mqppep_preproc: mqppep_preproc.xml annotate

annotate mqppep_preproc.xml @ 27:29775869faba draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488

author	eschen42
date	Wed, 26 Oct 2022 23:48:07 +0000
parents	7560a4e80a1e
children	872a0f9860ff

rev	line source
16 d9906288cc6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 7127d1511d45a8b22d4f50eee6db24d844371227" eschen42 parents: 13 diff changeset	1 <tool
d9906288cc6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 7127d1511d45a8b22d4f50eee6db24d844371227" eschen42 parents: 13 diff changeset	2 id="mqppep_preproc"
d9906288cc6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 7127d1511d45a8b22d4f50eee6db24d844371227" eschen42 parents: 13 diff changeset	3 name="MaxQuant Phosphopeptide Preprocessing"
d9906288cc6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 7127d1511d45a8b22d4f50eee6db24d844371227" eschen42 parents: 13 diff changeset	4 version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
d9906288cc6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 7127d1511d45a8b22d4f50eee6db24d844371227" eschen42 parents: 13 diff changeset	5 profile="21.05"
d9906288cc6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 7127d1511d45a8b22d4f50eee6db24d844371227" eschen42 parents: 13 diff changeset	6 >
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	7 <description>
23 7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	8 Prep phosphoproteomic MaxQuant output for statistical anlaysis.
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	9 </description>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	10 <macros>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	11 <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	12 </macros>
23 7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	13 <edam_topics>
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	14 <edam_topic>topic_0121</edam_topic><!-- Proteomics -->
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	15 <edam_topic>topic_3520</edam_topic><!-- Proteomics experiment-->
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	16 </edam_topics>
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	17 <edam_operations>
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	18 <edam_operation>operation_0338</edam_operation><!-- Sequence database search -->
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	19 <edam_operation>operation_0361</edam_operation><!-- Sequence annotation -->
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	20 <edam_operation>operation_3434</edam_operation><!-- Conversion -->
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	21 <edam_operation>operation_3436</edam_operation><!-- Aggregation -->
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	22 </edam_operations>
7 36f183e5e4ed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	23 <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	24 <command detect_errors="exit_code"><![CDATA[
23 7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	25 echo '--- localization-filter step:'
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	26 && (
16 d9906288cc6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 7127d1511d45a8b22d4f50eee6db24d844371227" eschen42 parents: 13 diff changeset	27 Rscript '$__tool_directory__/MaxQuantProcessingScript.R'
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	28 -i '$phosphoSites'
13 28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	29 #if $pst_py_selector == "y"
28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	30 --enriched Y
28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	31 #else
7 36f183e5e4ed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	32 --enriched ST
36f183e5e4ed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	33 #end if
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	34 --phosphoCol '$phosphocol_script'
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	35 --startCol '$startcol_script'
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	36 --intervalCol $intervalCol
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	37 --localProbCutoff $localProbCutoff
23 7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	38 --collapse_func $collapse_func
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	39 -o '$phosphoPepIntensities'
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	40 --locProbCutoffGraph $locProbCutoffGraph
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	41 --enrichGraph $enrichGraph
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	42 --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	43 --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	44 --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	45 --quant_data $quantData_tabular
23 7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	46 ) &&
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	47 echo '... end localization-filter.'
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	48 && (
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	49 echo '--- kinase-mapping step:'
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	50 ) && (
16 d9906288cc6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 7127d1511d45a8b22d4f50eee6db24d844371227" eschen42 parents: 13 diff changeset	51 perl '$__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	52 -i '$phosphoPepIntensities'
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	53 -f '$protein_fasta'
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	54 -n '$networkin'
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	55 -m '$p_sty_motifs'
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	56 -p '$psp_kinase_substrate'
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	57 -r '$psp_regulatory_sites'
13 28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	58 #if $pst_py_selector == "y"
28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	59 -P y
28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	60 #else
7 36f183e5e4ed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	61 -P sty
36f183e5e4ed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	62 #end if
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	63 -F $merge_function
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	64 -o '$mapped_phophopeptides'
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	65 -O '$melted_phophopeptide_map'
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	66 -D '$mqppep_output_sqlite'
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	67 -s '$species'
23 7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	68 ) &&
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	69 echo '... end kinase-mapping.'
