# HG changeset patch
# User proteore
# Date 1552484077 14400
# Node ID 034cfb96a4825d9951ed919565556e2335f56239
# Parent  299eb4a62e0c2fd7dc0b9992178b0b0f0c5289ae
planemo upload commit b052261cf5cd6c2413e301a19d5c95d9794f1e81-dirty

diff -r 299eb4a62e0c -r 034cfb96a482 Get_ms-ms_observations.xml
--- a/Get_ms-ms_observations.xml	Fri Feb 01 11:48:49 2019 -0500
+++ b/Get_ms-ms_observations.xml	Wed Mar 13 09:34:37 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="retr_pepatlas1" name="Get MS/MS observations in tissue/fluid" version="2019.02.01.1">
+<tool id="retr_pepatlas1" name="Get MS/MS observations in tissue/fluid" version="2019.02.26">
     <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_directory__+"/"+str(ref) for ref in str($atlas).split(",")])}
+        --atlas=${",".join([str(ref) if "peptide_atlas" in str(ref).split("/") else $__tool_directory__+"/"+str(ref) for ref in str($atlas).split(",")])}
         --output="$output"
     </command>
 
@@ -41,7 +41,9 @@
             <when value="file" >
                 <param name="file" type="data" format="txt,tabular" label="Select your file" help="" />
                 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
-                <param name="ncol" type="text" value="c1" label="Column of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />                
+                <param name="ncol" type="text" value="c1" label="Column of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on'>
+                    <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
+                </param>
             </when>
         </conditional>
         <!-- Peptide Atlas options -->
diff -r 299eb4a62e0c -r 034cfb96a482 peptide_atlas.loc.sample
--- a/peptide_atlas.loc.sample	Fri Feb 01 11:48:49 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,19 +0,0 @@
-#<id>   <name>  <tissue> <value>
-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
diff -r 299eb4a62e0c -r 034cfb96a482 proteore_peptide_atlas.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/proteore_peptide_atlas.loc.sample	Wed Mar 13 09:34:37 2019 -0400
@@ -0,0 +1,19 @@
+#<id>   <name>  <tissue> <value>
+Human_Adrenal_gland_2014-08	Human Adrenal gland 2014/08	Human_Adrenal_gland	tool-data/Human_Adrenal_gland_2014-08.tsv
+Human_Brain_2015-01	Human Brain 2015/01	Human_Brain	tool-data/Human_Brain_2015-01.tsv
+Human_Breast_2014-08	Human Breast 2014/08	Human_Breast	tool-data/Human_Breast_2014-08.tsv
+Human_CSF_2014-09	Human CSF 2014/09	Human_CSF	tool-data/Human_CSF_2014-09.tsv
+Human_Colon_cancer_2013-02	Human Colon cancer 2013/02	Human_Colon_cancer	tool-data/Human_Colon_cancer_2013-02.tsv
+Human_Digestive_system_2014-08	Human Digestive system 2014/08	Human_Digestive_system	tool-data/Human_Digestive_system_2014-08.tsv
+Human_Female_reproductive_system_2014-08	Human Female reproductive system 2014/08	Human_Female_reproductive_system	tool-data/Human_Female_reproductive_system_2014-08.tsv
+Human_Heart_2014-08	Human Heart 2014/08	Human_Heart	tool-data/Human_Heart_2014-08.tsv
+Human_Kidney_2014-08	Human Kidney 2014/08	Human_Kidney	tool-data/Human_Kidney_2014-08.tsv
+Human_Liver_2014-08	Human Liver 2014/08	Human_Liver	tool-data/Human_Liver_2014-08.tsv
+Human_Lung_2014-08	Human Lung 2014/08	Human_Lung	tool-data/Human_Lung_2014-08.tsv
+Human_Male_reproductive_system_2014-08	Human Male reproductive system 2014/08	Human_Male_reproductive_system	tool-data/Human_Male_reproductive_system_2014-08.tsv
+Human_Pancreas_2014-08	Human Pancreas 2014/08	Human_Pancreas	tool-data/Human_Pancreas_2014-08.tsv
+Human_Plasma_non_glyco_2017-04	Human Plasma non glyco 2017/04	Human_Plasma_non_glyco	tool-data/Human_Plasma_non_glyco_2017-04.tsv
+Human_Spleen_2014-08	Human Spleen 2014/08	Human_Spleen	tool-data/Human_Spleen_2014-08.tsv
+Human_Testis_2017-01	Human Testis 2017/01	Human_Testis	tool-data/Human_Testis_2017-01.tsv
+Human_Urinary_bladder_2014-08	Human Urinary bladder 2014/08	Human_Urinary_bladder	tool-data/Human_Urinary_bladder_2014-08.tsv
+Human_Urine_2014-08	Human Urine 2014/08	Human_Urine	tool-data/Human_Urine_2014-08.tsv
diff -r 299eb4a62e0c -r 034cfb96a482 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Fri Feb 01 11:48:49 2019 -0500
+++ b/tool_data_table_conf.xml.sample	Wed Mar 13 09:34:37 2019 -0400
@@ -1,8 +1,8 @@
 
 <tables>
     <!-- Location of peptide reference files for proteore_ms_observation -->
-    <table name='peptide_atlas' comment_char="#">
+    <table name='proteore_peptide_atlas' comment_char="#">
         <columns>id,name,tissue,value</columns>
-        <file path="tool-data/peptide_atlas.loc" />
+        <file path="tool-data/proteore_peptide_atlas.loc" />
     </table>
 </tables> 
\ No newline at end of file