mqppep_preproc: mqppep_preproc.xml annotate

annotate mqppep_preproc.xml @ 1:2ccb9727516b draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be

author	galaxyp
date	Fri, 28 Oct 2022 18:24:43 +0000
parents	ba62d93a9ef5
children	37203e501ea6

rev	line source
0 ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1 <tool
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2 id="mqppep_preproc"
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3 name="MaxQuant Phosphopeptide Preprocessing"
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	4 version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	5 profile="21.05"
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	6 >
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	7 <description>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	8 Prep phosphoproteomic MaxQuant output for statistical anlaysis.
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	9 </description>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	10 <macros>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	11 <import>macros.xml</import>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	12 </macros>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	13 <edam_topics>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	14 <edam_topic>topic_0121</edam_topic><!-- Proteomics -->
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	15 <edam_topic>topic_3520</edam_topic><!-- Proteomics experiment-->
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	16 </edam_topics>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	17 <edam_operations>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	18 <edam_operation>operation_0338</edam_operation><!-- Sequence database search -->
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	19 <edam_operation>operation_0361</edam_operation><!-- Sequence annotation -->
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	20 <edam_operation>operation_3434</edam_operation><!-- Conversion -->
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	21 <edam_operation>operation_3436</edam_operation><!-- Aggregation -->
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	22 </edam_operations>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	23 <expand macro="requirements"/>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	24 <command detect_errors="exit_code"><![CDATA[
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	25 echo '--- localization-filter step:'
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	26 && (
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	27 Rscript '$__tool_directory__/MaxQuantProcessingScript.R'
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	28 -i '$phosphoSites'
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	29 #if $pst_py_selector == "y"
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	30 --enriched Y
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	31 #else
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	32 --enriched ST
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	33 #end if
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	34 --phosphoCol '$phosphocol_script'
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	35 --startCol '$startcol_script'
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	36 --intervalCol $intervalCol
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	37 --localProbCutoff $localProbCutoff
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	38 --collapse_func $collapse_func
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	39 -o '$phosphoPepIntensities'
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	40 --locProbCutoffGraph $locProbCutoffGraph
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	41 --enrichGraph $enrichGraph
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	42 --locProbCutoffGraph_svg $locProbCutoffGraph_svg
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	43 --enrichGraph_svg $enrichGraph_svg
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	44 --filtered_data $filteredData_tabular
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	45 --quant_data $quantData_tabular
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	46 ) &&
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	47 echo '... end localization-filter.'
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	48 && (
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	49 echo '--- kinase-mapping step:'
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	50 ) && (
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	51 perl '$__tool_directory__/PhosphoPeptide_Upstream_Kinase_Mapping.pl'
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	52 -i '$phosphoPepIntensities'
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	53 -f '$protein_fasta'
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	54 -n '$networkin'
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	55 -m '$p_sty_motifs'
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	56 -p '$psp_kinase_substrate'
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	57 -r '$psp_regulatory_sites'
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	58 #if $pst_py_selector == "y"
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	59 -P y
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	60 #else
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	61 -P sty
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	62 #end if
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	63 -F $merge_function
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	64 -o '$mapped_phophopeptides'
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	65 -O '$melted_phophopeptide_map'
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	66 -D '$mqppep_output_sqlite'
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	67 -s '$species'
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	68 ) &&
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	69 echo '... end kinase-mapping.'
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	70 &&
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	71 echo '--- merge-and-filter step:'
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	72 && (
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	73 python '$__tool_directory__/mqppep_mrgfltr.py'
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	74 --phosphopeptides='$mapped_phophopeptides'
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	75 --ppep_mapping_db='$mqppep_output_sqlite'
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	76 --species='$species'
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	77 --mrgfltr_tab='$preproc_tab'
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	78 --mrgfltr_csv='$preproc_csv'
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	79 --mrgfltr_sqlite='$preproc_sqlite'
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	80 )
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	81 && echo '... end merge-and-filter.'
