annotate mqppep_preproc.xml @ 4:5c2beb4eb41c draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 1c1dbc5a9838e5cd45724b6e53246eb80437e1f1
author galaxyp
date Tue, 14 Feb 2023 17:37:36 +0000
parents b76c75521d91
children b889e05ce77d
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8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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1 <tool
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2 id="mqppep_preproc"
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3 name="MaxQuant Phosphopeptide Preprocessing"
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4 version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
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5 profile="21.05"
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6 >
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7 <description>
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8 Prep phosphoproteomic MaxQuant output for statistical anlaysis.
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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9 </description>
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10 <macros>
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11 <import>macros.xml</import>
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12 </macros>
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13 <edam_topics>
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14 <edam_topic>topic_0121</edam_topic><!-- Proteomics -->
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15 <edam_topic>topic_3520</edam_topic><!-- Proteomics experiment-->
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16 </edam_topics>
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17 <edam_operations>
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18 <edam_operation>operation_0338</edam_operation><!-- Sequence database search -->
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19 <edam_operation>operation_0361</edam_operation><!-- Sequence annotation -->
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20 <edam_operation>operation_3434</edam_operation><!-- Conversion -->
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21 <edam_operation>operation_3436</edam_operation><!-- Aggregation -->
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22 </edam_operations>
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23 <expand macro="requirements"/>
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24 <command detect_errors="exit_code"><![CDATA[
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25 echo '--- localization-filter step:'
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26 && (
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27 Rscript '$__tool_directory__/MaxQuantProcessingScript.R'
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28 -i '$phosphoSites'
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29 #if $pst_py_selector == "y"
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30 --enriched Y
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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31 #else
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32 --enriched ST
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33 #end if
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34 --phosphoCol '$phosphocol_script'
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35 --startCol '$startcol_script'
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36 --intervalCol $intervalCol
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37 --localProbCutoff $localProbCutoff
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38 --collapse_func $collapse_func
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39 -o '$phosphoPepIntensities'
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40 --locProbCutoffGraph $locProbCutoffGraph
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41 --enrichGraph $enrichGraph
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42 --locProbCutoffGraph_svg $locProbCutoffGraph_svg
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43 --enrichGraph_svg $enrichGraph_svg
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44 --filtered_data $filteredData_tabular
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45 --quant_data $quantData_tabular
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46 ) &&
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47 echo '... end localization-filter.'
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48 && (
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49 echo '--- kinase-mapping step:'
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50 ) && (
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51 perl '$__tool_directory__/PhosphoPeptide_Upstream_Kinase_Mapping.pl'
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52 -i '$phosphoPepIntensities'
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53 -f '$protein_fasta'
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54 -n '$networkin'
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55 -m '$p_sty_motifs'
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56 -p '$psp_kinase_substrate'
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57 -r '$psp_regulatory_sites'
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58 #if $pst_py_selector == "y"
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59 -P y
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60 #else
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61 -P sty
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62 #end if
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63 -F $merge_function
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64 -o '$mapped_phophopeptides'
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65 -O '$melted_phophopeptide_map'
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66 -D '$mqppep_output_sqlite'
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67 -s '$species'
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68 ) &&
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69 echo '... end kinase-mapping.'
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70 &&
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71 echo '--- merge-and-filter step:'
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72 && (
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73 python '$__tool_directory__/mqppep_mrgfltr.py'
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74 --phosphopeptides='$mapped_phophopeptides'
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75 --ppep_mapping_db='$mqppep_output_sqlite'
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76 --species='$species'
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77 --mrgfltr_tab='$preproc_tab'
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78 --mrgfltr_csv='$preproc_csv'
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79 --mrgfltr_sqlite='$preproc_sqlite'
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80 )
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81 && echo '... end merge-and-filter.'
