Mercurial > repos > proteore > proteore_ms_observation_pepatlas

changeset 3:e446b013c048 draft

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planemo upload commit 23c8d2008471f194131da1c7705c8bb0b6388236-dirty
author proteore
date Fri, 01 Feb 2019 11:34:12 -0500
parents 6ab9d2778f04
children 299eb4a62e0c
files Get_ms-ms_observations.xml peptide_atlas.loc.sample
diffstat 2 files changed, 44 insertions(+), 18 deletions(-) [+]
line wrap: on
line diff
--- a/Get_ms-ms_observations.xml	Tue Dec 18 09:50:50 2018 -0500
+++ b/Get_ms-ms_observations.xml	Fri Feb 01 11:34:12 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="retr_pepatlas1" name="Get MS/MS observations in tissue/fluid" version="2018.12.18">
+<tool id="retr_pepatlas1" name="Get MS/MS observations in tissue/fluid" version="2019.02.01">
     <description>[Peptide Atlas]</description>
     <requirements>
         <requirement type="package" version="3.4.1">R</requirement>
@@ -16,7 +16,7 @@
             --column_number="$input.ncol"
             --header="$input.header"
         #end if
-        --atlas=${",".join([$__tool_data_path__+"/"+str(ref) for ref in str($atlas).split(",")])}
+        --atlas=${",".join([$__tool_directory__+"/"+str(ref) for ref in str($atlas).split(",")])}
         --output="$output"
     </command>
 
@@ -46,7 +46,7 @@
         </conditional>
         <!-- Peptide Atlas options -->
         <param name="atlas" type="select" display="checkboxes" multiple="true" label="Proteomics dataset (biological sample)" optional="false" >
-            <options from_data_table="peptide_atlas">
+            <options from_data_table="proteore_peptide_atlas">
                 <filter type="sort_by" column="2"/>
             </options>
         </param>
@@ -91,13 +91,13 @@
 
 **Parameters**
 
-"Proteomics dataset (biological sample)": available human biological samples analyzed by MS/MS are the following: brain, heart, kidney, liver, plasma, urine and cerebrospinal fluid (CSF). 
+"Proteomics dataset (biological sample - date of downloading)": available human biological samples (tissue/organ/body fluid) analyzed by MS/MS and processed by Peptide Atlas are the following: adrenal gland, brain, breast, CSF (cerebrospinal fluid), colon cancer, digestive system, female and male reproductive system, heart, kidney, liver, lung, pancreas, plasma (non-glycosylated), spleen, testis, urinary bladder, urine. 
 
 ----
 
 **Output**
 
-Additional columns are created for each selected proteomics sample reporting the number of times all peptides corresponding to a protein have been observed by LC-MS/MS according to Peptide Atlas. 
+Additional columns are created for each selected proteomics sample reporting the total number of observation (called "ProteinProphet-adjusted N Obs") of all peptides detected by LC-MS/MS and assigned to a protein according to Peptide Atlas. 
 
 a “NA” means that no information has been reported suggesting that this protein has not been observed in the sample of interest.
 
@@ -105,7 +105,26 @@
 
 **Data source (release date)**
 
-Data were retrieved from Peptide Atlas release (January 2018) through their query interface.
+  Data source (release date)" - replace "MS/MS Proteomics dataset (also called "build") were retrieved from Peptide Atlas website through their query interface (in January 2019) with name and release date as follow:
+
+- Human Adrenal Gland 2014-08
+- Human Brain 2015-01
+- Human Breast 2014-08
+- Human CSF 2014-09
+- Human Colon Cancer 2013-02
+- Human Digestive System 2014-08
+- Human Female Reproductive System 2014-08
+- Human Heart 2014-08
+- Human Kidney 2014-08
+- Human Liver 2014-08
+- Human Lung 2014-08
+- Human Male Reproductive System 2014-08
+- Human Pancreas 2014-08
+- Human Plasma Non-Glyco 2017-04
+- Human Spleen 2014-08
+- Human Testis 2017-01
+- Human Urinary Bladder 2014-08
+- Human Urine 2014-08
 