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	82 ]]></command>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	83 <configfiles>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	84 <configfile name="phosphocol_script">$phosphoCol
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	85 </configfile>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	86 <configfile name="startcol_script">$startCol
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	87 </configfile>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	88 </configfiles>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	89 <inputs>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	90 <param name="phosphoSites" type="data" format="tabular"
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	91 label="Phospho (STY)Sites.txt"
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	92 help="Tabular 'Phospho (STY)Sites.txt' produced by MaxQuant"
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	93 />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	94 <param name="phosphoCol" type="text"
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	95 label="pattern for column 'Number of Phospho (STY)'"
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	96 help="PERL-compatible regular expression matching header of column having number of 'Phospho (STY)'"
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	97 value="^Number of Phospho [(]STY[)]$">
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	98 <sanitizer>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	99 <valid initial="string.printable">
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	100 <remove value="'"/>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	101 </valid>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	102 </sanitizer>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	103 </param>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	104 <param name="startCol" type="text"
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	105 label="pattern for first column of intensity values"
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	106 help="PERL-compatible regular expression matching column header having first sample intensity"
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	107 value="^Intensity[^_]">
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	108 <sanitizer>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	109 <valid initial="string.printable">
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	110 <remove value="'"/>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	111 </valid>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	112 </sanitizer>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	113 </param>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	114 <param name="intervalCol" type="integer" value="1" min="1"
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	115 label="Interval between the intensity column of samples"
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	116 help="E.g., 1 if subsequent column is next sample; 2 if next sample is two columns away, etc."/>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	117 <param name="pst_py_selector" type="select"
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	118 label="Phosphopeptide enrichment type"
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	119 help="Were samples enriched for pS and pT, or were they enriched for pY instead?"
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	120 >
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	121 <option value="st" selected="true">pST</option>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	122 <option value="y">pY</option>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	123 </param>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	124 <param name="collapse_func" type="select"
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	125 label="Intensity merge function"
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	126 help="When a peptide is multiply phosphorylated, how should intensities be merged? [default: sum]"
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	127 >
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	128 <option value="sum" selected="true">sum</option>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	129 <option value="mean">average</option>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	130 </param>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	131 <param name="localProbCutoff" type="float" value="0.75" min="0" max="1.0"
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	132 label="Localization Probability Cutoff"
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	133 help="See help below for an explanation."
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	134 />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	135 <param name="merge_function" type="select" label="intensity merge-function"
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	136 help="Specifies how intensities for identical phosphosites should be merged">
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	137 <option value="sum" selected="true">sum</option>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	138 <option value="average">average</option>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	139 </param>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	140 <param name="protein_fasta" type="data" format="fasta" label="UniProtKB/SwissProt FASTA database"
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	141 help="Sequence database; supply the same FASTA file as you supplied to by MaxQuant"
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	142 />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	143 <param name="networkin" type="data" format="tabular" label="NetworKIN file"
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	144 help="NetworKIN file; see help section below"/>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	145 <param name="p_sty_motifs" type="data" format="tabular" label="pSTY_Motifs file"
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	146 help="pS/pT/pY phosphorylation site motifs; see help section below"/>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	147 <param name="psp_kinase_substrate" type="data" format="tabular" label="PSP_Kinase_Substrate_Dataset"
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	148 help="'Kinase-substrate dataset'; see help section below"/>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	149 <param name="psp_regulatory_sites" type="data" format="tabular" label="PSP_Regulatory_sites"
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	150 help="'Regulatory sites'; see help section below"/>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	151 <param name="species"
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	152 type="text"
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	153 value = "human"
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	154 label="filter to limit PhosphoSitePlus records to indicated species"
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	155 help="(field may be empty) [default: human]. If you supply this parameter, use the species indentifier seen as a suffix in UniProtKB"
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	156 />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	157 </inputs>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	158 <outputs>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	159 <!-- localization filter -->
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	160 <data name="phosphoPepIntensities" format="tabular" label="${phosphoSites.name}.ppep_intensities" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	161 <data name="enrichGraph" format="pdf" label="${phosphoSites.name}.enrichment.pdf" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	162 <data name="locProbCutoffGraph" format="pdf" label="${phosphoSites.name}.locProbCutoff.pdf" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	163 <data name="enrichGraph_svg" format="svg" label="${phosphoSites.name}.enrichment.svg" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	164 <data name="locProbCutoffGraph_svg" format="svg" label="${phosphoSites.name}.locProbCutoff.svg" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	165 <data name="filteredData_tabular" format="tabular" label="${phosphoSites.name}.filteredData" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	166 <data name="quantData_tabular" format="tabular" label="${phosphoSites.name}.quantData" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	167 <!-- upstream kinase mapping -->
