Mercurial > repos > proteore > proteore_expression_levels_by_tissue

changeset 9:0a0f6c37f05e draft

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planemo upload commit 47b21d3d533a6729de0269f70b033f976419368c-dirty
author proteore
date Wed, 13 Mar 2019 09:15:52 -0400
parents 2c0bab71a436
children 48b767deb90b
files README.rst get_expression_profiles.xml proteore_protein_atlas_normal_tissue.loc.sample proteore_protein_atlas_tumor_tissue.loc.sample tool-data/proteinatlas.loc.sample tool_data_table_conf.xml.sample
diffstat 6 files changed, 26 insertions(+), 28 deletions(-) [+]
line wrap: on
line diff
--- a/README.rst	Tue Dec 18 09:48:29 2018 -0500
+++ b/README.rst	Wed Mar 13 09:15:52 2019 -0400
@@ -3,7 +3,7 @@
 
 **Authors**
 
-T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
+David Christiany, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
 
 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
 
--- a/get_expression_profiles.xml	Tue Dec 18 09:48:29 2018 -0500
+++ b/get_expression_profiles.xml	Wed Mar 13 09:15:52 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="sel_ann_hpa" name="Get expression profiles" version="2018.12.17">
+<tool id="sel_ann_hpa" name="Get expression profiles" version="2019.03.06">
     <description>by (normal or tumor) tissue/cell type [Human Protein Atlas]
     </description>
     <requirements>
@@ -8,7 +8,13 @@
     </stdio>
     <command interpreter="Rscript">
         $__tool_directory__/get_expression_profiles.R
-        --ref_file="$__tool_directory__/$options.proteinatlas"
+        
+        #if "protein_atlas" in str($options.proteinatlas).split("/")
+          --ref_file="$options.proteinatlas"
+        #else
+          --ref_file="$__tool_directory__/$options.proteinatlas"
+        #end if
+
         --input_type="$input.ids"
         #if $input.ids == "list"
             --input="$input.list"
@@ -51,7 +57,9 @@
             <when value="file" >
                 <param name="file" type="data" format="txt,tabular" label="" 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 number of IDs to map" 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 number of IDs to map" 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>
         <conditional name="options">
@@ -61,13 +69,7 @@
             </param>
             <when value="normal">
                 <param name="proteinatlas" type="select" label="Normal tissue HPA version" >
-                    <!--options from_file="proteinatlas.loc" >
-                        <column name="name" index="1"/>
-                        <column name="value" index="2"/>
-                        <filter type="remove_value" key="name" value="Full Human Protein Atlas (23/10/18)"/>
-                        <filter type="remove_value" key="name" value="HPA Tumor Tissue (23/10/18)"/>
-	                </options-->
-                    <option value="tool-data/HPA_normal_tissue_23-10-2018.tsv">HPA Normal Tissue (23/10/18)</option>
+                    <options from_data_table="proteore_protein_atlas_normal_tissue"/>
 	            </param>
                 <param name="normal_tissue" type="select" label="Select tissue(s)" multiple="True" display="checkboxes" optional="False">
                     <option value="adrenal gland" >Adrenal gland</option>
@@ -134,13 +136,7 @@
             </when>
             <when value="tumor">
                 <param name="proteinatlas" type="select" label="Tumor tissue HPA version" >
-                    <!--options from_file="proteinatlas.loc" >
-		                <column name="name" index="1" />
-		                <column name="value" index="2" />
-		                <filter type="remove_value" meta_ref="proteinatlas" key="name" value="Full Human Protein Atlas (23/10/18)" />
-                        <filter type="remove_value" meta_ref="proteinatlas" key="name" value="HPA Normal Tissue (23/10/18)" />
-	                </options-->
-                    <option value="tool-data/HPA_pathology_23-10-2018.tsv">HPA Tumor Tissue (23/10/18)</option>
+                    <options from_data_table="proteore_protein_atlas_tumor_tissue"/>
 	            </param>
                 <param name="cancer_tissue" type="select" label="Select cancer tissue(s)" multiple="True" display="checkboxes" optional="False">
                     <option value="breast cancer" >Breast cancer</option>
@@ -244,7 +240,7 @@
 
 **Authors**
 
-T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
+David Christiany, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
 
 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR
 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/proteore_protein_atlas_normal_tissue.loc.sample	Wed Mar 13 09:15:52 2019 -0400
@@ -0,0 +1,2 @@
+#<id>	<name>	<tissue>	<value>
+HPA_normal_tissue_19-07-2018	HPA normal tissue 19/07/2018	HPA_normal_tissue	/tool-data/HPA_normal_tissue_23-10-2018.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/proteore_protein_atlas_tumor_tissue.loc.sample	Wed Mar 13 09:15:52 2019 -0400
@@ -0,0 +1,2 @@
+#<id>	<name>	<tissue>	<value>
+HPA_pathology_19-07-2018	HPA pathology 19/07/2018	HPA_pathology	/tool-data/HPA_pathology_23-10-2018.tsv
--- a/tool-data/proteinatlas.loc.sample	Tue Dec 18 09:48:29 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-#This file lists the locations and dbkeys of Human Protein Atlas files.
-#<name>	<display_name (value)>          <file_path>
-#full	Full Human Protein Atlas (23/10/18)	tool-data/HPA_full_atlas_23-10-2018.tsv
-normal_tissue	HPA Normal Tissue (23/10/18)	tool-data/HPA_normal_tissue_23-10-2018.tsv
-pathology	HPA Tumor Tissue (23/10/18)	tool-data/HPA_pathology_23-10-2018.tsv
--- a/tool_data_table_conf.xml.sample	Tue Dec 18 09:48:29 2018 -0500
+++ b/tool_data_table_conf.xml.sample	Wed Mar 13 09:15:52 2019 -0400
@@ -1,7 +1,10 @@
 <tables>
-    <!-- Location of Human Protein Atlas -->
-    <table name="proteinatlas" comment_char="#">
-      <columns>name, value, path</columns>
-      <file path="tool-data/proteinatlas.loc" />
+    <table name="proteore_protein_atlas_normal_tissue" comment_char="#">
+      <columns>id, name, tissue, value</columns>
+      <file path="tool-data/proteore_protein_atlas_normal_tissue.loc" />
+    </table>
+    <table name="proteore_protein_atlas_tumor_tissue" comment_char="#">
+      <columns>id, name, tissue, value</columns>
+      <file path="tool-data/proteore_protein_atlas_tumor_tissue.loc" />
     </table>
 </tables>
\ No newline at end of file