23 7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	70 &&
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	71 echo '--- merge-and-filter step:'
23 7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	72 && (
16 d9906288cc6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 7127d1511d45a8b22d4f50eee6db24d844371227" eschen42 parents: 13 diff changeset	73 python '$__tool_directory__/mqppep_mrgfltr.py'
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	74 --phosphopeptides='$mapped_phophopeptides'
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	75 --ppep_mapping_db='$mqppep_output_sqlite'
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	76 --species='$species'
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	77 --mrgfltr_tab='$preproc_tab'
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	78 --mrgfltr_csv='$preproc_csv'
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	79 --mrgfltr_sqlite='$preproc_sqlite'
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	80 )
23 7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	81 && echo '... end merge-and-filter.'
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	82 ]]></command>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	83 <configfiles>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	84 <configfile name="phosphocol_script">$phosphoCol
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	85 </configfile>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	86 <configfile name="startcol_script">$startCol
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	87 </configfile>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	88 </configfiles>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	89 <inputs>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	90 <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	91 label="Phospho (STY)Sites.txt"
23 7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	92 help="Tabular 'Phospho (STY)Sites.txt' produced by MaxQuant"
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	93 />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	94 <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	95 label="pattern for column 'Number of Phospho (STY)'"
23 7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	96 help="PERL-compatible regular expression matching header of column having number of 'Phospho (STY)'"
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	97 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	98 <sanitizer>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	99 <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	100 <remove value="'"/>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	101 </valid>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	102 </sanitizer>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	103 </param>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	104 <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	105 label="pattern for first column of intensity values"
23 7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	106 help="PERL-compatible regular expression matching column header having first sample intensity"
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	107 value="^Intensity[^_]">
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	108 <sanitizer>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	109 <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	110 <remove value="'"/>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	111 </valid>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	112 </sanitizer>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	113 </param>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	114 <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	115 label="Interval between the intensity column of samples"
23 7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	116 help="E.g., 1 if subsequent column is next sample; 2 if next sample is two columns away, etc."/>
13 28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	117 <param name="pst_py_selector" type="select"
28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	118 label="Phosphopeptide enrichment type"
23 7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	119 help="Were samples enriched for pS and pT, or were they enriched for pY instead?"
7 36f183e5e4ed "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	120 >
13 28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	121 <option value="st" selected="true">pST</option>
28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	122 <option value="y">pY</option>
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	123 </param>
23 7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	124 <param name="collapse_func" type="select"
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	125 label="Intensity merge function"
23 7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	126 help="When a peptide is multiply phosphorylated, how should intensities be merged? [default: sum]"
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	127 >
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	128 <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	129 <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	130 </param>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	131 <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	132 label="Localization Probability Cutoff"
23 7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	133 help="See help below for an explanation."
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	134 />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	135 <param name="merge_function" type="select" label="intensity merge-function"
23 7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	136 help="Specifies how intensities for identical phosphosites should be merged">
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	137 <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	138 <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	139 </param>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	140 <param name="protein_fasta" type="data" format="fasta" label="UniProtKB/SwissProt FASTA database"
23 7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	141 help="Sequence database; supply the same FASTA file as you supplied to by MaxQuant"
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	142 />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	143 <param name="networkin" type="data" format="tabular" label="NetworKIN file"
23 7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	144 help="NetworKIN file; see help section below"/>
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	145 <param name="p_sty_motifs" type="data" format="tabular" label="pSTY_Motifs file"
23 7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	146 help="pS/pT/pY phosphorylation site motifs; see help section below"/>
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	147 <param name="psp_kinase_substrate" type="data" format="tabular" label="PSP_Kinase_Substrate_Dataset"
23 7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	148 help="'Kinase-substrate dataset'; see help section below"/>
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	149 <param name="psp_regulatory_sites" type="data" format="tabular" label="PSP_Regulatory_sites"
23 7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	150 help="'Regulatory sites'; see help section below"/>
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	151 <param name="species"
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	152 type="text"
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	153 value = "human"
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	154 label="filter to limit PhosphoSitePlus records to indicated species"
23 7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	155 help="(field may be empty) [default: human]. If you supply this parameter, use the species indentifier seen as a suffix in UniProtKB"
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	156 />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	157 </inputs>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	158 <outputs>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	159 <!-- localization filter -->
