}.ppep_intensities.ppep_mapping_sqlite"/> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
166 <!-- merge and filter --> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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167 <data name="preproc_tab" format="tabular" label="${phosphoSites.name}.ppep_intensities.ppep_map.preproc_tab" /> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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168 <data name="preproc_csv" format="csv" label="${phosphoSites.name}.ppep_intensities.ppep_map.preproc_csv" /> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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169 <data name="preproc_sqlite" format="sqlite" label="${phosphoSites.name}.ppep_intensities.ppep_map.preproc_sqlite" /> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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170 </outputs> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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171 <tests> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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172 <test> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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173 <param name="phosphoSites" ftype="tabular" value="test_input_for_preproc.tabular" /> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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174 <param name="protein_fasta" ftype="fasta" value="test_swissprot.fasta" /> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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175 <param name="networkin" ftype="tabular" value="test_networkin.tabular" /> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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176 <param name="p_sty_motifs" ftype="tabular" value="pSTY_motifs.tabular" /> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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177 <param name="psp_kinase_substrate" ftype="tabular" value="test_kinase_substrate.tabular" /> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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178 <param name="psp_regulatory_sites" ftype="tabular" value="test_regulatory_sites.tabular" /> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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179 <param name="pst_py_selector" value="st"/> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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180 <param name="merge_function" value="sum"/> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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181 |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
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|
182 <param name="phosphoCol" value="^Number of Phospho [(][STY][STY]*[)]$"/> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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183 <param name="startCol" value="^Intensity[^_]"/> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
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184 <param name="intervalCol" value="1"/> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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185 <param name="localProbCutoff" value="0.75"/> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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186 <param name="species" value="human"/> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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187 |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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188 <output name="phosphoPepIntensities"> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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189 <assert_contents> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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190 <has_text text="Phosphopeptide" /> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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191 <has_line_matching expression="AAAITDMADLEELSRLpSPLPPGpSPGSAAR.5416400.7101800.385280000.208060000.41426000.352400000" /> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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|
192 <has_line_matching expression="pSQKQEEENPAEETGEEK.0.0.8765300.0.2355900.14706000" /> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
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193 </assert_contents> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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|
194 </output> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
195 |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
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196 <output name="preproc_tab"> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
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|
197 <assert_contents> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
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|
198 <has_text text="SSRP1_HUMAN FACT complex subunit SSRP1" /> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
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199 <has_text text="AEBP2_HUMAN Isoform 2 of Zinc finger protein AEBP2" /> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
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|
200 <has_text text="molecular association, regulation" /> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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|
201 <has_text text="cell cycle regulation" /> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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202 <has_text text="PPP2CA(INDUCES)" /> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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203 <has_text text="SNCA(DISRUPTS)" /> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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204 <has_text text="CDK7" /> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
205 <has_text text="CK1alpha" /> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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|
206 <has_text text="CK2alpha" /> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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207 <has_text text="DNAPK" /> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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208 <has_text text="HIPK2" /> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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209 <has_text text="IKKalpha" /> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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210 <has_text text="PKCalpha" /> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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211 <has_text text="PKCbeta" /> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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changeset
|
212 <has_text text="PKC" /> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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213 <has_text text="CK2a2" /> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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214 <has_text text="CK2alpha" /> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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215 <has_text text="Csnk2a1" /> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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216 </assert_contents> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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217 </output> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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|
218 |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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219 <output name="melted_phophopeptide_map"> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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220 <assert_contents> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
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221 <has_text text="CDK7" /> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
222 <has_text text="CK1alpha" /> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
223 <has_text text="CK2alpha" /> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
224 <has_text text="DNAPK" /> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
