--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Build_tissue-specific_expression_dataset.xml	Thu Dec 13 03:59:41 2018 -0500
@@ -0,0 +1,210 @@
+<tool id="retrieve_from_hpa" name="Build tissue-specific expression dataset" version="2018.12.12">
+<description>[Human Protein Atlas](no input required)</description>
+<requirements>
+  <requirement type="package" version="3.4.1">R</requirement>
+</requirements>
+<stdio>
+  <exit_code range="1:" />
+</stdio>
+<command interpreter="Rscript">
+  $__tool_directory__/Build_tissue-specific_expression_dataset.R
+  --data_source="$input.data_source"
+  #if $input.data_source == "immuno"
+    --hpa_ref="$__tool_directory__/normal_tissue.tsv"
+    --tissue="$input.normal_tissue"
+    --level="$input.level"
+    --reliability="$input.reliability"
+  #else if $input.data_source == "rnaseq"
+    --hpa_ref="$__tool_directory__/rna_tissue.tsv"
+    --sample="$input.sample"
+  #end if
+  --output="$output"
+</command>
+
+<inputs>
+<conditional name="input">
+  <param name="data_source" type="select" label="Please choose experimental data source (antibody- or RNAseq-based)">
+    <option value="immuno">Expression profiles based on immunohistochemistry</option>
+    <option value="rnaseq">RNA levels based on RNA-seq</option>
+  </param>
+  <when value="immuno">
+    <param name="normal_tissue" type="select" label="Select tissue by clicking the dropdown menu below" multiple="True" optional="False">
+      <option value="adrenal gland" >Adrenal gland</option>
+      <option value="appendix" >Appendix</option>
+      <option value="bone marrow" >Bone marrow</option>
+      <option value="breast" >Breast</option>
+      <option value="bronchus" >Bronchus</option>
+      <option value="caudate" >Caudate</option>
+      <option value="cerebellum" >Cerebellum</option>
+      <option value="cerebral cortex" >Cerebral cortex</option>
+      <option value="cervix" >Cervix</option>
+      <option value="colon" >Colon</option>
+      <option value="duodenum" >Duodenum</option>
+      <option value="endometrium 1" >Endometrium 1</option>
+      <option value="endometrium 2" >Endometrium 2</option>
+      <option value="epididymis" >Epididymis</option>
+      <option value="esophagus" >Esophagus</option>
+      <option value="fallopian tube" >Fallopian tube</option>
+      <option value="gallbladder" >Gallbladder</option>
+      <option value="heart muscle" >Heart muscle</option>
+      <option value="hippocampus" >Hippocampus</option>
+      <option value="kidney" >Kidney</option>
+      <option value="liver" >Liver</option>
+      <option value="lung" >Lung</option>
+      <option value="lymph node" >Lymph node</option>
+      <option value="nasopharynx" >Nasopharynx</option>
+      <option value="oral mucosa" >Oral mucosa</option>
+      <option value="ovary" >Ovary</option>
+      <option value="pancreas" >Pancreas</option>
+      <option value="parathyroid gland" >Parathyroid gland</option>
+      <option value="placenta" >Placenta</option>
+      <option value="prostate" >Prostate</option>
+      <option value="rectum" >Rectum</option>
+      <option value="salivary gland" >Salivary gland</option>
+      <option value="seminal vesicle" >Seminal vesicle</option>
+      <option value="skeletal muscle" >Skeletal muscle</option>
+      <option value="skin 1" >Skin 1</option>
+      <option value="skin 2" >Skin 2</option>
+      <option value="small intestine" >Small intestine</option>
+      <option value="smooth muscle" >Smooth muscle</option>
+      <option value="soft tissue 1" >Soft tissue 1</option>
+      <option value="soft tissue 2" >Soft tissue 2</option>
+      <option value="spleen" >Spleen</option>
+      <option value="stomach 1" >Stomach 1</option>
+      <option value="stomach 2" >Stomach 2</option>
+      <option value="testis" >Testis</option>
+      <option value="thyroid gland" >Thyroid gland</option>
+      <option value="tonsil" >Tonsil</option>
+      <option value="urinary bladder" >Urinary bladder</option>
+      <option value="vagina" >Vagina</option>
+    </param>
+    <param name="level" type="select" label="Expression level" display="checkboxes" multiple="True" optional="False">
+      <option value="High" selected="true">High</option>
+      <option value="Medium">Medium</option>
+      <option value="Low">Low</option>
+      <option value="Not detected">Not detected</option>
+    </param>
+    <param name="reliability" type="select" label="Reliability score" display="checkboxes" multiple="True" optional="False">
+      <option value="Enhanced" selected="true">Enhanced</option>
+      <option value="Supported" selected="true">Supported</option>
+      <option value="Approved">Approved</option>
+      <option value="Uncertain">Uncertain</option>
+
+    </param>
+  </when>
+  <when value="rnaseq">
+    <param name="sample" type="select" label="Keep and annotate genes present in the following tissue(s)" multiple="True" optional="False">
+      <option value="adipose tissue">Adipose tissue</option>
+      <option value="adrenal gland">Adrenal gland</option>
+      <option value="appendix">Appendix</option>
+      <option value="bone marrow">Bone marrow</option>