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	160 <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	161 <data name="enrichGraph" format="pdf" label="${phosphoSites.name}.enrichment.pdf" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	162 <data name="locProbCutoffGraph" format="pdf" label="${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	163 <data name="enrichGraph_svg" format="svg" label="${phosphoSites.name}.enrichment.svg" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	164 <data name="locProbCutoffGraph_svg" format="svg" label="${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	165 <data name="filteredData_tabular" format="tabular" label="${phosphoSites.name}.filteredData" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	166 <data name="quantData_tabular" format="tabular" label="${phosphoSites.name}.quantData" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	167 <!-- upstream kinase mapping -->
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	168 <data name="mapped_phophopeptides" format="tabular" label="${phosphoSites.name}.ppep_intensities.ppep_map"/>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	169 <data name="melted_phophopeptide_map" format="tabular" label="${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	170 <data name="mqppep_output_sqlite" format="sqlite" label="${phosphoSites.name}.ppep_intensities.ppep_mapping_sqlite"/>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	171 <!-- merge and filter -->
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	172 <data name="preproc_tab" format="tabular" label="${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	173 <data name="preproc_csv" format="csv" label="${phosphoSites.name}.ppep_intensities.ppep_map.preproc_csv" />
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	174 <data name="preproc_sqlite" format="sqlite" label="${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	175 </outputs>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	176 <tests>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	177 <test>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	178 <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	179 <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	180 <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	181 <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	182 <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	183 <param name="psp_regulatory_sites" ftype="tabular" value="test_regulatory_sites.tabular" />
13 28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	184 <param name="pst_py_selector" value="st"/>
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	185 <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	186
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	187 <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	188 <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	189 <param name="intervalCol" value="1"/>
23 7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	190 <param name="collapse_func" value="sum"/>
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="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	192 <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	193
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	194 <output name="phosphoPepIntensities">
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	195 <assert_contents>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	196 <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	197 <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	198 <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	199 </assert_contents>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	200 </output>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	201
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	202 <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	203 <assert_contents>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	204 <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	205 <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	206 <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	207 <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	208 <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	209 <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	210 <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	211 <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	212 <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	213 <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	214 <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	215 <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	216 <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	217 <has_text text="PKCbeta" />
23 7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	218 <has_text text="PKC" />
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	219 <has_text text="CK2a2" />
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	220 <has_text text="CK2alpha" />
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	221 <has_text text="Csnk2a1" />
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	222 </assert_contents>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	223 </output>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	224
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	225 <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	226 <assert_contents>
23 7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	227 <has_text text="CDK7" />
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	228 <has_text text="CK1alpha" />
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	229 <has_text text="CK2alpha" />
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	230 <has_text text="DNAPK" />
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	231 <has_text text="HIPK2" />
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	232 <has_text text="IKKalpha" />
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	233 <has_text text="PKCalpha" />
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	234 <has_text text="PKCbeta" />
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	235 <has_text text="PKC" />
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	236 <has_text text="CK2a2" />
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	237 <has_text text="CK2alpha" />
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	238 <has_text text="Csnk2a1" />
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	239 </assert_contents>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	240 </output>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	241 </test>
13 28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	242 <test>
28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	243 <param name="phosphoSites" ftype="tabular" value="test_input_for_preproc.tabular" />
28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	244 <param name="protein_fasta" ftype="fasta" value="test_swissprot.fasta" />
28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	245 <param name="networkin" ftype="tabular" value="test_networkin.tabular" />
28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	246 <param name="p_sty_motifs" ftype="tabular" value="pSTY_motifs.tabular" />
28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	247 <param name="psp_kinase_substrate" ftype="tabular" value="test_kinase_substrate.tabular" />
28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	248 <param name="psp_regulatory_sites" ftype="tabular" value="test_regulatory_sites.tabular" />
28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	249 <param name="pst_py_selector" value="y"/>
28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	250 <param name="merge_function" value="sum"/>
28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	251
28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	252 <param name="phosphoCol" value="^Number of Phospho [(][STY][STY]*[)]$"/>
28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	253 <param name="startCol" value="^Intensity[^_]"/>
28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	254 <param name="intervalCol" value="1"/>