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82 ]]></command>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
83 <configfiles>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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84 <configfile name="phosphocol_script">$phosphoCol
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
85 </configfile>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
86 <configfile name="startcol_script">$startCol
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
87 </configfile>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
88 </configfiles>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
89 <inputs>
8dfd5d2b5903 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"
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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91 label="Phospho (STY)Sites.txt"
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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92 help="Tabular 'Phospho (STY)Sites.txt' produced by MaxQuant"
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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93 />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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94 <param name="phosphoCol" type="text"
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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95 label="pattern for column 'Number of Phospho (STY)'"
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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96 help="PERL-compatible regular expression matching header of column having number of 'Phospho (STY)'"
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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97 value="^Number of Phospho [(]STY[)]$">
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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diff changeset
98 <sanitizer>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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99 <valid initial="string.printable">
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
100 <remove value="&apos;"/>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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101 </valid>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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102 </sanitizer>
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103 </param>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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104 <param name="startCol" type="text"
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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105 label="pattern for first column of intensity values"
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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106 help="PERL-compatible regular expression matching column header having first sample intensity"
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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107 value="^Intensity[^_]">
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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108 <sanitizer>
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diff changeset
109 <valid initial="string.printable">
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diff changeset
110 <remove value="&apos;"/>
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galaxyp
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111 </valid>
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galaxyp
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112 </sanitizer>
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113 </param>
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114 <param name="intervalCol" type="integer" value="1" min="1"
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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115 label="Interval between the intensity column of samples"
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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116 help="E.g., 1 if subsequent column is next sample; 2 if next sample is two columns away, etc."/>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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117 <param name="pst_py_selector" type="select"
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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118 label="Phosphopeptide enrichment type"
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119 help="Were samples enriched for pS and pT, or were they enriched for pY instead?"
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120 >
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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121 <option value="st" selected="true">pST</option>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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122 <option value="y">pY</option>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
123 </param>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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124 <param name="collapse_func" type="select"
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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125 label="Intensity merge function"
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126 help="When a peptide is multiply phosphorylated, how should intensities be merged? [default: sum]"
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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127 >
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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128 <option value="sum" selected="true">sum</option>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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129 <option value="mean">average</option>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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130 </param>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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131 <param name="localProbCutoff" type="float" value="0.75" min="0" max="1.0"
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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132 label="Localization Probability Cutoff"
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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133 help="See help below for an explanation."
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134 />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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135 <param name="merge_function" type="select" label="intensity merge-function"
8dfd5d2b5903 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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136 help="Specifies how intensities for identical phosphosites should be merged">
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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137 <option value="sum" selected="true">sum</option>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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138 <option value="average">average</option>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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139 </param>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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140 <param name="protein_fasta" type="data" format="fasta" label="UniProtKB/SwissProt FASTA database"
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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141 help="Sequence database; supply the same FASTA file as you supplied to by MaxQuant"
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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142 />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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143 <param name="networkin" type="data" format="tabular" label="NetworKIN file"
8dfd5d2b5903 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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144 help="NetworKIN file; see help section below"/>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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145 <param name="p_sty_motifs" type="data" format="tabular" label="pSTY_Motifs file"
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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146 help="pS/pT/pY phosphorylation site motifs; see help section below"/>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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147 <param name="psp_kinase_substrate" type="data" format="tabular" label="PSP_Kinase_Substrate_Dataset"
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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148 help="'Kinase-substrate dataset'; see help section below"/>
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149 <param name="psp_regulatory_sites" type="data" format="tabular" label="PSP_Regulatory_sites"
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parents:
