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<tool id="retrieve_from_hpa" name="Retrieve tissue-specific expression data" version="0.1.0">
<description>
from HPA (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">
  $__tool_directory__/RetrieveFromHPA.R
  --data_source="$input.data_source"
  #if $input.data_source == "immuno"
    --hpa_ref="$__tool_directory__/HPA.normal.RData"
    --tissue="$input.normal_tissue"
    --level="$input.level"
    --reliability="$input.reliability"
  #else if $input.data_source == "rnaseq"
    --hpa_ref="$__tool_directory__/HPA.rnaTissue.RData"
    --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 immunohistochemisty</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="tabular" 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="retrieve_tissue_specific.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 [e-mail] for any questions or concerns about the Galaxy implementation of this tool.

]]></help>

<citations>
</citations>

</tool>