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	168 <data name="mapped_phophopeptides" format="tabular" label="${phosphoSites.name}.ppep_intensities.ppep_map"/>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	169 <data name="melted_phophopeptide_map" format="tabular" label="${phosphoSites.name}.ppep_intensities.melted"/>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	170 <data name="mqppep_output_sqlite" format="sqlite" label="${phosphoSites.name}.ppep_intensities.ppep_mapping_sqlite"/>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	171 <!-- merge and filter -->
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	172 <data name="preproc_tab" format="tabular" label="${phosphoSites.name}.ppep_intensities.ppep_map.preproc_tab" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	173 <data name="preproc_csv" format="csv" label="${phosphoSites.name}.ppep_intensities.ppep_map.preproc_csv" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	174 <data name="preproc_sqlite" format="sqlite" label="${phosphoSites.name}.ppep_intensities.ppep_map.preproc_sqlite" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	175 </outputs>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	176 <tests>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	177 <test>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	178 <param name="phosphoSites" ftype="tabular" value="test_input_for_preproc.tabular" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	179 <param name="protein_fasta" ftype="fasta" value="test_swissprot.fasta" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	180 <param name="networkin" ftype="tabular" value="test_networkin.tabular" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	181 <param name="p_sty_motifs" ftype="tabular" value="pSTY_motifs.tabular" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	182 <param name="psp_kinase_substrate" ftype="tabular" value="test_kinase_substrate.tabular" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	183 <param name="psp_regulatory_sites" ftype="tabular" value="test_regulatory_sites.tabular" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	184 <param name="pst_py_selector" value="st"/>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	185 <param name="merge_function" value="sum"/>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	186
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	187 <param name="phosphoCol" value="^Number of Phospho [(][STY][STY]*[)]$"/>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	188 <param name="startCol" value="^Intensity[^_]"/>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	189 <param name="intervalCol" value="1"/>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	190 <param name="collapse_func" value="sum"/>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	191 <param name="localProbCutoff" value="0.75"/>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	192 <param name="species" value="human"/>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	193
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	194 <output name="phosphoPepIntensities">
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	195 <assert_contents>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	196 <has_text text="Phosphopeptide" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	197 <has_line_matching expression="AAAITDMADLEELSRLpSPLPPGpSPGSAAR.5416400.7101800.385280000.208060000.41426000.352400000" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	198 <has_line_matching expression="pSQKQEEENPAEETGEEK.0.0.8765300.0.2355900.14706000" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	199 </assert_contents>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	200 </output>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	201
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	202 <output name="preproc_tab">
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	203 <assert_contents>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	204 <has_text text="SSRP1_HUMAN FACT complex subunit SSRP1" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	205 <has_text text="AEBP2_HUMAN Isoform 2 of Zinc finger protein AEBP2" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	206 <has_text text="molecular association, regulation" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	207 <has_text text="cell cycle regulation" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	208 <has_text text="PPP2CA(INDUCES)" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	209 <has_text text="SNCA(DISRUPTS)" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	210 <has_text text="CDK7" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	211 <has_text text="CK1alpha" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	212 <has_text text="CK2alpha" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	213 <has_text text="DNAPK" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	214 <has_text text="HIPK2" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	215 <has_text text="IKKalpha" />
ba62d93a9ef5 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" />
ba62d93a9ef5 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" />
ba62d93a9ef5 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" />
ba62d93a9ef5 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" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	220 <has_text text="CK2alpha" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	221 <has_text text="Csnk2a1" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	222 </assert_contents>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	223 </output>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	224
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	225 <output name="melted_phophopeptide_map">
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	226 <assert_contents>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	227 <has_text text="CDK7" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	228 <has_text text="CK1alpha" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	229 <has_text text="CK2alpha" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	230 <has_text text="DNAPK" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	231 <has_text text="HIPK2" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	232 <has_text text="IKKalpha" />
ba62d93a9ef5 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" />
ba62d93a9ef5 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" />
ba62d93a9ef5 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" />
ba62d93a9ef5 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" />
ba62d93a9ef5 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" />
ba62d93a9ef5 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" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	239 </assert_contents>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	240 </output>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	241 </test>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	242 <test>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	243 <param name="phosphoSites" ftype="tabular" value="test_input_for_preproc.tabular" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	244 <param name="protein_fasta" ftype="fasta" value="test_swissprot.fasta" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	245 <param name="networkin" ftype="tabular" value="test_networkin.tabular" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	246 <param name="p_sty_motifs" ftype="tabular" value="pSTY_motifs.tabular" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	247 <param name="psp_kinase_substrate" ftype="tabular" value="test_kinase_substrate.tabular" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	248 <param name="psp_regulatory_sites" ftype="tabular" value="test_regulatory_sites.tabular" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	249 <param name="pst_py_selector" value="y"/>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	250 <param name="merge_function" value="sum"/>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	251