225 <has_text text="HIPK2" /> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
226 <has_text text="IKKalpha" /> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
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227 <has_text text="PKCalpha" /> |
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228 <has_text text="PKCbeta" /> |
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229 <has_text text="PKC" /> |
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230 <has_text text="CK2a2" /> |
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231 <has_text text="CK2alpha" /> |
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232 <has_text text="Csnk2a1" /> |
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233 </assert_contents> |
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234 </output> |
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235 </test> |
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236 <test> |
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237 <param name="phosphoSites" ftype="tabular" value="test_input_for_preproc.tabular" /> |
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238 <param name="protein_fasta" ftype="fasta" value="test_swissprot.fasta" /> |
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239 <param name="networkin" ftype="tabular" value="test_networkin.tabular" /> |
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240 <param name="p_sty_motifs" ftype="tabular" value="pSTY_motifs.tabular" /> |
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241 <param name="psp_kinase_substrate" ftype="tabular" value="test_kinase_substrate.tabular" /> |
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242 <param name="psp_regulatory_sites" ftype="tabular" value="test_regulatory_sites.tabular" /> |
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243 <param name="pst_py_selector" value="y"/> |
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244 <param name="merge_function" value="sum"/> |
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245 |
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246 <param name="phosphoCol" value="^Number of Phospho [(][STY][STY]*[)]$"/> |
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247 <param name="startCol" value="^Intensity[^_]"/> |
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248 <param name="intervalCol" value="1"/> |
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249 <param name="localProbCutoff" value="0.75"/> |
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250 <param name="species" value="human"/> |
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251 |
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252 <output name="phosphoPepIntensities"> |
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253 <assert_contents> |
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254 <has_text text="Phosphopeptide" /> |
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255 <has_text text="pTYVDPFTpYEDPNQAVR" /> |
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256 </assert_contents> |
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257 </output> |
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258 |
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259 <output name="preproc_tab"> |
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260 <assert_contents> |
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261 <has_text text="pTYVDPFTpYEDPNQAVR" /> |
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262 <has_text text="EEKHLNQGVRpTYVDPFTYEDP" /> |
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263 <has_text text="GVRTYVDPFTpYEDPNQAVREF" /> |
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264 <has_text text="HLNQGVRtYVDPFTY" /> |
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265 <has_text text="TYVDPFTyEDPNQAV" /> |
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266 <has_text text="EPHA4" /> |
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267 <has_text text="pT595, pY602" /> |
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268 <has_text text="pT544, pY551" /> |
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269 <has_text text="P54764;" /> |
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270 <has_text text="P54764-2" /> |
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271 </assert_contents> |
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272 </output> |
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273 |
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274 <output name="melted_phophopeptide_map"> |
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275 <assert_contents> |
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276 <has_text text="EphA6" /> |
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277 <has_text text="EPHA4" /> |
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278 <has_text text="EphA4" /> |
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279 </assert_contents> |
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280 </output> |
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281 </test> |
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282 </tests> |
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283 <help><![CDATA[ |
1
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284 ============================================================= |
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285 **Phopsphoproteomic Enrichment Pipeline Preprocessing Steps** |
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286 ============================================================= |
0
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287 |
1
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288 *Overview* |
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289 ========== |
0
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290 |
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291 Prior to statistical analysis, it is necessary to perform |
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292 three steps to transform the MaxQuant output |
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293 for phosphoproteome-enriched samples. |
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294 |
1
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295 *Workflow position* |
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296 =================== |
0
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297 |
1
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298 Upstream tool |
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299 ============= |
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300 |
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301 The input dataset for this tool is the ``Phospho (STY)Sites.txt`` file that is produced: |
0
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302 |
1
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303 - by the Galaxy "MaxQuant" (``maxquant``) tool |
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304 - or by the Galaxy "Maxquant (using mqpar.xml)" (``maxquant_mqpar``) tool |
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305 - or by the desktop version of MaxQuant. |
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306 |
1
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307 Downstream tool |
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308 =============== |
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309 |
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310 The "MaxQuant Phosphopeptide ANOVA" tool (``mqppep_anova``) consumes the "preprocessed" output file ``preproc_tab`` that this tool produces. |
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311 |
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312 *Phopsphoproteomic Enrichment Pipeline Localization-Probability Cut-Off* |
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313 ======================================================================== |
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314 |
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315 This step applies a "localization-probability cut-off" for phosphopeptides for each phosphopeptide. |
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316 Higher values may reduce the number of peptides in the output. |
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317 The default value of 0.75 reflects the text of [Cheng 2018]: |
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318 |
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319 "For phosphopeptide identification, a localization probability cutoff is applied. This filter is performed to select for phosphopeptides with a high confidence (i.e., greater than 0.75) in phosphoresidue identification [Hogrebe 2018; Olsen 2006]. In other words, the summed probability of all other residues that could potentially contain the phospho-group is less than 0.25. This cutoff could be raised to increase the stringency of the phosphopeptide selection. In regard to the number of identifications, the expected number of pY peptides is in the hundreds, while the expected number of pST peptides is in the high thousands. These values reflect previously observed phosphoproteome distribution where about 2%, 12%, and 86% of the phosphosites are pY, pT, and pS, respectively [Olsen 2006]." |
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320 |
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321 This tool wraps an R script. written by Larry Cheng, that performs the following (in order): |
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322 |
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323 1. Remove contaminant and reverse sequence rows |
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324 2. Filters rows based on localization probability |
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325 3. Extract the quantitative data |
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326 4. Inserts a "p" before the phosphorylated residue(s) in each peptide sequence |
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327 5. Merges (aggregating by "sum" or "average") multiply-phosphorylated peptides |
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328 6. Filters output phosphopeptides based on enrichment |
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329 7. Produces an output file (in tabular format) that contains the phosphopeptide (first column) and its (possibly merged) mass spectral intensity for each sample. |
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330 |
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331 Note that the "ProTeomiX Quality Control Report" |
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332 [Bielow 2016] (available at `https://github.com/cbielow/PTXQC/ |
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333 <https://github.com/cbielow/PTXQC/>`_) is run by the Galaxy wrappers for MaxQuant, |
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334 so it is omitted here even though it was included in Larry Cheng's original script. |
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335 |
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336 |
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337 Input dataset |
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338 ============= |
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339 |
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340 Phospho (STY)Sites.txt |
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341 This is the ``MaxQuant Phospho (STY)Sites.txt`` file produced by MaxQuant. |
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342 If you use the desktop version of MaxQuant, you will find this file in the ``txt`` folder. |
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343 |
1
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344 Input parameters |
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345 ================ |
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346 |
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347 Localization probability cutoff |
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348 Minimum localization probability; see above. |
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349 |
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350 Intensity merge-function |
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351 Specifies how intensities for identical phosphosites should be merged. Choosing "sum" means that relative intensities reflect number of phospho-*residues*; choosing "average" means that relative intensities reflect number of phospho-*peptides*. |
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352 |
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353 Output datasets |
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354 =============== |
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355 |
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356 ``ppep_intensities`` |
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357 Data table (in tabular format) presenting, for each sample, the mass-spectral intensity of each phopshopeptide having localization probability greater than the cutoff. |
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358 |
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359 ``enrichment.pdf`` |
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360 Graph (in PDF format) presenting non-zero proportions of pS, pT, and pY among the phosphosites; note that a phosphopeptide may have multiple phosphosite. |
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361 |
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362 ``locProbCutoff.pdf`` |
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363 Graph (in PDF format) contrasting proportion of phosphopeptides above the localization probability cutoff with the proportion below. |
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364 |
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365 ``enrichment.svg`` |
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366 Enrichment graph (in downloadable "scalable vector graphics" format) for incorporation into documents. |
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367 |
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368 ``locProbCutoff.svg`` |
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369 Localization probability cutoff graph (in downloadable "scalable vector graphics" format) for incorporation into documents. |
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370 |
0
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371 ``filteredData`` |
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372 Data table (in tabular format) comprising rows of the ``phosphSites`` input file that are not flagged as contaminants or reversed sequences. |
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373 |
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374 ``quantData`` |
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375 Data table (in tabular format) comprising rows of the ``filteredData`` file whose localization probability exceeds the **Localization Probability Cutoff** parameter. |
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376 |
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377 Authors |
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378 ======= |
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379 |
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380 ``Nicholas A. Graham`` |
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381 (`ORCiD 0000-0002-6811-1941 <https://orcid.org/0000-0002-6811-1941>`_) initiated the original script. |
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382 |
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383 ``Larry C. Cheng`` |
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384 (`ORCiD 0000-0002-6922-6433 <https://orcid.org/0000-0002-6922-6433>`_) updated the original script. |
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385 |
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386 ``Arthur C. Eschenlauer`` |
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387 (`ORCiD 0000-0002-2882-0508 <https://orcid.org/0000-0002-2882-0508>`_) adapted the script to run in Galaxy. |
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388 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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389 ``James E. Johnson`` |
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390 (University of Minnesota Supercomputing Institute) adapted the script to run in Galaxy. |
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391 |
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392 |
1
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393 *Phopsphoproteomic Enrichment Pipeline Upstream Kinase Mapping* |
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394 =============================================================== |
0
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395 |
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396 This step searches phosphopeptides against several databases for known or predicted sites. |