23 7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	255 <param name="collapse_func" value="sum"/>
13 28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	256 <param name="localProbCutoff" value="0.75"/>
28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	257 <param name="species" value="human"/>
28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	258
28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	259 <output name="phosphoPepIntensities">
28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	260 <assert_contents>
28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	261 <has_text text="Phosphopeptide" />
28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	262 <has_text text="pTYVDPFTpYEDPNQAVR" />
28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	263 </assert_contents>
28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	264 </output>
28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	265
28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	266 <output name="preproc_tab">
28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	267 <assert_contents>
28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	268 <has_text text="pTYVDPFTpYEDPNQAVR" />
28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	269 <has_text text="EEKHLNQGVRpTYVDPFTYEDP" />
28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	270 <has_text text="GVRTYVDPFTpYEDPNQAVREF" />
28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	271 <has_text text="HLNQGVRtYVDPFTY" />
28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	272 <has_text text="TYVDPFTyEDPNQAV" />
28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	273 <has_text text="EPHA4" />
28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	274 <has_text text="pT595, pY602" />
28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	275 <has_text text="pT544, pY551" />
28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	276 <has_text text="P54764;" />
28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	277 <has_text text="P54764-2" />
28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	278 </assert_contents>
28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	279 </output>
28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	280
28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	281 <output name="melted_phophopeptide_map">
28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	282 <assert_contents>
23 7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	283 <has_text text="EphA6" />
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	284 <has_text text="EPHA4" />
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	285 <has_text text="EphA4" />
13 28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	286 </assert_contents>
28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	287 </output>
28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	288 </test>
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	289 </tests>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	290 <help><![CDATA[
27 29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	291 =============================================================
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	292 Phopsphoproteomic Enrichment Pipeline Preprocessing Steps
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	293 =============================================================
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	294
27 29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	295 Overview
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	296 ==========
0 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 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	299 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	300 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	301
27 29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	302 Workflow position
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	303 ===================
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	304
27 29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	305 Upstream tool
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	306 =============
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	307
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	308 The input dataset for this tool is the ``Phospho (STY)Sites.txt`` file that is produced:
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	309
27 29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	310 - by the Galaxy "MaxQuant" (``maxquant``) tool
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	311 - or by the Galaxy "Maxquant (using mqpar.xml)" (``maxquant_mqpar``) tool
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	312 - or by the desktop version of MaxQuant.
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	313
27 29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	314 Downstream tool
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	315 ===============
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	316
27 29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	317 The "MaxQuant Phosphopeptide ANOVA" tool (``mqppep_anova``) consumes the "preprocessed" output file ``preproc_tab`` that this tool produces.
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	318
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	319 Phopsphoproteomic Enrichment Pipeline Localization-Probability Cut-Off
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	320 ========================================================================
0 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 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	323 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	324 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	325
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	326 "For phosphopeptide identification, a localization probability cutoff is applied. This filter is performed to select for phosphopeptides with a high confidence (i.e., greater than 0.75) in phosphoresidue identification [Hogrebe 2018; Olsen 2006]. In other words, the summed probability of all other residues that could potentially contain the phospho-group is less than 0.25. This cutoff could be raised to increase the stringency of the phosphopeptide selection. In regard to the number of identifications, the expected number of pY peptides is in the hundreds, while the expected number of pST peptides is in the high thousands. These values reflect previously observed phosphoproteome distribution where about 2%, 12%, and 86% of the phosphosites are pY, pT, and pS, respectively [Olsen 2006]."
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	327
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	328 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	329
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	330 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	331 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	332 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	333 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	334 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	335 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	336 7. Produces an output file (in tabular format) that contains the phosphopeptide (first column) and its (possibly merged) mass spectral intensity for each sample.
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 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	339 [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	340 <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	341 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	342
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	343
27 29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	344 Input dataset
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	345 =============
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	346
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	347 Phospho (STY)Sites.txt
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	348 This is the ``MaxQuant Phospho (STY)Sites.txt`` file produced by MaxQuant.
