Mercurial > repos > proteore > proteore_expression_rnaseq_abbased
changeset 4:3f9057cdfdde draft
planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
| author | proteore |
|---|---|
| date | Thu, 13 Dec 2018 03:56:46 -0500 |
| parents | d7d2a4512059 |
| children | e919b55188ab |
| files | add_expression_data.xml expression_rnaseq_abbased.xml |
| diffstat | 2 files changed, 146 insertions(+), 146 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/add_expression_data.xml Thu Dec 13 03:56:46 2018 -0500 @@ -0,0 +1,146 @@ +<tool id="rna_abbased_data" name="Add expression data" version="2018.12.12"> +<description> (RNAseq or Immuno-assays)[Human Protein Atlas] +</description> +<requirements> + <requirement type="package" version="3.4.1">R</requirement> +</requirements> +<stdio> + <exit_code range="1:" /> +</stdio> +<command><![CDATA[ + + #if $inputtype.filetype == "copy_paste": + + Rscript $__tool_directory__/add_expression_HPA.R --inputtype="copypaste" --input='$inputtype.genelist' --atlas="$__tool_directory__/proteinatlas.csv" --select='$options.hpaparams' --output='$output' + + #else + + Rscript $__tool_directory__/add_expression_HPA.R --inputtype="tabfile" --input='$inputtype.genelist' --header='$inputtype.header' --atlas="$__tool_directory__/proteinatlas.csv" --column='$inputtype.column' --select='$options.hpaparams' --output='$output' + + #end if + + +]]></command> + +<inputs> + <conditional name="inputtype"> + <param name="filetype" type="select" label="Enter your list of Ensembl gene ID"> + <option value="file_all" selected="true">Input file containing your IDs</option> + <option value="copy_paste">Copy/paste your list of IDs</option> + </param> + <when value="copy_paste"> + <param name="genelist" type="text" label="Enter a list of identifiers"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping initial="none"> + <add source="'" target="__sq__"/> + </mapping> + </sanitizer> + </param> + </when> + <when value="file_all"> + <param name="genelist" type="data" format="txt,tabular" label="Choose your file" help="This file must imperatively have 1 column filled with Ensembl Gene IDs (ENSG). Please use the ID_Converter tool if this is not the case."/> + <param name="column" type="text" label="Please specify the column where are your Ensembl gene IDs (e.g : Enter c1 if ENSG ID are in column n°1)" value="c1"/> + <param name="header" type="select" label="Does your file have a header?" multiple="false" optional="false"> + <option value="true" selected="true">Yes</option> + <option value="false" selected="false">No</option> + </param> + </when> + </conditional> + <section name="options" title="RNAseq/Ab-based expression data" expanded="True"> + <param name="hpaparams" type="select" label="Choose the information from RNAseq/ab-based data you want to add to your list (see below for details)" multiple="True" display="checkboxes"> + <option value="Gene" selected="true">Gene name</option> + <option value="Gene description" selected="false">Gene description</option> + <option value="Evidence">Evidence (at protein level, at transcript level or no evidence)</option> + <option value="Antibody">Antibody reference</option> + <option value="RNA tissue category">RNA tissue category</option> + <option value="Reliability (IH)">IH detection level</option> + <option value="Reliability (IF)">IF detection level</option> + <option value="Subcellular location">Subcellular location</option> + <option value="RNA TS TPM">RNA tissue specificity abundance in 'Transcript Per Million'</option> + <option value="TPM max in non-specific">RNA non-specific tissue abundance in 'Transcript Per Million'</option> + </param> + </section> + +</inputs> + + +<outputs> + <data name="output" format="tsv" label=""/> +</outputs> + +<tests> + <test> + <conditional name="inputtype"> + <param name="filetype " value="file_all"/> + <param name="genelist" value="ID_Converter_Lacombe_et_al_2017_OK.txt"/> + <param name="column" value="c8"/> + <param name="header" value="TRUE"/> + </conditional> + <section name="options"> + <param name="hpaparams" value="Gene,Gene.description,Evidence,Antibody,RNA.tissue.category,Reliability.IH,Reliability.IF,Subcellular.location,RNA.TS.TPM,TPM.max.in.non.specific"/> + </section> + <output name="output" file="Get_annotation_RNAseq.txt"/> + </test> +</tests> + +<help><![CDATA[ + +This tool