comparison add_expression_data.xml @ 14:133309fd6875 draft

"planemo upload commit c4edbc8a0ffd86395f088cb5b6592f77db658ac7"

13:0b279190f90d

<tool id="rna_abbased_data" name="Add expression data" version="2019.06.27">
<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 IDs (Ensembl gene IDs only, e.g. ENSG00000064787)" help="Copy/paste or from a file (e.g. table)"> 
      <option value="file_all" selected="true">Input file containing your IDs</option>
      <option value="copy_paste">Copy/paste your list of IDs</option> 
    </param>

      <param name="hpaparams" type="select" label="Select information to add to your list" multiple="True" display="checkboxes" optional="false" > 
          <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>

- 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.

-----

**Output**

The output is a tabular file containing initial columns and new columns with annotation from HPA.  

-----

**Data sources (release date)**

HPA source file (data are based on the Human Protein Atlas version 18.1 and Ensembl version 88.38):  http://www.proteinatlas.org/download/proteinatlas.tab.gz

-----

.. class:: infomark

14:133309fd6875

<tool id="rna_abbased_data" name="Add expression data" version="2020.01.24">
<description> (RNAseq or Immuno-assays)[Human Protein Atlas]
</description>
<requirements>
  <requirement type="package" version="3.4.4">R</requirement>
</requirements>
<stdio>
  <exit_code range="1:" />
</stdio>
<command><![CDATA[

    Rscript $__tool_directory__/add_expression_HPA.R
    --input='$inputtype.genelist'
    --select='$options.hpaparams'
    --output='$output' 
    
    #if $inputtype.filetype == "copy_paste": 
        --inputtype="copypaste"    
    #else 
        --inputtype="tabfile" 
        --header='$inputtype.header' 
        --column='$inputtype.column'  
    #end if

    #if "protein_atlas" in str($ref_file).split("/")
    --atlas="$ref_file"
    #else 
    --atlasf="$__tool_directory__/$ref_file"
    #end if

]]></command>

<inputs>
    <param name="ref_file" type="select" label="HPA source file version" >
        <options from_data_table="proteore_protein_full_atlas">
            <filter type="sort_by" column="0"/>
        </options>
    </param>
  <conditional name="inputtype">
    <param name="filetype" type="select" label="Enter your IDs (Ensembl gene IDs only, e.g. ENSG00000064787)" help="Copy/paste or from a file (e.g. table)"> 
      <option value="file_all" selected="true">Input file containing your IDs</option>
      <option value="copy_paste">Copy/paste your list of IDs</option> 
    </param>

      <param name="hpaparams" type="select" label="Select information to add to your list" multiple="True" display="checkboxes" optional="false" > 
          <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 specificity">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 tissue specific NX">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' (only for 23/10/2018 release)</option>
    </param>
  </section>

</inputs>

- 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' (only available from 23/10/2018 release): please refer to http://www.proteinatlas.org/about/assays+annotation#rna.

-----

**Output**

The output is a tabular file containing initial columns and new columns with annotation from HPA.  

-----

**HPA source file version (release date)**

Release date 23/10/2018: data are based on the Human Protein Atlas version 18.1 and Ensembl version 88.38

Release date 21/01/2020: a subset of the data in the Human Protein Atlas version 19.1

downloaded from:  http://www.proteinatlas.org/download/proteinatlas.tab.gz

-----

.. class:: infomark