mqppep_preproc: mqppep_preproc.xml annotate

annotate mqppep_preproc.xml @ 7:36f183e5e4ed draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"

author	eschen42
date	Tue, 15 Mar 2022 00:35:55 +0000
parents	b91809a18dbe
children	28a126da9b28

rev	line source
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	1 <tool id="mqppep_preproc" name="MaxQuant Phosphopeptide Preprocessing" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	2 <description>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	3 Transform the output of MaxQuant for phosphoproteome-enriched samples to prepare it for statistical anlaysis.
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	4 </description>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	5 <macros>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	6 <import>macros.xml</import>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	7 </macros>
7 36f183e5e4ed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	8 <expand macro="requirements"/>
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	9 <command detect_errors="exit_code"><![CDATA[
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	10 (
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	11 echo '--- localization-filter step:'
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	12 ) && (
4 8be24b489992 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182-dirty" eschen42 parents: 0 diff changeset	13 \$CONDA_PREFIX/bin/Rscript '$__tool_directory__/MaxQuantProcessingScript.R'
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	14 -i '$phosphoSites'
7 36f183e5e4ed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	15 #if $pst_not_py:
36f183e5e4ed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	16 --enriched ST
36f183e5e4ed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	17 #else
36f183e5e4ed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	18 --enriched Y
36f183e5e4ed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	19 #end if
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	20 --phosphoCol '$phosphocol_script'
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	21 --startCol '$startcol_script'
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	22 --intervalCol $intervalCol
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	23 --localProbCutoff $localProbCutoff
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	24 --collapse_func $collapseFunc
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	25 -o '$phosphoPepIntensities'
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	26 --locProbCutoffGraph $locProbCutoffGraph
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	27 --enrichGraph $enrichGraph
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	28 --locProbCutoffGraph_svg $locProbCutoffGraph_svg
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	29 --enrichGraph_svg $enrichGraph_svg
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	30 --filtered_data $filteredData_tabular
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	31 --quant_data $quantData_tabular
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	32 ) && (
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	33 echo '... end localization-filter.'
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	34 ) && (
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	35 echo '--- kinase-mapping step:'
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	36 ) && (
5 b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf" eschen42 parents: 4 diff changeset	37 \$CONDA_PREFIX/bin/perl '$__tool_directory__/PhosphoPeptide_Upstream_Kinase_Mapping.pl'
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	38 -i '$phosphoPepIntensities'
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	39 -f '$protein_fasta'
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	40 -n '$networkin'
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	41 -m '$p_sty_motifs'
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	42 -p '$psp_kinase_substrate'
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	43 -r '$psp_regulatory_sites'
7 36f183e5e4ed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	44 #if $pst_not_py:
36f183e5e4ed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	45 -P sty
36f183e5e4ed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	46 #else
36f183e5e4ed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	47 -P y
36f183e5e4ed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	48 #end if
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	49 -F $merge_function
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	50 -o '$mapped_phophopeptides'
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	51 -O '$melted_phophopeptide_map'
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	52 -D '$mqppep_output_sqlite'
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	53 -s '$species'
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	54 ) && (
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	55 echo '... end kinase-mapping.'
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	56 ) && (
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	57 echo '--- merge-and-filter step:'
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	58 ) && (
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	59 \$CONDA_PREFIX/bin/python '$__tool_directory__/mqppep_mrgfltr.py'
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	60 --phosphopeptides='$mapped_phophopeptides'
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	61 --ppep_mapping_db='$mqppep_output_sqlite'
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	62 --species='$species'
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	63 --mrgfltr_tab='$preproc_tab'
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	64 --mrgfltr_csv='$preproc_csv'
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	65 --mrgfltr_sqlite='$preproc_sqlite'
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	66 ) && (
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	67 echo '... end merge-and-filter.'