 ----
 
--- a/peptide_atlas.loc.sample	Tue Dec 18 09:50:50 2018 -0500
+++ b/peptide_atlas.loc.sample	Fri Feb 01 11:34:12 2019 -0500
@@ -1,12 +1,19 @@
-#This file lists the locations name and values of reference files 
-#for number of MS/MS observations in a tissue
-#This is a tab separated file (TAB, not 4 spaces !)
-#
-#<tissue>   <name>  <value>
-Human_Brain     Human Brain 25/07/2018  peptide_atlas/Human_Brain_25-07-2018.tsv
-Human_CSF       Human CSF 25/07/2018    peptide_atlas/Human_CSF_25-07-2018.tsv
-Human_Heart     Human Heart 25/07/2018  peptide_atlas/Human_Heart_25-07-2018.tsv
-Human_Kidney    Human Kidney 25/07/2018 peptide_atlas/Human_Kidney_25-07-2018.tsv
-Human_Liver     Human Liver 25/07/2018  peptide_atlas/Human_Liver_25-07-2018.tsv
-Human_Plasma    Human Plasma 25/07/2018 peptide_atlas/Human_Plasma_25-07-2018.tsv
-Human_Urine     Human Urine 25/07/2018  peptide_atlas/Human_Urine_25-07-2018.tsv
+#<id>   <name>  <value> <path>
+Human_Adrenal_gland_2014-08 Human Adrenal gland 2014/08	Human_Adrenal_gland	tool-data/peptide_atlas/Human_Adrenal_gland_2014-08.tsv
+Human_Brain_2015-01 Human Brain 2015/01	Human_Brain	tool-data/peptide_atlas/Human_Brain_2015-01.tsv
+Human_Breast_2014-08    Human Breast 2014/08	Human_Breast	tool-data/peptide_atlas/Human_Breast_2014-08.tsv
+Human_CSF_2014-09   Human CSF 2014/09	Human_CSF	tool-data/peptide_atlas/Human_CSF_2014-09.tsv
+Human_Colon_cancer_2013-02  Human Colon cancer 2013/02	Human_Colon_cancer	tool-data/peptide_atlas/Human_Colon_cancer_2013-02.tsv
+Human_Digestive_system_2014-08	Human Digestive system 2014/08	Human_Digestive_system	tool-data/peptide_atlas/Human_Digestive_system_2014-08.tsv
+Human_Female_reproductive_system_2014-08	Human Female reproductive system 2014/08	Human_Female_reproductive_system	tool-data/peptide_atlas/Human_Female_reproductive_system_2014-08.tsv
+Human_Heart_2014-08 Human Heart 2014/08	Human_Heart	tool-data/peptide_atlas/Human_Heart_2014-08.tsv
+Human_Kidney_2014-08	Human Kidney 2014/08	Human_Kidney	tool-data/peptide_atlas/Human_Kidney_2014-08.tsv
+Human_Liver_2014-08	Human Liver 2014/08	Human_Liver	tool-data/peptide_atlas/Human_Liver_2014-08.tsv
+Human_Lung_2014-08	Human Lung 2014/08	Human_Lung	tool-data/peptide_atlas/Human_Lung_2014-08.tsv
+Human_Male_reproductive_system_2014-08	Human Male reproductive system 2014/08	Human_Male_reproductive_system	tool-data/peptide_atlas/Human_Male_reproductive_system_2014-08.tsv
+Human_Pancreas_2014-08	Human Pancreas 2014/08	Human_Pancreas	tool-data/peptide_atlas/Human_Pancreas_2014-08.tsv
+Human_Plasma_non_glyco_2017-04	Human Plasma non glyco 2017/04	Human_Plasma_non_glyco	tool-data/peptide_atlas/Human_Plasma_non_glyco_2017-04.tsv
+Human_Spleen_2014-08	Human Spleen 2014/08	Human_Spleen	tool-data/peptide_atlas/Human_Spleen_2014-08.tsv
+Human_Testis_2017-01	Human Testis 2017/01	Human_Testis	tool-data/peptide_atlas/Human_Testis_2017-01.tsv
+Human_Urinary_bladder_2014-08	Human Urinary bladder 2014/08	Human_Urinary_bladder	tool-data/peptide_atlas/Human_Urinary_bladder_2014-08.tsv
+Human_Urine_2014-08	Human Urine 2014/08	Human_Urine	tool-data/peptide_atlas/Human_Urine_2014-08.tsv