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150 help="'Regulatory sites'; see help section below"/>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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151 <param name="species"
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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152 type="text"
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153 value = "human"
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154 label="filter to limit PhosphoSitePlus records to indicated species"
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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155 help="(field may be empty) [default: human]. If you supply this parameter, use the species indentifier seen as a suffix in UniProtKB"
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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156 />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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157 </inputs>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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158 <outputs>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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diff changeset
159 <!-- localization filter -->
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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160 <data name="phosphoPepIntensities" format="tabular" label="${phosphoSites.name}.ppep_intensities" />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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161 <data name="enrichGraph" format="pdf" label="${phosphoSites.name}.enrichment.pdf" />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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162 <data name="locProbCutoffGraph" format="pdf" label="${phosphoSites.name}.locProbCutoff.pdf" />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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163 <data name="enrichGraph_svg" format="svg" label="${phosphoSites.name}.enrichment.svg" />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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parents:
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164 <data name="locProbCutoffGraph_svg" format="svg" label="${phosphoSites.name}.locProbCutoff.svg" />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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165 <data name="filteredData_tabular" format="tabular" label="${phosphoSites.name}.filteredData" />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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166 <data name="quantData_tabular" format="tabular" label="${phosphoSites.name}.quantData" />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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167 <!-- upstream kinase mapping -->
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168 <data name="mapped_phophopeptides" format="tabular" label="${phosphoSites.name}.ppep_intensities.ppep_map"/>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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169 <data name="melted_phophopeptide_map" format="tabular" label="${phosphoSites.name}.ppep_intensities.melted"/>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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170 <data name="mqppep_output_sqlite" format="sqlite" label="${phosphoSites.name}.ppep_intensities.ppep_mapping_sqlite"/>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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171 <!-- merge and filter -->
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172 <data name="preproc_tab" format="tabular" label="${phosphoSites.name}.ppep_intensities.ppep_map.preproc_tab" />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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173 <data name="preproc_csv" format="csv" label="${phosphoSites.name}.ppep_intensities.ppep_map.preproc_csv" />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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174 <data name="preproc_sqlite" format="sqlite" label="${phosphoSites.name}.ppep_intensities.ppep_map.preproc_sqlite" />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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175 </outputs>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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176 <tests>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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177 <test>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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178 <param name="phosphoSites" ftype="tabular" value="test_input_for_preproc.tabular" />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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179 <param name="protein_fasta" ftype="fasta" value="test_swissprot.fasta" />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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180 <param name="networkin" ftype="tabular" value="test_networkin.tabular" />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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181 <param name="p_sty_motifs" ftype="tabular" value="pSTY_motifs.tabular" />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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182 <param name="psp_kinase_substrate" ftype="tabular" value="test_kinase_substrate.tabular" />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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183 <param name="psp_regulatory_sites" ftype="tabular" value="test_regulatory_sites.tabular" />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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184 <param name="pst_py_selector" value="st"/>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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185 <param name="merge_function" value="sum"/>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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186
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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187 <param name="phosphoCol" value="^Number of Phospho [(][STY][STY]*[)]$"/>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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188 <param name="startCol" value="^Intensity[^_]"/>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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189 <param name="intervalCol" value="1"/>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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190 <param name="collapse_func" value="sum"/>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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191 <param name="localProbCutoff" value="0.75"/>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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192 <param name="species" value="human"/>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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193
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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194 <output name="phosphoPepIntensities">
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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195 <assert_contents>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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196 <has_text text="Phosphopeptide" />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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197 <has_line_matching expression="AAAITDMADLEELSRLpSPLPPGpSPGSAAR.5416400.7101800.385280000.208060000.41426000.352400000" />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
198 <has_line_matching expression="pSQKQEEENPAEETGEEK.0.0.8765300.0.2355900.14706000" />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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199 </assert_contents>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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200 </output>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
201
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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diff changeset
202 <output name="preproc_tab">
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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diff changeset
203 <assert_contents>
8dfd5d2b5903 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="SSRP1_HUMAN FACT complex subunit SSRP1" />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
205 <has_text text="AEBP2_HUMAN Isoform 2 of Zinc finger protein AEBP2" />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
206 <has_text text="molecular association, regulation" />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
207 <has_text text="cell cycle regulation" />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
208 <has_text text="PPP2CA(INDUCES)" />
8dfd5d2b5903 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="SNCA(DISRUPTS)" />
8dfd5d2b5903 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="CDK7" />
8dfd5d2b5903 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="CK1alpha" />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