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	68 )
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	69 ]]></command>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	70 <configfiles>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	71 <configfile name="phosphocol_script">$phosphoCol
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	72 </configfile>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	73 <configfile name="startcol_script">$startCol
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	74 </configfile>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	75 </configfiles>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	76 <inputs>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	77 <param name="phosphoSites" type="data" format="tabular"
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	78 label="Phospho (STY)Sites.txt"
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	79 help="[phosphoSites] Tabular 'Phospho (STY)Sites.txt' produced by MaxQuant"
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	80 />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	81 <param name="phosphoCol" type="text"
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	82 label="pattern for column 'Number of Phospho (STY)'"
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	83 help="[phosphoCol] PERL-compatible regular expression matching header of column having number of 'Phospho (STY)'"
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	84 value="^Number of Phospho [(]STY[)]$">
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	85 <sanitizer>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	86 <valid initial="string.printable">
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	87 <remove value="'"/>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	88 </valid>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	89 </sanitizer>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	90 </param>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	91 <param name="startCol" type="text"
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	92 label="pattern for first column of intensity values"
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	93 help="[startCol] PERL-compatible regular expression matching column header having first sample intensity"
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	94 value="^Intensity[^_]">
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	95 <sanitizer>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	96 <valid initial="string.printable">
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	97 <remove value="'"/>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	98 </valid>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	99 </sanitizer>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	100 </param>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	101 <param name="intervalCol" type="integer" value="1" min="1"
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	102 label="Interval between the intensity column of samples"
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	103 help="[intervalCol] E.g., 1 if subsequent column is next sample; 2 if next sample is two columns away, etc."/>
7 36f183e5e4ed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	104 <!-- pst_not_py is true when chosing pS/pT, false when choosing pY -->
36f183e5e4ed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	105 <param name="pst_not_py" type="boolean"
36f183e5e4ed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	106 checked="true"
36f183e5e4ed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	107 label="Phospho enrichment pS/pT (rather than pY)"
36f183e5e4ed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	108 help="True when samples were enriched for pS and pT; false when enriched for pY"
36f183e5e4ed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	109 >
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	110 </param>
7 36f183e5e4ed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	111 <!--
36f183e5e4ed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	112 <conditional name="py_pst">
36f183e5e4ed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	113 <param name="pst_not_py" type="select"
36f183e5e4ed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	114 label="Phospho enrichment type"
36f183e5e4ed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	115 help="[enriched] Were samples enriched for pS and pT, or were they enriched for pY?"
36f183e5e4ed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	116 >
36f183e5e4ed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	117 <option value="st" selected="true">pST</option>
36f183e5e4ed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	118 <option value="y">pY</option>
36f183e5e4ed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	119 </param>
36f183e5e4ed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	120 <when value="st">
36f183e5e4ed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	121 <param name="enriched" type="text" value="ST" />
36f183e5e4ed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	122 <param name="phospho_type" type="text" value="sty" />
36f183e5e4ed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	123 </when>
36f183e5e4ed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	124 <when value="y">
36f183e5e4ed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	125 <param name="enriched" type="text" value="Y" />
36f183e5e4ed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	126 <param name="phospho_type" type="text" value="y" />
36f183e5e4ed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	127 </when>
36f183e5e4ed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	128 </conditional>
36f183e5e4ed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	129 -->
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	130 <param name="collapseFunc" type="select"
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	131 label="Intensity merge function"
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	132 help="[collapseFunc] When a peptide is multiply phosphorylated, how should intensities be merged? [default: sum]"
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	133 >
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	134 <option value="sum" selected="true">sum</option>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	135 <option value="mean">average</option>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	136 </param>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	137 <param name="localProbCutoff" type="float" value="0.75" min="0" max="1.0"
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	138 label="Localization Probability Cutoff"
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	139 help="[localProbCutoff] See help below for an explanation."
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	140 />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	141 <param name="merge_function" type="select" label="intensity merge-function"
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	142 help="[merge_function] Specifies how intensities for identical phosphosites should be merged">
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	143 <option value="sum" selected="true">sum</option>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	144 <option value="average">average</option>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	145 </param>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	146 <param name="protein_fasta" type="data" format="fasta" label="UniProtKB/SwissProt FASTA database"
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	147 help="[protein_fasta] Sequence database; supply the same FASTA file as you supplied to by MaxQuant"
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	148 />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	149 <param name="networkin" type="data" format="tabular" label="NetworKIN file"
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	150 help="[networkin] NetworKIN file; see help section below"/>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	151 <param name="p_sty_motifs" type="data" format="tabular" label="pSTY_Motifs file"
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	152 help="[p_sty_motifs] pS/pT/pY phosphorylation site motifs; see help section below"/>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	153 <param name="psp_kinase_substrate" type="data" format="tabular" label="PSP_Kinase_Substrate_Dataset"
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	154 help="[psp_kinase_substrate] 'Kinase-substrate dataset'; see help section below"/>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	155 <param name="psp_regulatory_sites" type="data" format="tabular" label="PSP_Regulatory_sites"
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	156 help="[psp_regulatory_sites] 'Regulatory sites'; see help section below"/>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	157 <param name="species"
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	158 type="text"
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	159 value = "human"
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	160 label="filter to limit PhosphoSitePlus records to indicated species"
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	161 help="[species] (field may be empty) [default: human]"
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	162 />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	163 </inputs>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	164 <outputs>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	165 <!-- localization filter -->
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	166 <data name="phosphoPepIntensities" format="tabular" label="${phosphoSites.name}.ppep_intensities" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	167 <data name="enrichGraph" format="pdf" label="${phosphoSites.name}.enrichment.pdf" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	168 <data name="locProbCutoffGraph" format="pdf" label="${phosphoSites.name}.locProbCutoff.pdf" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	169 <data name="enrichGraph_svg" format="svg" label="${phosphoSites.name}.enrichment.svg" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	170 <data name="locProbCutoffGraph_svg" format="svg" label="${phosphoSites.name}.locProbCutoff.svg" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	171 <data name="filteredData_tabular" format="tabular" label="${phosphoSites.name}.filteredData" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	172 <data name="quantData_tabular" format="tabular" label="${phosphoSites.name}.quantData" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	173 <!-- upstream kinase mapping -->
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	174 <data name="mapped_phophopeptides" format="tabular" label="${phosphoSites.name}.ppep_intensities.ppep_map"/>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	175 <data name="melted_phophopeptide_map" format="tabular" label="${phosphoSites.name}.ppep_intensities.melted"/>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	176 <data name="mqppep_output_sqlite" format="sqlite" label="${phosphoSites.name}.ppep_intensities.ppep_mapping_sqlite"/>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	177 <!-- merge and filter -->
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	178 <data name="preproc_tab" format="tabular" label="${phosphoSites.name}.ppep_intensities.ppep_map.preproc_tab" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	179 <data name="preproc_csv" format="csv" label="${phosphoSites.name}.ppep_intensities.ppep_map.preproc_csv" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	180 <data name="preproc_sqlite" format="sqlite" label="${phosphoSites.name}.ppep_intensities.ppep_map.preproc_sqlite" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	181 </outputs>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	182 <tests>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	183 <test>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	184 <param name="phosphoSites" ftype="tabular" value="test_input_for_preproc.tabular" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	185 <param name="protein_fasta" ftype="fasta" value="test_swissprot.fasta" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	186 <param name="networkin" ftype="tabular" value="test_networkin.tabular" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	187 <param name="p_sty_motifs" ftype="tabular" value="pSTY_motifs.tabular" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	188 <param name="psp_kinase_substrate" ftype="tabular" value="test_kinase_substrate.tabular" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	189 <param name="psp_regulatory_sites" ftype="tabular" value="test_regulatory_sites.tabular" />
7 36f183e5e4ed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	190 <param name="pst_not_py" value="true"/>
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	191 <param name="merge_function" value="sum"/>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	192
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	193 <param name="phosphoCol" value="^Number of Phospho [(][STY][STY]*[)]$"/>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	194 <param name="startCol" value="^Intensity[^_]"/>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	195 <param name="intervalCol" value="1"/>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	196 <param name="collapseFunc" value="sum"/>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	197 <param name="localProbCutoff" value="0.75"/>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	198 <param name="species" value="human"/>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	199
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	200 <output name="phosphoPepIntensities">
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	201 <assert_contents>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	202 <has_text text="Phosphopeptide" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	203 <has_line_matching expression="AAAITDMADLEELSRLpSPLPPGpSPGSAAR.5416400.7101800.385280000.208060000.41426000.352400000" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	204 <has_line_matching expression="pSQKQEEENPAEETGEEK.0.0.8765300.0.2355900.14706000" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	205 </assert_contents>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	206 </output>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	207
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	208 <output name="preproc_tab">
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	209 <assert_contents>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	210 <has_text text="SSRP1_HUMAN FACT complex subunit SSRP1" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	211 <has_text text="AEBP2_HUMAN Isoform 2 of Zinc finger protein AEBP2" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	212 <has_text text="molecular association, regulation" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	213 <has_text text="cell cycle regulation" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	214 <has_text text="PPP2CA(INDUCES)" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	215 <has_text text="SNCA(DISRUPTS)" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	216 <has_text text="Casein Kinase II substrate" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	217 <has_text text="PKC kinase substrate" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	218 <has_text text="PKCiota" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	219 <has_text text="Csnk2a1" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	220 <has_text text="CDK7" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	221 <has_text text="CK1alpha" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	222 <has_text text="CK2a2" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	223 <has_text text="CK2alpha" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	224 <has_text text="DNAPK" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	225 <has_text text="HIPK2" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	226 <has_text text="IKKalpha" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	227 <has_text text="PKCalpha" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	228 <has_text text="PKCbeta" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	229 </assert_contents>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	230 </output>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	231
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	232 <output name="melted_phophopeptide_map">
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	233 <assert_contents>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	234 <has_text text="CDK7_NetworKIN" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	235 <has_text text="CK1alpha_NetworKIN" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	236 <has_text text="CK2a2_NetworKIN" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	237 <has_text text="CK2alpha_NetworKIN" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	238 <has_text text="DNAPK_NetworKIN" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	239 <has_text text="HIPK2_NetworKIN" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	240 <has_text text="IKKalpha_NetworKIN" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	241 <has_text text="PKCalpha_NetworKIN" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	242 <has_text text="PKCbeta_NetworKIN" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	243 <has_text text="PKC kinase substrate motif" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	244 <has_text text="Casein Kinase II substrate motif" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	245 <has_text text="Csnk2a1_PhosphoSite" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	246 </assert_contents>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	247 </output>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	248 </test>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	249 </tests>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	250 <help><![CDATA[
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	251 =========================================================
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	252 Phopsphoproteomic Enrichment Pipeline Preprocessing Steps
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	253 =========================================================
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	254
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	255 Overview
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	256
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	257 Prior to statistical analysis, it is necessary to perform
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	258 three steps to transform the MaxQuant output
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	259 for phosphoproteome-enriched samples.
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	260
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	261 Workflow position
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	262
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	263 ``upstream tool``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	264 The input data file for this tool is the ``Phospho (STY)Sites.txt`` file that is produced:
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	265
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	266 - by the Galaxy "MaxQuant" (``maxquant``) tool
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	267 - or by the Galaxy "Maxquant (using mqpar.xml)" (``maxquant_mqpar``) tool
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	268 - or by the desktop version of MaxQuant.