+      <option value="breast">Breast</option>
+      <option value="cerebral cortex">Cerebral cortex</option>
+      <option value="cervix, uterine">Cervix, uterine</option>
+      <option value="colon">Colon</option>
+      <option value="duodenum">Duodenum</option>
+      <option value="endometrium">Endometrium</option>
+      <option value="epididymis">Epididymis</option>
+      <option value="esophagus">Esophagus</option>
+      <option value="fallopian tube">Fallopian tube</option>
+      <option value="gallbladder">Gallbladder</option>
+      <option value="heart muscle">Heart muscle</option>
+      <option value="kidney">Kidney</option>
+      <option value="liver">Liver</option>
+      <option value="lung">Lung</option>
+      <option value="lymph node">Lymph node</option>
+      <option value="ovary">Ovary</option>
+      <option value="pancreas">Pancreas</option>
+      <option value="parathyroid gland">Parathyroid gland</option>
+      <option value="placenta">Placenta</option>
+      <option value="prostate">Prostate</option>
+      <option value="rectum">Rectum</option>
+      <option value="salivary gland">Salivary gland</option>
+      <option value="seminal vesicle">Seminal vesicle</option>
+      <option value="skeletal muscle">Skeletal muscle</option>
+      <option value="skin">Skin</option>
+      <option value="small intestine">Small intestine</option>
+      <option value="smooth muscle">Smooth muscle</option>
+      <option value="spleen">Spleen</option>
+      <option value="stomach">Stomach</option>
+      <option value="testis">Testis</option>
+      <option value="thyroid gland">Thyroid gland</option>
+      <option value="tonsil">Tonsil</option>
+      <option value="rinary bladder">Urinary bladder</option>
+    </param>
+  </when>
+</conditional>
+</inputs>
+
+<outputs>
+  <data name="output" format="tsv" label=""/>
+</outputs>
+
+<tests>
+  <test>
+    <conditional name="input">
+      <param name="data_source" value="immuno"/>
+      <param name="normal_tissue" value="lung,ovary"/>
+      <param name="level" value="High"/>
+      <param name="reliability" value="Approved,Supported"/>
+    </conditional>
+    <output name="output" file="test.txt"/>
+  </test>
+</tests>
+
+<help><![CDATA[
+
+This tool allows to retrieve information from Human Protein Atlas (https://www.proteinatlas.org/) 
+regarding the expression profiles of human genes both at the mRNA and protein levels 
+without any input required. It could be used to:
+
+* Select a list of proteins highly expressed in a given tissue for data mining or comparison purpose in terms of expected protein content from one tissue to another
+
+* Build a "reference" proteome restricted to a given tissue (for instance for GO analysis as a reference background restricted to a biological sample)
+
+The resources from Human Protein Atlas that can be queried are the following:
+
+1. Human normal tissue data: expression profiles for proteins in human tissues based on immunohistochemisty using tissue micro arrays measured in 58 tissues and 82 cell types.
+
+   The tab-separated file includes Ensembl gene identifier ("Gene"), tissue name ("Tissue"), annotated cell type ("Cell type"), expression value ("Level"), and the gene reliability of the expression value ("Reliability score").
+
+   The reliability score is divided into Enhanced, Supported, Approved, or Uncertain with the following definitions:
+
+   * Enhanced: One or several antibodies with non-overlapping epitopes targeting the same gene have obtained enhanced validation based on orthogonal or independent antibody validation method.
+
+   * Supported: Consistency with RNA-seq and/or protein/gene characterization data, in combination with similar staining pattern if independent antibodies are available.
+
+   * Approved: Consistency with RNA-seq data in combination with inconsistency with, or lack of, protein/gene characterization data. Alternatively, consistency with protein/gene characterization data in combination with inconsistency with RNA-seq data. If independent antibodies are available, the staining pattern is partly similar or dissimilar.
+
+   * Uncertain:
+
+     Inconsistency with, or lack of, RNA-seq and/or protein/gene characterization data, in combination with dissimilar staining pattern if independent antibodies are available.
+
+   The data is based on The Human Protein Atlas version 18 and Ensembl version 88.38.
+
+2. RNA levels based on RNA-seq data: RNA levels measured in 64 cell lines and 37 tissues based on RNA-seq experiments. The tab-separated file includes Ensembl gene identifier ("Gene"), analysed sample ("Sample") and transcripts per million ("Value" and "Unit").
+   
+   The data is based on The Human Protein Atlas version 18 and Ensembl version 88.38.
+
+   For more information: https://www.proteinatlas.org/about/help
+
+-----
+
+.. class:: infomark
+
+**Authors**
+
+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
+
+This work has been partially funded through the French National Agency for Research (ANR) IFB project.
+
+Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
+
+]]></help>
+
+<citations>
+</citations>
+
+</tool>