212 <has_text text="CK2alpha" />
8dfd5d2b5903 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="DNAPK" />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
214 <has_text text="HIPK2" />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
215 <has_text text="IKKalpha" />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
216 <has_text text="PKCalpha" />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
217 <has_text text="PKCbeta" />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
218 <has_text text="PKC" />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
219 <has_text text="CK2a2" />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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220 <has_text text="CK2alpha" />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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221 <has_text text="Csnk2a1" />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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222 </assert_contents>
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223 </output>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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diff changeset
224
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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225 <output name="melted_phophopeptide_map">
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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226 <assert_contents>
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galaxyp
parents:
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227 <has_text text="CDK7" />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
228 <has_text text="CK1alpha" />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
229 <has_text text="CK2alpha" />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
230 <has_text text="DNAPK" />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
231 <has_text text="HIPK2" />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
232 <has_text text="IKKalpha" />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
233 <has_text text="PKCalpha" />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
234 <has_text text="PKCbeta" />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
235 <has_text text="PKC" />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
236 <has_text text="CK2a2" />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
237 <has_text text="CK2alpha" />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
238 <has_text text="Csnk2a1" />
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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239 </assert_contents>
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240 </output>
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galaxyp
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241 </test>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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242 <test>
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243 <param name="phosphoSites" ftype="tabular" value="test_input_for_preproc.tabular" />
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244 <param name="protein_fasta" ftype="fasta" value="test_swissprot.fasta" />
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245 <param name="networkin" ftype="tabular" value="test_networkin.tabular" />
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246 <param name="p_sty_motifs" ftype="tabular" value="pSTY_motifs.tabular" />
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247 <param name="psp_kinase_substrate" ftype="tabular" value="test_kinase_substrate.tabular" />
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248 <param name="psp_regulatory_sites" ftype="tabular" value="test_regulatory_sites.tabular" />
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249 <param name="pst_py_selector" value="y"/>
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250 <param name="merge_function" value="sum"/>
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251
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252 <param name="phosphoCol" value="^Number of Phospho [(][STY][STY]*[)]$"/>
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253 <param name="startCol" value="^Intensity[^_]"/>
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254 <param name="intervalCol" value="1"/>
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255 <param name="collapse_func" value="sum"/>
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256 <param name="localProbCutoff" value="0.75"/>
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257 <param name="species" value="human"/>
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258
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259 <output name="phosphoPepIntensities">
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260 <assert_contents>
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261 <has_text text="Phosphopeptide" />
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262 <has_text text="pTYVDPFTpYEDPNQAVR" />
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263 </assert_contents>
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264 </output>
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265
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266 <output name="preproc_tab">
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267 <assert_contents>
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268 <has_text text="pTYVDPFTpYEDPNQAVR" />
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269 <has_text text="EEKHLNQGVRpTYVDPFTYEDP" />
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270 <has_text text="GVRTYVDPFTpYEDPNQAVREF" />
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271 <has_text text="HLNQGVRtYVDPFTY" />
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272 <has_text text="TYVDPFTyEDPNQAV" />
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273 <has_text text="EPHA4" />
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274 <has_text text="pT595, pY602" />
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275 <has_text text="pT544, pY551" />
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276 <has_text text="P54764;" />
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277 <has_text text="P54764-2" />
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278 </assert_contents>
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279 </output>
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280
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281 <output name="melted_phophopeptide_map">
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282 <assert_contents>
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283 <has_text text="EphA6" />
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284 <has_text text="EPHA4" />
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285 <has_text text="EphA4" />
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286 </assert_contents>
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287 </output>
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288 </test>
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289 </tests>
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290 <help><![CDATA[
1
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291 =============================================================
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292 **Phopsphoproteomic Enrichment Pipeline Preprocessing Steps**
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293 =============================================================
0
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294
1
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295 *Overview*
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296 ==========
0
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297
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298 Prior to statistical analysis, it is necessary to perform
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299 three steps to transform the MaxQuant output
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300 for phosphoproteome-enriched samples.
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301
1
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302 *Workflow position*
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303 ===================
0
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304
1
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305 Upstream tool
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306 =============
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307
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308 The input dataset for this tool is the ``Phospho (STY)Sites.txt`` file that is produced:
0
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309
1
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310 - by the Galaxy "MaxQuant" (``maxquant``) tool
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311 - or by the Galaxy "Maxquant (using mqpar.xml)" (``maxquant_mqpar``) tool
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312 - or by the desktop version of MaxQuant.