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	252 <param name="phosphoCol" value="^Number of Phospho [(][STY][STY]*[)]$"/>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	253 <param name="startCol" value="^Intensity[^_]"/>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	254 <param name="intervalCol" value="1"/>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	255 <param name="collapse_func" value="sum"/>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	256 <param name="localProbCutoff" value="0.75"/>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	257 <param name="species" value="human"/>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	258
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	259 <output name="phosphoPepIntensities">
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	260 <assert_contents>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	261 <has_text text="Phosphopeptide" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	262 <has_text text="pTYVDPFTpYEDPNQAVR" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	263 </assert_contents>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	264 </output>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	265
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	266 <output name="preproc_tab">
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	267 <assert_contents>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	268 <has_text text="pTYVDPFTpYEDPNQAVR" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	269 <has_text text="EEKHLNQGVRpTYVDPFTYEDP" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	270 <has_text text="GVRTYVDPFTpYEDPNQAVREF" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	271 <has_text text="HLNQGVRtYVDPFTY" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	272 <has_text text="TYVDPFTyEDPNQAV" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	273 <has_text text="EPHA4" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	274 <has_text text="pT595, pY602" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	275 <has_text text="pT544, pY551" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	276 <has_text text="P54764;" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	277 <has_text text="P54764-2" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	278 </assert_contents>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	279 </output>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	280
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	281 <output name="melted_phophopeptide_map">
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	282 <assert_contents>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	283 <has_text text="EphA6" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	284 <has_text text="EPHA4" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	285 <has_text text="EphA4" />
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	286 </assert_contents>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	287 </output>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	288 </test>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	289 </tests>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	290 <help><![CDATA[
1 2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	291 =============================================================
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	292 Phopsphoproteomic Enrichment Pipeline Preprocessing Steps
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	293 =============================================================
0 ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	294
1 2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	295 Overview
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	296 ==========
0 ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	297
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	298 Prior to statistical analysis, it is necessary to perform
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	299 three steps to transform the MaxQuant output
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	300 for phosphoproteome-enriched samples.
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	301
1 2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	302 Workflow position
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	303 ===================
0 ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	304
1 2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	305 Upstream tool
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	306 =============
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	307
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	308 The input dataset for this tool is the ``Phospho (STY)Sites.txt`` file that is produced:
0 ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	309
1 2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	310 - by the Galaxy "MaxQuant" (``maxquant``) tool
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	311 - or by the Galaxy "Maxquant (using mqpar.xml)" (``maxquant_mqpar``) tool
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	312 - or by the desktop version of MaxQuant.
0 ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	313
1 2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	314 Downstream tool
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	315 ===============
0 ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	316
1 2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	317 The "MaxQuant Phosphopeptide ANOVA" tool (``mqppep_anova``) consumes the "preprocessed" output file ``preproc_tab`` that this tool produces.
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	318
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	319 Phopsphoproteomic Enrichment Pipeline Localization-Probability Cut-Off
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	320 ========================================================================
0 ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	321
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	322 This step applies a "localization-probability cut-off" for phosphopeptides for each phosphopeptide.
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	323 Higher values may reduce the number of peptides in the output.
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	324 The default value of 0.75 reflects the text of [Cheng 2018]:
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	325
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	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]."
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	327
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	328 This tool wraps an R script. written by Larry Cheng, that performs the following (in order):
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	329
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	330 1. Remove contaminant and reverse sequence rows
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	331 2. Filters rows based on localization probability
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	332 3. Extract the quantitative data
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	333 4. Inserts a "p" before the phosphorylated residue(s) in each peptide sequence
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	334 5. Merges (aggregating by "sum" or "average") multiply-phosphorylated peptides
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	335 6. Filters output phosphopeptides based on enrichment
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	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.
