Mercurial > repos > proteore > proteore_expression_levels_by_tissue
diff get_expression_profiles.xml @ 8:2c0bab71a436 draft
planemo upload commit 5e13878e9679f3f5ba8e482b9108249a43f3355e-dirty
| author | proteore |
|---|---|
| date | Tue, 18 Dec 2018 09:48:29 -0500 |
| parents | |
| children | 0a0f6c37f05e |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_expression_profiles.xml Tue Dec 18 09:48:29 2018 -0500 @@ -0,0 +1,258 @@ +<tool id="sel_ann_hpa" name="Get expression profiles" version="2018.12.17"> + <description>by (normal or tumor) tissue/cell type [Human Protein Atlas] + </description> + <requirements> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command interpreter="Rscript"> + $__tool_directory__/get_expression_profiles.R + --ref_file="$__tool_directory__/$options.proteinatlas" + --input_type="$input.ids" + #if $input.ids == "list" + --input="$input.list" + #else + --input="$input.file" + --column_number="$input.ncol" + --header="$input.header" + #end if + + #if $options.database == "normal" + --atlas="normal" + --tissue="$options.normal_tissue" + --level="$options.level" + --reliability="$options.reliability" + #else if $options.database == "tumor" + --atlas="cancer" + --cancer="$options.cancer_tissue" + #end if + --not_mapped="$not_mapped" + --output="$hpa_output" + </command> + <inputs> + <conditional name="input" > + <param name="ids" type="select" label="Enter your IDs (ENSG IDs only)" help="Copy/paste or from a file (e.g. table)" > + <option value="list">Copy/paste your IDs</option> + <option value="file" selected="true">Input file containing your IDs</option> + </param> + <when value="list" > + <param name="list" type="text" label="Copy/paste your IDs" help='IDs must be separated by spaces into the form field, for example: ENSG00000174876 ENSG00000178372 ENSG00000159763' > + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping initial="none"> + <add source="'" target="__sq__"/> + </mapping> + </sanitizer> + </param> + </when> + <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' /> + </when> + </conditional> + <conditional name="options"> + <param name="database" type="select" label="Human Protein Atlas (normal or tumor tissue)"> + <option value="normal">Human Normal Tissue</option> + <option value="tumor">Human Tumor Tissue</option> + </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> + </param> + <param name="normal_tissue" type="select" label="Select tissue(s)" multiple="True" display="checkboxes" 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="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> + </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> + <option value="carcinoid" >Carcinoid</option> + <option value="cervical cancer" >Cervical cancer</option> + <option value="colorectal cancer" >Colorectal cancer</option> + <option value="endometrial cancer" >Endometrial cancer</option> + <option value="glioma" >Glioma</option> + <option value="head and neck cancer" >Head and neck cancer</option> + <option value="liver cancer" >Liver cancer</option> + <option value="lung cancer" >Lung cancer</option> + <option value="lymphoma" >Lymphoma</option> + <option value="melanoma" >Melanoma</option> + <option value="ovarian cancer" >Ovarian cancer</option> + <option value="pancreatic cancer" >Pancreatic cancer</option> + <option value="prostate cancer" >Prostate cancer</option> + <option value="renal cancer" >Renal cancer</option> + <option value="skin cancer" >Skin cancer</option> + <option value="stomach cancer" >Stomach cancer</option> + <option value="testis cancer" >Testis cancer</option> + <option value="thyroid cancer" >Thyroid cancer</option> + <option value="urothelial cancer" >Urothelial cancer</option> + </param> + </when> + </conditional> + <param name="not_mapped" type="boolean" truevalue="true" falsevalue="false" label="Keep IDs not found in HPA?" checked="true"/> + </inputs> + <outputs> + <data name="hpa_output" format="tsv" label="" /> + </outputs> + <tests> + <test> + <conditional name="input"> + <param name="ids" value="file"/> + <param name="file" value="ID_Converter_FKW_Lacombe_et_al_2017_OK.txt"/> + <param name="header" value="true"/> + <param name="ncol" value="c8"/> + </conditional> + <conditional name="options"> + <param name="database" value="normal"/> + <param name="proteinatlas" value="normal_tissue.tsv"/> + <param name="normal_tissue" value="bronchus,lung,nasopharynx,salivary gland"/> + <param name="level" value="Not detected,Medium,High,Low"/> + <param name="reliability" value="Approved,Supported,Uncertain"/> + </conditional> + <param name="not_mapped" value="true" /> + <output name="hpa_output" file="Expres_levels_Lacombe_et_al_2017_OK.txt"/> + </test> + </tests> + <help><![CDATA[ + +**Description** + +This tool allows to retrieve expression profiles (normal or tumor tissue) from Human Protein Atlas (https://www.proteinatlas.org/) + +**Input** + +A list of ENSG (Ensembl gene) IDs must be entered (either via a copy/paste or by choosing a file); if it's not the case, please use the ID_Converter tool of ProteoRE. + +----- + +**Parameters** + +"Human Protein Atlas (normal or tumor tissue)": two resources are currently available + +* **Human normal tissue data**: expression profiles for proteins in human tissues based on immunohistochemisty using tissue micro arrays. + +**Output** will be in the form: a 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"). + +* **Human tumor tissue data**: staining profiles for proteins in human tumor tissue based on immunohistochemisty using tissue micro arrays and log-rank P value for Kaplan-Meier analysis of correlation between mRNA expression level and patient survival. + +**Ouptut** will be in the form: The tab-separated file includes Ensembl gene identifier ("Gene"), gene name ("Gene name"), tumor name ("Cancer"), the number of patients annotated for different staining levels ("High", "Medium", "Low" & "Not detected") and log-rank p values for patient survival and mRNA correlation ("prognostic - favourable", "unprognostic - favourable", "prognostic - unfavourable", "unprognostic - unfavourable"). + +"Select tissue(s)": information from more than one tissue can be retrieved + +"Keep IDs not found in HPA?": ENSG ID not found in Human Protein Atlas will be returned in the output file in the form of "NA" (default is "No") + +----- + +**Reliability score (only for normal tissue)** + +Reliability score is divided into Enhanced, Supported, Approved, or Uncertain with respect to the definitions from HPA: + +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. + +----- + +**Data sources (release date)** + +Both normal and tumor tissues data are based on the Human Protein Atlas version 18 and Ensembl version 88.38. + +----- + +.. 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, FR + +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>