0
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313
1
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314 Downstream tool
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315 ===============
0
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316
1
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317 The "MaxQuant Phosphopeptide ANOVA" tool (``mqppep_anova``) consumes the "preprocessed" output file ``preproc_tab`` that this tool produces.
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318
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319 *Phopsphoproteomic Enrichment Pipeline Localization-Probability Cut-Off*
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320 ========================================================================
0
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321
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322 This step applies a "localization-probability cut-off" for phosphopeptides for each phosphopeptide.
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323 Higher values may reduce the number of peptides in the output.
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324 The default value of 0.75 reflects the text of [Cheng 2018]:
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325
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326 "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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327
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328 This tool wraps an R script. written by Larry Cheng, that performs the following (in order):
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329
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330 1. Remove contaminant and reverse sequence rows
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331 2. Filters rows based on localization probability
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332 3. Extract the quantitative data
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333 4. Inserts a "p" before the phosphorylated residue(s) in each peptide sequence
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334 5. Merges (aggregating by "sum" or "average") multiply-phosphorylated peptides
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335 6. Filters output phosphopeptides based on enrichment
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336 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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337
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338 Note that the "ProTeomiX Quality Control Report"
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339 [Bielow 2016] (available at `https://github.com/cbielow/PTXQC/
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340 <https://github.com/cbielow/PTXQC/>`_) is run by the Galaxy wrappers for MaxQuant,
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341 so it is omitted here even though it was included in Larry Cheng's original script.
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342
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343
1
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344 Input dataset
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345 =============
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346
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347 Phospho (STY)Sites.txt
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348 This is the ``MaxQuant Phospho (STY)Sites.txt`` file produced by MaxQuant.
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349 If you use the desktop version of MaxQuant, you will find this file in the ``txt`` folder.
0
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350
1
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351 Input parameters
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352 ================
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353
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354 Localization probability cutoff
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355 Minimum localization probability; see above.
0
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356
1
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357 Intensity merge-function
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358 Specifies how intensities for identical phosphosites should be merged; see above.
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359
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360 Output datasets
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361 ===============
0
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362
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363 ``ppep_intensities``
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364 Data table (in tabular format) presenting, for each sample, the mass-spectral intensity of each phopshopeptide having localization probability greater than the cutoff.
1
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365
0
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366 ``enrichment.pdf``
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367 Graph (in PDF format) presenting non-zero proportions of pS, pT, and pY among the phosphosites; note that a phosphopeptide may have multiple phosphosite.
1
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368
0
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369 ``locProbCutoff.pdf``
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370 Graph (in PDF format) contrasting proportion of phosphopeptides above the localization probability cutoff with the proportion below.
1
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371
0
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372 ``enrichment.svg``
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373 Enrichment graph (in downloadable "scalable vector graphics" format) for incorporation into documents.
1
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374
0
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375 ``locProbCutoff.svg``
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376 Localization probability cutoff graph (in downloadable "scalable vector graphics" format) for incorporation into documents.
1
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377
0
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378 ``filteredData``
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379 Data table (in tabular format) comprising rows of the ``phosphSites`` input file that are not flagged as contaminants or reversed sequences.
1
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380
0
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381 ``quantData``
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382 Data table (in tabular format) comprising rows of the ``filteredData`` file whose localization probability exceeds the **Localization Probability Cutoff** parameter.
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383
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384 Authors
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385 =======
0
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386
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387 ``Nicholas A. Graham``
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388 (`ORCiD 0000-0002-6811-1941 <https://orcid.org/0000-0002-6811-1941>`_) initiated the original script.
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389
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390 ``Larry C. Cheng``
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391 (`ORCiD 0000-0002-6922-6433 <https://orcid.org/0000-0002-6922-6433>`_) updated the original script.
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392
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393 ``Arthur C. Eschenlauer``
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394 (`ORCiD 0000-0002-2882-0508 <https://orcid.org/0000-0002-2882-0508>`_) adapted the script to run in Galaxy.