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397 |
1
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398 Input databases |
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399 =============== |
0
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400 |
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401 ``networkin`` |
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402 This table is the result of filtering the NetworkKIN database [Linding 2007; Horn 2014] for cutoff score > 2.0. The ENSEMBL data used to generate the file were from Ensembl, `ensembl.org <https://web.archive.org/web/20220308011159/http://useast.ensembl.org/index.html>`_ [Howe 2021]. |
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403 |
1
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404 To generate this file: |
0
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405 |
1
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406 (1) Download the "precomputed data for all available kinase predictors against ENSEMBL" (available at the NetworkKIN predictions link on the downloads page at https://web.archive.org/web/20200208000403/http://networkin.info/download/networkin_human_predictions_3.1.tsv.xz; N.B.: "Commercial users are requested to contact the authors before using the data on the networkin.info website"); |
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407 (2) Decompress the .tsv.xz with file with "unxz" (from XZ Utils `https://tukaani.org/xz/ <https://tukaani.org/xz/>`_); |
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408 (3) Filter out the rows having "network_kin" less than 2.0. |
0
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409 |
1
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410 The result should be a tab-separated file with the following columns: |
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411 |
1
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412 - ``#substrate`` |
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413 - ``position`` |
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414 - ``id`` |
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415 - ``networkin_score`` |
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416 - ``tree`` |
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417 - ``netphorest_group`` |
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418 - ``netphorest_score`` |
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419 - ``string_identifier`` |
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420 - ``string_score`` |
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421 - ``substrate_name`` |
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422 - ``sequence`` |
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423 - ``string_path`` |
0
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424 |
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425 |
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426 ``p_sty_motifs`` |
1
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427 This database merges motif patterns from [Amanchy 2007] and Phosida [Gnad 2011]. |
0
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428 |
1
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429 The Amanchy data are adapted from `https://web.archive.org/web/*/http://hprd.org/serine_motifs <https://web.archive.org/web/*/http://hprd.org/serine_motifs>`_ and `https://web.archive.org/web/*/http://hprd.org/tyrosine_motifs <https://web.archive.org/web/*/http://hprd.org/tyrosine_motifs>`_ (both links cite the reference where each motif was published), and the patterns are translated into Perl regular expression format (`https://perldoc.perl.org/perlre <https://perldoc.perl.org/perlre>`_). |
0
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430 |
1
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431 The Phosida data are adapted (translated to Perl-formatted regular expressions) from `http://pegasus.biochem.mpg.de/phosida/help/motifs.aspx <http://pegasus.biochem.mpg.de/phosida/help/motifs.aspx>`_ (this link cites the reference where each motif was published). |
0
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432 |
1
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433 This file has three tab-separated columns (and no header): |
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434 |
1
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435 - column 1 is an (ignored) identifier |
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436 - column 2 is a Perl regular expression |
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437 - column 3 is a descriptor. |
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438 |
1
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439 For two examples: |
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440 |
1
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441 ``2<TAB>R.R..(pS|pT)<TAB>Akt kinase substrate motif (HPRD)`` |
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442 |
1
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443 ``10<TAB>R..(pS|pT)V<TAB>CAMK2_Phosida`` |
0
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444 |
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445 ``psp_kinase_substrate`` |
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446 'Kinase-substrate dataset: experimentally determined substrates, sequences, cognate kinases, and metadata curated from the literature' [Hornbeck 2011]. This tabular-formatted file may be downloaded for non-commercial purposes as 'Kinase_Substrate_Dataset.gz' from `https://www.phosphosite.org/staticDownloads.action <https://www.phosphosite.org/staticDownloads.action>`_. |
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447 |
1
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448 Data extracted from PhosphoSitePlus(R), created by Cell Signaling Technology Inc. PhosphoSitePlus is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License (`https://creativecommons.org/licenses/by-nc-sa/3.0/ <https://creativecommons.org/licenses/by-nc-sa/3.0/>`_). Attribution must be given in written, oral and digital presentations to PhosphoSitePlus, www.phosphosite.org. Written documents should additionally cite: |
0
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449 |
1
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450 Hornbeck PV, Kornhauser JM, Tkachev S, Zhang B, Skrzypek E, Murray B, Latham V, Sullivan M (2012) PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res. 40, D261-D270.; www.phosphosite.org. |
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451 |
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452 ``psp_regulatory_sites`` |
1
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453 'Regulatory sites: information curated from the literature about modification sites shown to regulate molecular functions, biological processes, and molecular interactions including protein-protein interactions' [Hornbeck 2011]. This tabular-formatted file may be downloaded for non-commercial purposes as 'Regulatory_sites.gz' from `https://www.phosphosite.org/staticDownloads.action <https://www.phosphosite.org/staticDownloads.action>`_. |
0
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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454 |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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parents:
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|
455 Terms of use and citatation are as for the ``psp_kinase_substrate`` file. |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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456 |
1
2ccb9727516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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457 Output datasets |
2ccb9727516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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|
458 =============== |
0
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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459 |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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460 ``ppep_map`` |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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461 Data table (in tabular format, consumed by the merge/filter step) presenting, for each phosphopeptide, the kinase mappings, the mass-spectral intensities for each sample, and the metadata from UniProtKB/SwissProt, phospho-sites, phospho-motifs, and regulatory sites. Data in the columns marked "``Domain``", "``ON_...``", or "``..._PhosphoSite``" are available subject to the following terms: |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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parents:
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462 |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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parents:
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463 "PhosphoSitePlus\ |reg| (PSP) was created by Cell Signaling Technology Inc. It is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License(`https://creativecommons.org/licenses/by-nc-sa/3.0/ <https://creativecommons.org/licenses/by-nc-sa/3.0/>`_). When using PSP data or analyses in printed publications or in online resources, the following acknowledgements must be included: (a) the words 'PhosphoSitePlus(R), www.phosphosite.org' must be included at appropriate places in the text or webpage, and (b) citation of [Hornbeck 2011 (`PMID: 25514926 <https://pubmed.ncbi.nlm.nih.gov/25514926>`_)] must be included in the bibliography." |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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464 |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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465 |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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466 ``melted`` |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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467 Data table (in tabular format) presenting, for each phosphopeptide, the gene and one of the phospho-motifs or kinase-substrate sites. |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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468 |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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469 ``ppep_mapping_sqlite`` |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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470 SQLite database (consumed by the merge/filter step). |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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471 |
1
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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472 Authors |
2ccb9727516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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473 ======= |
0
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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474 |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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475 ``Nicholas A. Graham`` |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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changeset
|
476 (`ORCiD 0000-0002-6811-1941 <https://orcid.org/0000-0002-6811-1941>`_) wrote the original script. |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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477 |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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changeset
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478 ``Arthur C. Eschenlauer`` |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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changeset
|
479 (`ORCiD 0000-0002-2882-0508 <https://orcid.org/0000-0002-2882-0508>`_) adapted the script to run in Galaxy. |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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480 |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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481 |
1
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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|
482 *Phopsphoproteomic Enrichment Pipeline Merge and Filter* |
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483 ======================================================== |
0
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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484 |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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485 This step merges mapped metadata into metadata for phosphopeptides, filtering by species. |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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486 |
1
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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487 Input parameters |
2ccb9727516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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488 ================ |
0
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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489 |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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490 ``species`` |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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491 Limit PhosphoSitesPlus to indicated species. Default: **human** |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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492 |
1
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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493 Output datasets |
2ccb9727516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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|
494 =============== |
0
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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495 |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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496 ``preproc_tab`` |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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497 Phosphopeptides annotated with SwissProt and phosphosite metadata, in tabular format. This file is designed to be consumed by the downstream ANOVA tool. Some data in the columns marked "PSP" are available subject to the following terms: |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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|
498 |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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parents:
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499 "PhosphoSitePlus\ |reg| (PSP) was created by Cell Signaling Technology Inc. It is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License(`https://creativecommons.org/licenses/by-nc-sa/3.0/ <https://creativecommons.org/licenses/by-nc-sa/3.0/>`_). When using PSP data or analyses in printed publications or in online resources, the following acknowledgements must be included: (a) the words 'PhosphoSitePlus(R), www.phosphosite.org' must be included at appropriate places in the text or webpage, and (b) citation of [Hornbeck 2011 (`PMID: 25514926 <https://pubmed.ncbi.nlm.nih.gov/25514926>`_)] must be included in the bibliography." |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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parents:
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changeset
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500 |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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parents:
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501 ``preproc_csv`` |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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502 Phosphopeptides annotated with SwissProt and phosphosite metadata, in CSV format. |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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503 |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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504 ``preproc_sqlite`` |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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|
505 ``ppep_mapping_sqlite`` updated with annotations, in SQLite format. |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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506 |
1
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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|
507 Authors |
2ccb9727516b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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|
508 ======= |
0
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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|
509 |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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parents:
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|