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	349 If you use the desktop version of MaxQuant, you will find this file in the ``txt`` folder.
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	350
27 29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	351 Input parameters
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	352 ================
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	353
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	354 Localization probability cutoff
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	355 Minimum localization probability; see above.
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	356
27 29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	357 Intensity merge-function
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	358 Specifies how intensities for identical phosphosites should be merged; see above.
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	359
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	360 Output datasets
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	361 ===============
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	362
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	363 ``ppep_intensities``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	364 Data table (in tabular format) presenting, for each sample, the mass-spectral intensity of each phopshopeptide having localization probability greater than the cutoff.
27 29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	365
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	366 ``enrichment.pdf``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	367 Graph (in PDF format) presenting non-zero proportions of pS, pT, and pY among the phosphosites; note that a phosphopeptide may have multiple phosphosite.
27 29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	368
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	369 ``locProbCutoff.pdf``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	370 Graph (in PDF format) contrasting proportion of phosphopeptides above the localization probability cutoff with the proportion below.
27 29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	371
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	372 ``enrichment.svg``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	373 Enrichment graph (in downloadable "scalable vector graphics" format) for incorporation into documents.
27 29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	374
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	375 ``locProbCutoff.svg``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	376 Localization probability cutoff graph (in downloadable "scalable vector graphics" format) for incorporation into documents.
27 29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	377
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	378 ``filteredData``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	379 Data table (in tabular format) comprising rows of the ``phosphSites`` input file that are not flagged as contaminants or reversed sequences.
27 29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	380
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	381 ``quantData``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	382 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	383
27 29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	384 Authors
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	385 =======
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	386
23 7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	387 ``Nicholas A. Graham``
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	388 (`ORCiD 0000-0002-6811-1941 <https://orcid.org/0000-0002-6811-1941>`_) initiated the original script.
7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	389
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	390 ``Larry C. Cheng``
23 7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	391 (`ORCiD 0000-0002-6922-6433 <https://orcid.org/0000-0002-6922-6433>`_) updated the original script.
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	392
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	393 ``Arthur C. Eschenlauer``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	394 (`ORCiD 0000-0002-2882-0508 <https://orcid.org/0000-0002-2882-0508>`_) adapted the script to run in Galaxy.
13 28a126da9b28 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 7 diff changeset	395
22 43f1fd0ff86b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 00881af5b1373174e5afe706add2f33b8614828c" eschen42 parents: 16 diff changeset	396 ``James E. Johnson``
43f1fd0ff86b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 00881af5b1373174e5afe706add2f33b8614828c" eschen42 parents: 16 diff changeset	397 (University of Minnesota Supercomputing Institute) adapted the script to run in Galaxy.
43f1fd0ff86b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 00881af5b1373174e5afe706add2f33b8614828c" eschen42 parents: 16 diff changeset	398
43f1fd0ff86b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 00881af5b1373174e5afe706add2f33b8614828c" eschen42 parents: 16 diff changeset	399
27 29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	400 Phopsphoproteomic Enrichment Pipeline Upstream Kinase Mapping
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	401 ===============================================================
0 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 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	404
27 29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	405 Input databases
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	406 ===============
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	407
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	408 ``networkin``
5 b91809a18dbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf" eschen42 parents: 4 diff changeset	409 This table is the result of filtering the NetworkKIN database [Linding 2007; Horn 2014] for cutoff score > 2.0. The ENSEMBL data used to generate the file were from Ensembl, `ensembl.org <https://web.archive.org/web/20220308011159/http://useast.ensembl.org/index.html>`_ [Howe 2021].
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	410
27 29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	411 To generate this file:
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	412
27 29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	413 (1) Download the "precomputed data for all available kinase predictors against ENSEMBL" (available at the NetworkKIN predictions link on the downloads page at https://web.archive.org/web/20200208000403/http://networkin.info/download/networkin_human_predictions_3.1.tsv.xz; N.B.: "Commercial users are requested to contact the authors before using the data on the networkin.info website");
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	414 (2) Decompress the .tsv.xz with file with "unxz" (from XZ Utils `https://tukaani.org/xz/ <https://tukaani.org/xz/>`_);
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	415 (3) Filter out the rows having "network_kin" less than 2.0.