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395
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396 ``James E. Johnson``
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397 (University of Minnesota Supercomputing Institute) adapted the script to run in Galaxy.
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398
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399
1
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400 *Phopsphoproteomic Enrichment Pipeline Upstream Kinase Mapping*
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401 ===============================================================
0
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402
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403 This step searches phosphopeptides against several databases for known or predicted sites.
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404
1
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405 Input databases
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406 ===============
0
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407
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408 ``networkin``
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409 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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410
1
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411 To generate this file:
0
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412
1
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413 (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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414 (2) Decompress the .tsv.xz with file with "unxz" (from XZ Utils `https://tukaani.org/xz/ <https://tukaani.org/xz/>`_);
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415 (3) Filter out the rows having "network_kin" less than 2.0.
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416
1
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417 The result should be a tab-separated file with the following columns:
0
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418
1
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419 - ``#substrate``
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420 - ``position``
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421 - ``id``
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422 - ``networkin_score``
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423 - ``tree``
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424 - ``netphorest_group``
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425 - ``netphorest_score``
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426 - ``string_identifier``
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427 - ``string_score``
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428 - ``substrate_name``
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429 - ``sequence``
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430 - ``string_path``
0
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431
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432
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433 ``p_sty_motifs``
1
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434 This database merges motif patterns from [Amanchy 2007] and Phosida [Gnad 2011].
0
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435
1
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436 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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437
1
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438 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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439
1
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440 This file has three tab-separated columns (and no header):
0
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441
1
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442 - column 1 is an (ignored) identifier
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443 - column 2 is a Perl regular expression
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444 - column 3 is a descriptor.
0
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445
1
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446 For two examples:
0
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447
1
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448 ``2<TAB>R.R..(pS|pT)<TAB>Akt kinase substrate motif (HPRD)``
0
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449
1
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450 ``10<TAB>R..(pS|pT)V<TAB>CAMK2_Phosida``
0
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451
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452 ``psp_kinase_substrate``
1
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453 '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>`_.
0
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454
1
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455 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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456
1
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457 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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458
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459 ``psp_regulatory_sites``
1
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460 '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>`_.
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461
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462 Terms of use and citatation are as for the ``psp_kinase_substrate`` file.
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463
1
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464 Output datasets
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465 ===============
0
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466
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467 ``ppep_map``
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468 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:
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469
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470 "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."
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471
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472
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473 ``melted``
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474 Data table (in tabular format) presenting, for each phosphopeptide, the gene and one of the phospho-motifs or kinase-substrate sites.
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475
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476 ``ppep_mapping_sqlite``
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477 SQLite database (consumed by the merge/filter step).
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478
1
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479 Authors
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480 =======
0
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481
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482 ``Nicholas A. Graham``
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483 (`ORCiD 0000-0002-6811-1941 <https://orcid.org/0000-0002-6811-1941>`_) wrote the original script.
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484
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485 ``Arthur C. Eschenlauer``
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
486 (`ORCiD 0000-0002-2882-0508 <https://orcid.org/0000-0002-2882-0508>`_) adapted the script to run in Galaxy.
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
487
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
488
1
b76c75521d91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents: 0
diff changeset
489 *Phopsphoproteomic Enrichment Pipeline Merge and Filter*
b76c75521d91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents: 0
diff changeset
490 ========================================================
0
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
491
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
492 This step merges mapped metadata into metadata for phosphopeptides, filtering by species.
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
493
1
b76c75521d91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents: 0
diff changeset
494 Input parameters
b76c75521d91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents: 0
diff changeset
495 ================
0
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
496
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
497 ``species``
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
498 Limit PhosphoSitesPlus to indicated species. Default: **human**
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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parents:
diff changeset
499
1
b76c75521d91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents: 0
diff changeset
500 Output datasets
b76c75521d91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents: 0
diff changeset
501 ===============
0
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
502
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
503 ``preproc_tab``
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
504 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:
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
505
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
506 "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."
