Mercurial > repos > proteore > proteore_expression_levels_by_tissue
diff get_expression_profiles.xml @ 12:56c93d1fc8fd draft
planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty
| author | proteore |
|---|---|
| date | Fri, 28 Jun 2019 05:10:08 -0400 |
| parents | 6e85f07c20ee |
| children | 2173192d4824 |
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--- a/get_expression_profiles.xml Wed Mar 13 09:30:12 2019 -0400 +++ b/get_expression_profiles.xml Fri Jun 28 05:10:08 2019 -0400 @@ -1,4 +1,4 @@ -<tool id="sel_ann_hpa" name="Get expression profiles" version="2019.03.13"> +<tool id="sel_ann_hpa" name="Get expression profiles" version="2019.06.27"> <description>by (normal or tumor) tissue/cell type [Human Protein Atlas] </description> <requirements> @@ -38,7 +38,7 @@ </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)" > + <param name="ids" type="select" label="Enter your IDs (Ensembl gene ID only; e.g. ENSG00000163631)" 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> @@ -68,8 +68,10 @@ <option value="tumor">Human Tumor Tissue</option> </param> <when value="normal"> - <param name="proteinatlas" type="select" label="Normal tissue HPA version" > - <options from_data_table="proteore_protein_atlas_normal_tissue"/> + <param name="proteinatlas" type="select" label="Normal tissue HPA version 18.1" > + <options from_data_table="proteore_protein_atlas_normal_tissue"> + <filter type="sort_by" column="0"/> + </options> </param> <param name="normal_tissue" type="select" label="Select tissue(s)" multiple="True" display="checkboxes" optional="False"> <option value="adrenal gland" >Adrenal gland</option> @@ -123,7 +125,7 @@ </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="Medium" selected="true">Medium</option> <option value="Low">Low</option> <option value="Not detected">Not detected</option> </param> @@ -135,8 +137,10 @@ </param> </when> <when value="tumor"> - <param name="proteinatlas" type="select" label="Tumor tissue HPA version" > - <options from_data_table="proteore_protein_atlas_tumor_tissue"/> + <param name="proteinatlas" type="select" label="Tumor tissue HPA version 18.1" > + <options from_data_table="proteore_protein_atlas_tumor_tissue"> + <filter type="sort_by" column="0"/> + </options> </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> @@ -194,7 +198,13 @@ **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. +A list of Ensembl gene IDs (e.g. ENSG00000163631) 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. + +A line can contains multiple ids if separated by ";". + +.. class:: warningmark + +In copy/paste mode, the number of IDs considered in input is limited to 5000. ----- @@ -232,7 +242,7 @@ **Data sources (release date)** -Both normal and tumor tissues data are based on the Human Protein Atlas version 18 and Ensembl version 88.38. +Both normal and tumor tissues data are based on the Human Protein Atlas version 18.1 and Ensembl version 88.38. More information: https://www.proteinatlas.org/about/download ----- @@ -246,7 +256,7 @@ 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: contact@proteore.org for any questions or concerns about this tool. ]]></help> <citations>