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	337
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	338 Note that the "ProTeomiX Quality Control Report"
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	339 [Bielow 2016] (available at `https://github.com/cbielow/PTXQC/
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	340 <https://github.com/cbielow/PTXQC/>`_) is run by the Galaxy wrappers for MaxQuant,
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	341 so it is omitted here even though it was included in Larry Cheng's original script.
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	342
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	343
1 2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	344 Input dataset
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	345 =============
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	346
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	347 Phospho (STY)Sites.txt
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	348 This is the ``MaxQuant Phospho (STY)Sites.txt`` file produced by MaxQuant.
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	349 If you use the desktop version of MaxQuant, you will find this file in the ``txt`` folder.
0 ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	350
1 2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	351 Input parameters
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	352 ================
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	353
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	354 Localization probability cutoff
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	355 Minimum localization probability; see above.
0 ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	356
1 2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	357 Intensity merge-function
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	358 Specifies how intensities for identical phosphosites should be merged; see above.
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	359
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	360 Output datasets
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	361 ===============
0 ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	362
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	363 ``ppep_intensities``
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	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 2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	365
0 ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	366 ``enrichment.pdf``
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	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 2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	368
0 ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	369 ``locProbCutoff.pdf``
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	370 Graph (in PDF format) contrasting proportion of phosphopeptides above the localization probability cutoff with the proportion below.
1 2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	371
0 ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	372 ``enrichment.svg``
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	373 Enrichment graph (in downloadable "scalable vector graphics" format) for incorporation into documents.
1 2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	374
0 ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	375 ``locProbCutoff.svg``
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	376 Localization probability cutoff graph (in downloadable "scalable vector graphics" format) for incorporation into documents.
1 2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	377
0 ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	378 ``filteredData``
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	379 Data table (in tabular format) comprising rows of the ``phosphSites`` input file that are not flagged as contaminants or reversed sequences.
1 2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	380
0 ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	381 ``quantData``
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	382 Data table (in tabular format) comprising rows of the ``filteredData`` file whose localization probability exceeds the Localization Probability Cutoff parameter.
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	383
1 2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	384 Authors
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	385 =======
0 ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	386
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	387 ``Nicholas A. Graham``
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	388 (`ORCiD 0000-0002-6811-1941 <https://orcid.org/0000-0002-6811-1941>`_) initiated the original script.
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	389
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	390 ``Larry C. Cheng``
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	391 (`ORCiD 0000-0002-6922-6433 <https://orcid.org/0000-0002-6922-6433>`_) updated the original script.
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	392
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	393 ``Arthur C. Eschenlauer``
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	394 (`ORCiD 0000-0002-2882-0508 <https://orcid.org/0000-0002-2882-0508>`_) adapted the script to run in Galaxy.
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	395
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	396 ``James E. Johnson``
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	397 (University of Minnesota Supercomputing Institute) adapted the script to run in Galaxy.
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	398
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	399
1 2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	400 Phopsphoproteomic Enrichment Pipeline Upstream Kinase Mapping
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	401 ===============================================================
0 ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	402
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	403 This step searches phosphopeptides against several databases for known or predicted sites.
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	404
1 2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	405 Input databases
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	406 ===============
0 ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	407
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	408 ``networkin``
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	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].
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	410
1 2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	411 To generate this file:
0 ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	412
1 2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	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");
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	414 (2) Decompress the .tsv.xz with file with "unxz" (from XZ Utils `https://tukaani.org/xz/ <https://tukaani.org/xz/>`_);
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	415 (3) Filter out the rows having "network_kin" less than 2.0.
0 ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	416
1 2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	417 The result should be a tab-separated file with the following columns:
0 ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	418
1 2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	419 - ``#substrate``
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	420 - ``position``
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	421 - ``id``
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	422 - ``networkin_score``
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	423 - ``tree``
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	424 - ``netphorest_group``
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	425 - ``netphorest_score``
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	426 - ``string_identifier``
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	427 - ``string_score``
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	428 - ``substrate_name``
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	429 - ``sequence``
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	430 - ``string_path``
0 ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	431
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	432
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	433 ``p_sty_motifs``
1 2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	434 This database merges motif patterns from [Amanchy 2007] and Phosida [Gnad 2011].