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
507
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
508 ``preproc_csv``
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
509 Phosphopeptides annotated with SwissProt and phosphosite metadata, in CSV format.
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
510
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
511 ``preproc_sqlite``
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
512 ``ppep_mapping_sqlite`` updated with annotations, in SQLite format.
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
513
1
b76c75521d91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents: 0
diff changeset
514 Authors
b76c75521d91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents: 0
diff changeset
515 =======
0
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
516
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
517 ``Nicholas A. Graham``
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
518 (`ORCiD 0000-0002-6811-1941 <https://orcid.org/0000-0002-6811-1941>`_) initiated the original script.
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
519
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
520 ``Larry C. Cheng``
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
521 (`ORCiD 0000-0002-6922-6433 <https://orcid.org/0000-0002-6922-6433>`_) updated the original script.
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
522
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
523 ``Arthur C. Eschenlauer``
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
524 (`ORCiD 0000-0002-2882-0508 <https://orcid.org/0000-0002-2882-0508>`_) adapted the script to run in Galaxy.
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
525
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
526 .. |reg| unicode:: U+000AE .. REGISTERED SIGN
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
527 ]]></help>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
528 <citations>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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parents:
diff changeset
529 <!-- upstream kinase mapping -->
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
530 <!-- Amanchy, R., Periaswamy, B., Mathivanan, S. et al. A curated compendium of phosphorylation motifs. PMID: 17344875 -->
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
531 <citation type="doi">10.1038/nbt0307-285</citation>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
532 <!-- Aken 2016 "The Ensembl gene annotation system." PMID: 33137190 -->
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
533 <citation type="doi">10.1093/database/baw093</citation>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
534 <!-- localization filter -->
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
535 <!-- Bielow_2016 "Proteomics Quality Control: Quality Control Software for MaxQuant Results" PMID: 26653327 -->
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
536 <citation type="doi">10.1021/acs.jproteome.5b00780</citation>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
537 <!-- all three -->
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
538 <!-- Cheng 2018 "Phosphopeptide Enrichment ..." PMID: 30124664 -->
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
539 <citation type="doi">10.3791/57996</citation>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
540 <!-- localization and upstream kinase mapping -->
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
541 <!-- Cox 2014 "Accurate proteome-wide label-free quantification ..." PMID: 24942700 -->
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
542 <citation type="doi">10.1074/mcp.M113.031591</citation>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
543 <!-- Cox 2008 "MaxQuant enables high peptide identification rates ..." PMID: 19029910 -->
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
544 <!-- upstream kinase mapping -->
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
545 <citation type="doi">10.1038/nbt.1511</citation>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
546 <!-- Gnad 2011 "PHOSIDA 2011: the posttranslational modification database." PMID: 21081558 -->
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
547 <citation type="doi">10.1093/nar/gkq1159</citation>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
548 <!-- localization filter -->
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
549 <!-- Hogrebe_2018 "Benchmarking common quantification strategies for large-scale phosphoproteomics" PMID: 29535314 -->
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
550 <citation type="doi">10.1038/s41467-018-03309-6</citation>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
551 <!-- upstream kinase mapping -->
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
552 <!-- Horn 2014 "KinomeXplorer: an integrated platform for kinome biology studies." PMID: 24874572 -->
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
553 <citation type="doi">10.1038/nmeth.2968</citation>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
554 <!-- upstream kinase mapping and merge and filter -->
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
555 <!-- Hornbeck 2012 "PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse." PMID: 22135298 -->
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
556 <citation type="doi">10.1093/nar/gkr1122</citation>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
557 <!-- upstream kinase mapping -->
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
558 <!-- Linding 2007 "Systematic discovery of in vivo phosphorylation networks." PMID: 17570479 -->
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
559 <citation type="doi">10.1016/j.cell.2007.05.052</citation>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
560 <!-- localization filter -->
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
561 <!-- Olsen_2006 "Global, in vivo, and site-specific phosphorylation dynamics in signaling networks" PMID: 17081983 -->
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
562 <citation type="doi">10.1016/j.cell.2006.09.026</citation>
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
563 </citations>
8dfd5d2b5903 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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564 </tool>