adds expression information (RNAseq- or antibody-based experiments) from the Human Protein Atlas (HPA) database (https://www.proteinatlas.org/) to your protein list. + +**Input** + +Input can be either a list of Ensembl gene ids (copy/paste) or a file containing multiple fields but with **at least one column of Ensembl gene IDs**. If your input file contains other type of IDs, please use the ID_Converter tool to create a column of Ensembl gene IDs. + +**Databases** + +HPA source file (Human Protein Atlas version 18): http://www.proteinatlas.org/download/proteinatlas.tab.gz + +**Annotation** + +- Gene name: according to the HGNC (Hugo Gene Nomenclature Committee) + +- Gene description: entry description (full text) + +- Evidence: at protein level, at transcript level or no evidence + +- Antibody reference: reference of the HPA antibody used for immunohistochemistry and immunocytochemistry/IF + +- RNA tissue category: categories based on RNA-Seq data to estimate the transcript abundance of each protein-coding gene in tissues. For more information, please refer to http://www.proteinatlas.org/about/assays+annotation#rna . + +- IH detection level: level of detection of the protein associated to the coding gene tissues based on immunofluorescency. For more information, please refer to http://www.proteinatlas.org/about/assays+annotation#if . + +- IF detection level:level of detection of the protein associated to the coding gene tissues based on immunohistochemistry. For more information, please refer to http://www.proteinatlas.org/about/assays+annotation#ih . + +- Subcellular location:according to HPA data. For more information, please refer to https://www.proteinatlas.org/about/assays+annotation#ifa + +- RNA tissue specificity abundance in 'Transcript Per Million': For each gene is reported the tissue specificity abundance in 'Transcript Per Million' (TPM) as the sum of the TPM values of all its protein-coding transcripts. + +- RNA non-specific tissue abundance in 'Transcript Per Million': please refer to http://www.proteinatlas.org/about/assays+annotation#rna. + +**Outputs** + +The output is a tabular file. The initial columns are kept and new columns are added according to what type of annotation data you chose. + +----- + +.. class:: infomark + +**Authors** + +Lisa Peru, 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>
--- a/expression_rnaseq_abbased.xml Thu Dec 06 05:26:20 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,146 +0,0 @@ -<tool id="rna_abbased_data" name="Add human expression data" version="2018.12.04"> -<description> (RNAseq and Immuno-assays data from Human Protein Atlas) -</description> -<requirements> - <requirement type="package" version="3.4.1">R</requirement> -</requirements> -<stdio> - <exit_code range="1:" /> -</stdio> -<command><![CDATA[ - - #if $inputtype.filetype == "copy_paste": - - Rscript $__tool_directory__/add_expression_HPA.R --inputtype="copypaste" --input='$inputtype.genelist' --atlas="$__tool_directory__/proteinatlas.csv" --select='$options.hpaparams' --output='$output' - - #else - - Rscript $__tool_directory__/add_expression_HPA.R --inputtype="tabfile" --input='$inputtype.genelist' --header='$inputtype.header' --atlas="$__tool_directory__/proteinatlas.csv" --column='$inputtype.column' --select='$options.hpaparams' --output='$output' - - #end if - - -]]></command> - -<inputs> - <conditional name="inputtype"> - <param name="filetype" type="select" label="Enter your list of Ensembl gene ID"> - <option value="file_all" selected="true">Input file containing your IDs</option> - <option value="copy_paste">Copy/paste your list of IDs</option> - </param> - <when value="copy_paste"> - <param name="genelist" type="text" label="Enter a list of identifiers"> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - </valid> - <mapping initial="none"> - <add source="'" target="__sq__"/> - </mapping> - </sanitizer> - </param> - </when> - <when value="file_all"> - <param name="genelist" type="data" format="txt,tabular" label="Choose your file" help="This file must imperatively have 1 column filled with Ensembl Gene IDs (ENSG). Please use the ID_Converter tool if this is not the case."