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	416
27 29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	417 The result should be a tab-separated file with the following columns:
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	418
27 29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	419 - ``#substrate``
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	420 - ``position``
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	421 - ``id``
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	422 - ``networkin_score``
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	423 - ``tree``
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	424 - ``netphorest_group``
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	425 - ``netphorest_score``
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	426 - ``string_identifier``
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	427 - ``string_score``
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	428 - ``substrate_name``
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	429 - ``sequence``
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	430 - ``string_path``
0 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
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	433 ``p_sty_motifs``
27 29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	434 This database merges motif patterns from [Amanchy 2007] and Phosida [Gnad 2011].
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	435
27 29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	436 The Amanchy data are adapted from `https://web.archive.org/web//http://hprd.org/serine_motifs <https://web.archive.org/web//http://hprd.org/serine_motifs>`_ and `https://web.archive.org/web//http://hprd.org/tyrosine_motifs <https://web.archive.org/web//http://hprd.org/tyrosine_motifs>`_ (both links cite the reference where each motif was published), and the patterns are translated into Perl regular expression format (`https://perldoc.perl.org/perlre <https://perldoc.perl.org/perlre>`_).
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	437
27 29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	438 The Phosida data are adapted (translated to Perl-formatted regular expressions) from `http://pegasus.biochem.mpg.de/phosida/help/motifs.aspx <http://pegasus.biochem.mpg.de/phosida/help/motifs.aspx>`_ (this link cites the reference where each motif was published).
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	439
27 29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	440 This file has three tab-separated columns (and no header):
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	441
27 29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	442 - column 1 is an (ignored) identifier
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	443 - column 2 is a Perl regular expression
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	444 - column 3 is a descriptor.
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	445
27 29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	446 For two examples:
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	447
27 29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	448 ``2<TAB>R.R..(pS\|pT)<TAB>Akt kinase substrate motif (HPRD)``
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	449
27 29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	450 ``10<TAB>R..(pS\|pT)V<TAB>CAMK2_Phosida``
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	451
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	452 ``psp_kinase_substrate``
27 29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	453 'Kinase-substrate dataset: experimentally determined substrates, sequences, cognate kinases, and metadata curated from the literature' [Hornbeck 2011]. This tabular-formatted file may be downloaded for non-commercial purposes as 'Kinase_Substrate_Dataset.gz' from `https://www.phosphosite.org/staticDownloads.action <https://www.phosphosite.org/staticDownloads.action>`_.
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	454
27 29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	455 Data extracted from PhosphoSitePlus(R), created by Cell Signaling Technology Inc. PhosphoSitePlus is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License (`https://creativecommons.org/licenses/by-nc-sa/3.0/ <https://creativecommons.org/licenses/by-nc-sa/3.0/>`_). Attribution must be given in written, oral and digital presentations to PhosphoSitePlus, www.phosphosite.org. Written documents should additionally cite:
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	456
27 29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	457 Hornbeck PV, Kornhauser JM, Tkachev S, Zhang B, Skrzypek E, Murray B, Latham V, Sullivan M (2012) PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res. 40, D261-D270.; www.phosphosite.org.
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	458
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	459 ``psp_regulatory_sites``
27 29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	460 'Regulatory sites: information curated from the literature about modification sites shown to regulate molecular functions, biological processes, and molecular interactions including protein-protein interactions' [Hornbeck 2011]. This tabular-formatted file may be downloaded for non-commercial purposes as 'Regulatory_sites.gz' from `https://www.phosphosite.org/staticDownloads.action <https://www.phosphosite.org/staticDownloads.action>`_.