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	269
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	270 ``downstream tool``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	271 The "MaxQuant Phosphopeptide ANOVA" tool (``mqppep_anova``) consumes the ``merged/filtered`` output file ``preproc_tab`` that this tool produces.
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	272
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	273 ======================================================================
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	274 Phopsphoproteomic Enrichment Pipeline Localization-Probability Cut-Off
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	275 ======================================================================
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	276
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	277 This step applies a "localization-probability cut-off" for phosphopeptides for each phosphopeptide.
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	278 Higher values may reduce the number of peptides in the output.
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	279 The default value of 0.75 reflects the text of [Cheng 2018]:
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	280
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	281 "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]."
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	282
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	283 This tool wraps an R script. written by Larry Cheng, that performs the following (in order):
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	284
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	285 1. Remove contaminant and reverse sequence rows
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	286 2. Filters rows based on localization probability
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	287 3. Extract the quantitative data
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	288 4. Inserts a "p" before the phosphorylated residue(s) in each peptide sequence
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	289 5. Merges (aggregating by "sum" or "average") multiply-phosphorylated peptides
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	290 6. Filters output phosphopeptides based on enrichment
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	291 7. Produces an output file (in tabular format) that contains the phosphopeptide (first column) and its (possibly merged) mass spectral intensity for each sample.
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	292
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	293 Note that the "ProTeomiX Quality Control Report"
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	294 [Bielow 2016] (available at `https://github.com/cbielow/PTXQC/
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	295 <https://github.com/cbielow/PTXQC/>`_) is run by the Galaxy wrappers for MaxQuant,
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	296 so it is omitted here even though it was included in Larry Cheng's original script.
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	297
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	298
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	299 Input dataset
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	300
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	301 ``phosphoSites``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	302 This is the ``MaxQuant Phospho (STY)Sites.txt`` file produced by MaxQuant.
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	303 If you use the desktop version of MaxQuant, you will find this file in the ``txt`` folder.
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	304
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	305 Output datasets
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	306
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	307 ``ppep_intensities``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	308 Data table (in tabular format) presenting, for each sample, the mass-spectral intensity of each phopshopeptide having localization probability greater than the cutoff.
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	309 ``enrichment.pdf``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	310 Graph (in PDF format) presenting non-zero proportions of pS, pT, and pY among the phosphosites; note that a phosphopeptide may have multiple phosphosite.
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	311 ``locProbCutoff.pdf``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	312 Graph (in PDF format) contrasting proportion of phosphopeptides above the localization probability cutoff with the proportion below.
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	313 ``enrichment.svg``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	314 Enrichment graph (in downloadable "scalable vector graphics" format) for incorporation into documents.
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	315 ``locProbCutoff.svg``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	316 Localization probability cutoff graph (in downloadable "scalable vector graphics" format) for incorporation into documents.
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	317 ``filteredData``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	318 Data table (in tabular format) comprising rows of the ``phosphSites`` input file that are not flagged as contaminants or reversed sequences.
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	319 ``quantData``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	320 Data table (in tabular format) comprising rows of the ``filteredData`` file whose localization probability exceeds the Localization Probability Cutoff parameter.
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	321
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	322 Authors
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	323
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	324 ``Larry C. Cheng``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	325 (`ORCiD 0000-0002-6922-6433 <https://orcid.org/0000-0002-6922-6433>`_) wrote the original script.
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	326
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	327 ``Arthur C. Eschenlauer``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	328 (`ORCiD 0000-0002-2882-0508 <https://orcid.org/0000-0002-2882-0508>`_) adapted the script to run in Galaxy.
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	329
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	330 =============================================================
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	331 Phopsphoproteomic Enrichment Pipeline Upstream Kinase Mapping
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	332 =============================================================
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	333
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	334 This step searches phosphopeptides against several databases for known or predicted sites.
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	335
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	336 Input databases
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	337
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	338 ``networkin``
5 b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf" eschen42 parents: 4 diff changeset	339 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].