510 ``Nicholas A. Graham`` |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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parents:
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changeset
|
511 (`ORCiD 0000-0002-6811-1941 <https://orcid.org/0000-0002-6811-1941>`_) initiated the original script. |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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|
512 |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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|
513 ``Larry C. Cheng`` |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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parents:
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changeset
|
514 (`ORCiD 0000-0002-6922-6433 <https://orcid.org/0000-0002-6922-6433>`_) updated the original script. |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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parents:
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changeset
|
515 |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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parents:
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changeset
|
516 ``Arthur C. Eschenlauer`` |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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changeset
|
517 (`ORCiD 0000-0002-2882-0508 <https://orcid.org/0000-0002-2882-0508>`_) adapted the script to run in Galaxy. |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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parents:
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changeset
|
518 |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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parents:
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|
519 .. |reg| unicode:: U+000AE .. REGISTERED SIGN |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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|
520 ]]></help> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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|
521 <citations> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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parents:
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522 <!-- upstream kinase mapping --> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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|
523 <!-- Amanchy, R., Periaswamy, B., Mathivanan, S. et al. A curated compendium of phosphorylation motifs. PMID: 17344875 --> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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parents:
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changeset
|
524 <citation type="doi">10.1038/nbt0307-285</citation> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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parents:
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|
525 <!-- Aken 2016 "The Ensembl gene annotation system." PMID: 33137190 --> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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parents:
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526 <citation type="doi">10.1093/database/baw093</citation> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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527 <!-- localization filter --> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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528 <!-- Bielow_2016 "Proteomics Quality Control: Quality Control Software for MaxQuant Results" PMID: 26653327 --> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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529 <citation type="doi">10.1021/acs.jproteome.5b00780</citation> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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530 <!-- all three --> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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531 <!-- Cheng 2018 "Phosphopeptide Enrichment ..." PMID: 30124664 --> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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changeset
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532 <citation type="doi">10.3791/57996</citation> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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533 <!-- localization and upstream kinase mapping --> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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534 <!-- Cox 2014 "Accurate proteome-wide label-free quantification ..." PMID: 24942700 --> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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changeset
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535 <citation type="doi">10.1074/mcp.M113.031591</citation> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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536 <!-- Cox 2008 "MaxQuant enables high peptide identification rates ..." PMID: 19029910 --> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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537 <!-- upstream kinase mapping --> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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538 <citation type="doi">10.1038/nbt.1511</citation> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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539 <!-- Gnad 2011 "PHOSIDA 2011: the posttranslational modification database." PMID: 21081558 --> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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540 <citation type="doi">10.1093/nar/gkq1159</citation> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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541 <!-- localization filter --> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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542 <!-- Hogrebe_2018 "Benchmarking common quantification strategies for large-scale phosphoproteomics" PMID: 29535314 --> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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543 <citation type="doi">10.1038/s41467-018-03309-6</citation> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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544 <!-- upstream kinase mapping --> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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545 <!-- Horn 2014 "KinomeXplorer: an integrated platform for kinome biology studies." PMID: 24874572 --> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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546 <citation type="doi">10.1038/nmeth.2968</citation> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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547 <!-- upstream kinase mapping and merge and filter --> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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548 <!-- Hornbeck 2012 "PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse." PMID: 22135298 --> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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549 <citation type="doi">10.1093/nar/gkr1122</citation> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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550 <!-- upstream kinase mapping --> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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551 <!-- Linding 2007 "Systematic discovery of in vivo phosphorylation networks." PMID: 17570479 --> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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552 <citation type="doi">10.1016/j.cell.2007.05.052</citation> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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553 <!-- localization filter --> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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554 <!-- Olsen_2006 "Global, in vivo, and site-specific phosphorylation dynamics in signaling networks" PMID: 17081983 --> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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555 <citation type="doi">10.1016/j.cell.2006.09.026</citation> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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parents:
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556 </citations> |
ba62d93a9ef5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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557 </tool> |