0 ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	435
1 2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	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 ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	437
1 2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	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 ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	439
1 2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	440 This file has three tab-separated columns (and no header):
0 ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	441
1 2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	442 - column 1 is an (ignored) identifier
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	443 - column 2 is a Perl regular expression
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	444 - column 3 is a descriptor.
0 ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	445
1 2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	446 For two examples:
0 ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	447
1 2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	448 ``2<TAB>R.R..(pS\|pT)<TAB>Akt kinase substrate motif (HPRD)``
0 ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	449
1 2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	450 ``10<TAB>R..(pS\|pT)V<TAB>CAMK2_Phosida``
0 ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	451
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	452 ``psp_kinase_substrate``
1 2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	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 ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	454
1 2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	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 ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	456
1 2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	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.
0 ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	458
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	459 ``psp_regulatory_sites``
1 2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	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>`_.
0 ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	461
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	462 Terms of use and citatation are as for the ``psp_kinase_substrate`` file.
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	463
1 2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	464 Output datasets
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	465 ===============
0 ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	466
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	467 ``ppep_map``
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	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:
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	469
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	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."
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	471
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	472
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	473 ``melted``
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	474 Data table (in tabular format) presenting, for each phosphopeptide, the gene and one of the phospho-motifs or kinase-substrate sites.
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	475
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	476 ``ppep_mapping_sqlite``
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	477 SQLite database (consumed by the merge/filter step).
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	478
1 2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	479 Authors
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	480 =======
0 ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	481
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	482 ``Nicholas A. Graham``
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	483 (`ORCiD 0000-0002-6811-1941 <https://orcid.org/0000-0002-6811-1941>`_) wrote the original script.
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	484
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	485 ``Arthur C. Eschenlauer``
ba62d93a9ef5 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.
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	487
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	488
1 2ccb9727516b 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
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	490 ========================================================
0 ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	491
ba62d93a9ef5 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.
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	493
1 2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	494 Input parameters
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	495 ================
0 ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	496
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	497 ``species``
ba62d93a9ef5 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
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	499
1 2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	500 Output datasets
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	501 ===============
0 ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	502
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	503 ``preproc_tab``
ba62d93a9ef5 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:
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	505
ba62d93a9ef5 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."
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	507
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	508 ``preproc_csv``
ba62d93a9ef5 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.
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	510
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	511 ``preproc_sqlite``
ba62d93a9ef5 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.
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	513
1 2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	514 Authors
2ccb9727516b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	515 =======
0 ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	516
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	517 ``Nicholas A. Graham``
ba62d93a9ef5 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.
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	519
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	520 ``Larry C. Cheng``
ba62d93a9ef5 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.
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	522
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	523 ``Arthur C. Eschenlauer``
ba62d93a9ef5 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.
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	525
ba62d93a9ef5 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
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	527 ]]></help>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	528 <citations>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	529 <!-- upstream kinase mapping -->
ba62d93a9ef5 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 -->
ba62d93a9ef5 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>
ba62d93a9ef5 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 -->
ba62d93a9ef5 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>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	534 <!-- localization filter -->
ba62d93a9ef5 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 -->
ba62d93a9ef5 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>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	537 <!-- all three -->
ba62d93a9ef5 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 -->
ba62d93a9ef5 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>
ba62d93a9ef5 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 -->
ba62d93a9ef5 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 -->
ba62d93a9ef5 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>
ba62d93a9ef5 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 -->
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	544 <!-- upstream kinase mapping -->
ba62d93a9ef5 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>
ba62d93a9ef5 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 -->
ba62d93a9ef5 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>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	548 <!-- localization filter -->
ba62d93a9ef5 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 -->
ba62d93a9ef5 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>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	551 <!-- upstream kinase mapping -->
ba62d93a9ef5 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 -->
ba62d93a9ef5 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>
ba62d93a9ef5 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 -->
ba62d93a9ef5 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 -->
ba62d93a9ef5 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>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	557 <!-- upstream kinase mapping -->
ba62d93a9ef5 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 -->
ba62d93a9ef5 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>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	560 <!-- localization filter -->
ba62d93a9ef5 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 -->
ba62d93a9ef5 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>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	563 </citations>
ba62d93a9ef5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	564 </tool>

Mercurial > repos > galaxyp > mqppep_preproc

annotate mqppep_preproc.xml @ 1:2ccb9727516b draft