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	340
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	341 To generate this file:
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	342
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	343 (1) Download the "precomputed data for all available kinase predictors against ENSEMBL" [available at the NetworkKIN predictions link on the downloads page at `https://networkin.info/download.shtml <https://networkin.info/download.shtml>`_] (N.B.: "Commercial users are requested to contact the authors before using the data on this website");
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	344
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	345 (2) Decompress the .tsv.xz with file with "unxz" (from XZ Utils `https://tukaani.org/xz/ <https://tukaani.org/xz/>`_);
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	346
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	347 (3) Filter out the rows having "network_kin" less than 2.0.
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	348
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	349 The result should be a tab-separated file with the following columns:
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	350
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	351 1. ``#substrate``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	352 2. ``position``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	353 3. ``id``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	354 4. ``networkin_score``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	355 5. ``tree``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	356 6. ``netphorest_group``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	357 7. ``netphorest_score``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	358 8. ``string_identifier``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	359 9. ``string_score``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	360 10. ``substrate_name``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	361 11. ``sequence``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	362 12. ``string_path``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	363
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	364
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	365 ``p_sty_motifs``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	366 This database merges motif patterns from [Amanchy 2007] and Phosida [Gnad 2011].
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	367
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	368 The Amanchy data are adapted from `http://hprd.org/serine_motifs <http://hprd.org/serine_motifs>`_ and `http://hprd.org/tyrosine_motifs <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>`_).
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	369
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	370 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).
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	371
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	372 This file has three tab-separated columns (and no header):
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	373
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	374 1. column 1 is an (ignored) identifier
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	375 2. column 2 is a Perl regular expression
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	376 3. column 3 is a descriptor.
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	377
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	378 For two examples:
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	379
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	380 ``2<TAB>R.R..(pS\|pT)<TAB>Akt kinase substrate motif (HPRD)``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	381
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	382 ``10<TAB>R..(pS\|pT)V<TAB>CAMK2_Phosida``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	383
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	384 ``psp_kinase_substrate``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	385 '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>`_.
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	386
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	387 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:
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	388
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	389 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.
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	390
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	391 ``psp_regulatory_sites``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	392 '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>`_.
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	393
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	394 Terms of use and citatation are as for the ``psp_kinase_substrate`` file.
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	395
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	396 Output datasets
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	397
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	398 ``ppep_map``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	399 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:
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	400
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	401 "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."
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	402
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	403
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	404 ``melted``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	405 Data table (in tabular format) presenting, for each phosphopeptide, the gene and one of the phospho-motifs or kinase-substrate sites.
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	406
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	407 ``ppep_mapping_sqlite``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	408 SQLite database (consumed by the merge/filter step).
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	409
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	410 Authors
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	411
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	412 ``Nicholas A. Graham``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	413 (`ORCiD 0000-0002-6811-1941 <https://orcid.org/0000-0002-6811-1941>`_) wrote the original script.
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	414
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	415 ``Arthur C. Eschenlauer``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	416 (`ORCiD 0000-0002-2882-0508 <https://orcid.org/0000-0002-2882-0508>`_) adapted the script to run in Galaxy.
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	417
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	418
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	419 ======================================================
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	420 Phopsphoproteomic Enrichment Pipeline Merge and Filter
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	421 ======================================================
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	422
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	423 This step merges mapped metadata into metadata for phosphopeptides, filtering by species.
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	424
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	425 Input parameters
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	426
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	427 ``species``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	428 Limit PhosphoSitesPlus to indicated species. Default: human
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	429
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	430 Output datasets
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	431
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	432 ``preproc_tab``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	433 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:
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	434
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	435 "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."
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	436
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	437 ``preproc_csv``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	438 Phosphopeptides annotated with SwissProt and phosphosite metadata, in CSV format.
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	439
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	440 ``preproc_sqlite``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	441 ``ppep_mapping_sqlite`` updated with annotations, in SQLite format.