/> - <param name="column" type="text" label="Please specify the column where are your Ensembl gene IDs (e.g : Enter c1 if ENSG ID are in column n°1)" value="c1"/> - <param name="header" type="select" label="Does your file have a header?" multiple="false" optional="false"> - <option value="true" selected="true">Yes</option> - <option value="false" selected="false">No</option> - </param> - </when> - </conditional> - <section name="options" title="RNAseq/Ab-based expression data" expanded="True"> - <param name="hpaparams" type="select" label="Choose the information from RNAseq/ab-based data you want to add to your list (see below for details)" multiple="True" display="checkboxes"> - <option value="Gene" selected="true">Gene name</option> - <option value="Gene description" selected="false">Gene description</option> - <option value="Evidence">Evidence (at protein level, at transcript level or no evidence)</option> - <option value="Antibody">Antibody reference</option> - <option value="RNA tissue category">RNA tissue category</option> - <option value="Reliability (IH)">IH detection level</option> - <option value="Reliability (IF)">IF detection level</option> - <option value="Subcellular location">Subcellular location</option> - <option value="RNA TS TPM">RNA tissue specificity abundance in 'Transcript Per Million'</option> - <option value="TPM max in non-specific">RNA non-specific tissue abundance in 'Transcript Per Million'</option> - </param> - </section> - -</inputs> - - -<outputs> - <data name="output" format="tsv" label=""/> -</outputs> - -<tests> - <test> - <conditional name="inputtype"> - <param name="filetype " value="file_all"/> - <param name="genelist" value="ID_Converter_Lacombe_et_al_2017_OK.txt"/> - <param name="column" value="c8"/> - <param name="header" value="TRUE"/> - </conditional> - <section name="options"> - <param name="hpaparams" value="Gene,Gene.description,Evidence,Antibody,RNA.tissue.category,Reliability.IH,Reliability.IF,Subcellular.location,RNA.TS.TPM,TPM.max.in.non.specific"/> - </section> - <output name="output" file="Get_annotation_RNAseq.txt"/> - </test> -</tests> - -<help><![CDATA[ - -This tool adds expression information (RNAseq- or antibody-based experiments) from the Human Protein Atlas (HPA) database (https://www.proteinatlas.org/) to your protein list. - -**Input** - -Input can be either a list of Ensembl gene ids (copy/paste) or a file containing multiple fields but with **at least one column of Ensembl gene IDs**. If your input file contains other type of IDs, please use the ID_Converter tool to create a column of Ensembl gene IDs. - -**Databases** - -HPA source file (Human Protein Atlas version 18): http://www.proteinatlas.org/download/proteinatlas.tab.gz - -**Annotation** - -- Gene name: according to the HGNC (Hugo Gene Nomenclature Committee) - -- Gene description: entry description (full text) - -- Evidence: at protein level, at transcript level or no evidence - -- Antibody reference: reference of the HPA antibody used for immunohistochemistry and immunocytochemistry/IF - -- RNA tissue category: categories based on RNA-Seq data to estimate the transcript abundance of each protein-coding gene in tissues. For more information, please refer to http://www.proteinatlas.org/about/assays+annotation#rna . - -- IH detection level: level of detection of the protein associated to the coding gene tissues based on immunofluorescency. For more information, please refer to http://www.proteinatlas.org/about/assays+annotation#if . - -- IF detection level:level of detection of the protein associated to the coding gene tissues based on immunohistochemistry. For more information, please refer to http://www.proteinatlas.org/about/assays+annotation#ih . - -- Subcellular location:according to HPA data. For more information, please refer to https://www.proteinatlas.org/about/assays+annotation#ifa - -- RNA tissue specificity abundance in 'Transcript Per Million': For each gene is reported the tissue specificity abundance in 'Transcript Per Million' (TPM) as the sum of the TPM values of all its protein-coding transcripts. - -- RNA non-specific tissue abundance in 'Transcript Per Million': please refer to http://www.proteinatlas.org/about/assays+annotation#rna. - -**Outputs** - -The output is a tabular file. The initial columns are kept and new columns are added according to what type of annotation data you chose. - ------ - -.. class:: infomark - -**Authors** - -Lisa Peru, 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>