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	461
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	462 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	463
27 29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	464 Output datasets
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	465 ===============
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	466
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	467 ``ppep_map``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	468 Data table (in tabular format, consumed by the merge/filter step) presenting, for each phosphopeptide, the kinase mappings, the mass-spectral intensities for each sample, and the metadata from UniProtKB/SwissProt, phospho-sites, phospho-motifs, and regulatory sites. Data in the columns marked "``Domain``", "``ON_...``", or "``..._PhosphoSite``" are available subject to the following terms:
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	469
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	470 "PhosphoSitePlus\ \|reg\| (PSP) was created by Cell Signaling Technology Inc. It is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License(`https://creativecommons.org/licenses/by-nc-sa/3.0/ <https://creativecommons.org/licenses/by-nc-sa/3.0/>`_). When using PSP data or analyses in printed publications or in online resources, the following acknowledgements must be included: (a) the words 'PhosphoSitePlus(R), www.phosphosite.org' must be included at appropriate places in the text or webpage, and (b) citation of [Hornbeck 2011 (`PMID: 25514926 <https://pubmed.ncbi.nlm.nih.gov/25514926>`_)] must be included in the bibliography."
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	471
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	472
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	473 ``melted``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	474 Data table (in tabular format) presenting, for each phosphopeptide, the gene and one of the phospho-motifs or kinase-substrate sites.
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	475
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	476 ``ppep_mapping_sqlite``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	477 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	478
27 29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	479 Authors
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	480 =======
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	481
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	482 ``Nicholas A. Graham``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	483 (`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	484
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	485 ``Arthur C. Eschenlauer``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	486 (`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	487
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	488
27 29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	489 Phopsphoproteomic Enrichment Pipeline Merge and Filter
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	490 ========================================================
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	491
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	492 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	493
27 29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	494 Input parameters
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	495 ================
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	496
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	497 ``species``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	498 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	499
27 29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	500 Output datasets
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	501 ===============
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	502
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	503 ``preproc_tab``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	504 Phosphopeptides annotated with SwissProt and phosphosite metadata, in tabular format. This file is designed to be consumed by the downstream ANOVA tool. Some data in the columns marked "PSP" are available subject to the following terms:
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	505
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	506 "PhosphoSitePlus\ \|reg\| (PSP) was created by Cell Signaling Technology Inc. It is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License(`https://creativecommons.org/licenses/by-nc-sa/3.0/ <https://creativecommons.org/licenses/by-nc-sa/3.0/>`_). When using PSP data or analyses in printed publications or in online resources, the following acknowledgements must be included: (a) the words 'PhosphoSitePlus(R), www.phosphosite.org' must be included at appropriate places in the text or webpage, and (b) citation of [Hornbeck 2011 (`PMID: 25514926 <https://pubmed.ncbi.nlm.nih.gov/25514926>`_)] must be included in the bibliography."
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	507
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	508 ``preproc_csv``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	509 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	510
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	511 ``preproc_sqlite``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	512 ``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	513
27 29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	514 Authors
29775869faba planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	515 =======
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	516
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	517 ``Nicholas A. Graham``
23 7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	518 (`ORCiD 0000-0002-6811-1941 <https://orcid.org/0000-0002-6811-1941>`_) initiated the original script.
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	519
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	520 ``Larry C. Cheng``
23 7560a4e80a1e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 22 diff changeset	521 (`ORCiD 0000-0002-6922-6433 <https://orcid.org/0000-0002-6922-6433>`_) updated the original script.
0 2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	522
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	523 ``Arthur C. Eschenlauer``
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	524 (`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	525
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	526 .. \|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	527 ]]></help>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	528 <citations>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	529 <!-- upstream kinase mapping -->
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	530 <!-- 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	531 <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	532 <!-- 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	533 <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	534 <!-- localization filter -->
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	535 <!-- 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	536 <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	537 <!-- all three -->
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	538 <!-- 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	539 <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	540 <!-- 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	541 <!-- 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	542 <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	543 <!-- 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	544 <!-- upstream kinase mapping -->
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	545 <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	546 <!-- 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	547 <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	548 <!-- localization filter -->
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	549 <!-- 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	550 <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	551 <!-- upstream kinase mapping -->
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	552 <!-- 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	553 <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	554 <!-- 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	555 <!-- Hornbeck 2012 "PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse." PMID: 22135298 -->
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	556 <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	557 <!-- upstream kinase mapping -->
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	558 <!-- 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	559 <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	560 <!-- localization filter -->
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	561 <!-- 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	562 <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	563 </citations>
2c7e1b167736 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	564 </tool>

Mercurial > repos > eschen42 > mqppep_preproc

annotate mqppep_preproc.xml @ 27:29775869faba draft