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	442
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	443 Authors
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	444
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	445 ``Nicholas A. Graham``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	446 (`ORCiD 0000-0002-6811-1941 <https://orcid.org/0000-0002-6811-1941>`_) may have initiated the original script.
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	447
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	448 ``Larry C. Cheng``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	449 (`ORCiD 0000-0002-6922-6433 <https://orcid.org/0000-0002-6922-6433>`_) may have updated the original script.
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	450
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	451 ``Arthur C. Eschenlauer``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	452 (`ORCiD 0000-0002-2882-0508 <https://orcid.org/0000-0002-2882-0508>`_) adapted the script to run in Galaxy.
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	453
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	454 .. \|reg\| unicode:: U+000AE .. REGISTERED SIGN
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	455 ]]></help>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	456 <citations>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	457 <!-- upstream kinase mapping -->
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	458 <!-- Amanchy, R., Periaswamy, B., Mathivanan, S. et al. A curated compendium of phosphorylation motifs. PMID: 17344875 -->
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	459 <citation type="doi">10.1038/nbt0307-285</citation>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	460 <!-- Aken 2016 "The Ensembl gene annotation system." PMID: 33137190 -->
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	461 <citation type="doi">10.1093/database/baw093</citation>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	462 <!-- localization filter -->
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	463 <!-- Bielow_2016 "Proteomics Quality Control: Quality Control Software for MaxQuant Results" PMID: 26653327 -->
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	464 <citation type="doi">10.1021/acs.jproteome.5b00780</citation>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	465 <!-- all three -->
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	466 <!-- Cheng 2018 "Phosphopeptide Enrichment ..." PMID: 30124664 -->
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	467 <citation type="doi">10.3791/57996</citation>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	468 <!-- localization and upstream kinase mapping -->
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	469 <!-- Cox 2014 "Accurate proteome-wide label-free quantification ..." PMID: 24942700 -->
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	470 <citation type="doi">10.1074/mcp.M113.031591</citation>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	471 <!-- Cox 2008 "MaxQuant enables high peptide identification rates ..." PMID: 19029910 -->
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	472 <!-- upstream kinase mapping -->
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	473 <citation type="doi">10.1038/nbt.1511</citation>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	474 <!-- Gnad 2011 "PHOSIDA 2011: the posttranslational modification database." PMID: 21081558 -->
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	475 <citation type="doi">10.1093/nar/gkq1159</citation>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	476 <!-- localization filter -->
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	477 <!-- Hogrebe_2018 "Benchmarking common quantification strategies for large-scale phosphoproteomics" PMID: 29535314 -->
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	478 <citation type="doi">10.1038/s41467-018-03309-6</citation>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	479 <!-- upstream kinase mapping -->
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	480 <!-- Horn 2014 "KinomeXplorer: an integrated platform for kinome biology studies." PMID: 24874572 -->
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	481 <citation type="doi">10.1038/nmeth.2968</citation>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	482 <!-- upstream kinase mapping and merge and filter -->
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	483 <!-- Hornbeck 2012 "PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse." PMID: 22135298 -->
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	484 <citation type="doi">10.1093/nar/gkr1122</citation>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	485 <!-- upstream kinase mapping -->
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	486 <!-- Linding 2007 "Systematic discovery of in vivo phosphorylation networks." PMID: 17570479 -->
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	487 <citation type="doi">10.1016/j.cell.2007.05.052</citation>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	488 <!-- localization filter -->
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	489 <!-- Olsen_2006 "Global, in vivo, and site-specific phosphorylation dynamics in signaling networks" PMID: 17081983 -->
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	490 <citation type="doi">10.1016/j.cell.2006.09.026</citation>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	491 </citations>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	492 </tool>

Mercurial > repos > eschen42 > mqppep_preproc

annotate mqppep_preproc.xml @ 7:36f183e5e4ed draft