# HG changeset patch
# User dchristiany
# Date 1548688161 18000
# Node ID 93338a36da6e77878c868b0a323bc33ea4ae2550
# Parent  a4811c440b45bb94c97778629529f4cd4180cfb4
planemo upload commit c89c5deac442c0c2aa52b24f2c5af4b290773fc0-dirty

diff -r a4811c440b45 -r 93338a36da6e data_manager/resource_building.xml
--- a/data_manager/resource_building.xml	Mon Jan 28 09:43:02 2019 -0500
+++ b/data_manager/resource_building.xml	Mon Jan 28 10:09:21 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2019.01.25.7" tool_type="manage_data">
+<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2019.01.25.8" tool_type="manage_data">
 <description>
 to create or update reference files for proteore tools
 </description>
@@ -152,13 +152,24 @@
 
 For 'Peptide Atlas':
 
-* `Human liver <"https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetPeptides?atlas_build_id=472&display_options=ShowMappings&organism_id=2&sample_category_id=1&QUERY_NAME=AT_GetPeptides&output_mode=tsv&apply_action=QUERY">`_.
-* `Human brain <"https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetPeptides?atlas_build_id=472&display_options=ShowMappings&organism_id=2&sample_category_id=2&QUERY_NAME=AT_GetPeptides&output_mode=tsv&apply_action=QUERY">`_.
-* `Human heart <"https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetPeptides?atlas_build_id=472&display_options=ShowMappings&organism_id=2&sample_category_id=3&QUERY_NAME=AT_GetPeptides&output_mode=tsv&apply_action=QUERY">`_.
-* `Human kidney <"https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetPeptides?atlas_build_id=472&display_options=ShowMappings&organism_id=2&sample_category_id=4&QUERY_NAME=AT_GetPeptides&output_mode=tsv&apply_action=QUERY">`_.
-* `Human plasma <"https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetPeptides?atlas_build_id=472&display_options=ShowMappings&organism_id=2&sample_category_id=5&QUERY_NAME=AT_GetPeptides&output_mode=tsv&apply_action=QUERY">`_.
-* `Human urine <"https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetPeptides?atlas_build_id=472&display_options=ShowMappings&organism_id=2&sample_category_id=6&QUERY_NAME=AT_GetPeptides&output_mode=tsv&apply_action=QUERY">`_.
-* `Human CSF <"https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetPeptides?atlas_build_id=472&display_options=ShowMappings&organism_id=2&sample_category_id=7&QUERY_NAME=AT_GetPeptides&output_mode=tsv&apply_action=QUERY">`_.
+
+* `Human Adrenal gland proteome <"https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=432&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY">`_.
+* `Human Brain proteome <"https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=441&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY">`_.
+* `Human Breast Proteome <"https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=427&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY">`_.
+* `Human CSF proteome <"https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=434&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY">`_.
+* `Human Digestive System proteome<"https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=429&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY">`_.
+* `Human female reproductive system proteome <"https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=430&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY">`_.
+* `Human Heart proteome <"https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=418&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY">`_.
+* `Human Kidney man Kidney Proteome <"https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=424&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY">`_.
+* `Human Liver proteome <"https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=425&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY">`_.
+* `Human Lung proteome <"https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=419&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY">`_.
+* `Human Male Reproductive System proteome <"https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=431&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY">`_.
+* `Human Pancreas proteome <"https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=420&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY">`_.
+* `Human Plasma Non-Glyco proteome <"https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=465&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY">`_.
+* `Human Spleen proteome <"https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=421&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY">`_.
+* `Human Testis and spermatozoa samples <"https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=463&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY">`_.
+* `Human Urinary Bladder proteome <"https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=422&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY">`_.
+* `Human Urine proteome <"https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id=423&display_options=ShowAbundances&organism_id=2&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY">`_.
 
 For ID mapping: