comparison add_expression_data.xml @ 11:e109cacd75b2 draft

planemo upload commit f91a292f92a3e75996e6f4502fa090961727c235-dirty

10:7b9a4ec7ec54

<tool id="rna_abbased_data" name="Add expression data" version="2018.12.18">
<description> (RNAseq or Immuno-assays)[Human Protein Atlas]
</description>
<requirements>
  <requirement type="package" version="3.4.1">R</requirement>
</requirements>

          <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>

  <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>

11:e109cacd75b2

<tool id="rna_abbased_data" name="Add expression data" version="2019.01.02">
<description> (RNAseq or Immuno-assays)[Human Protein Atlas]
</description>
<requirements>
  <requirement type="package" version="3.4.1">R</requirement>
</requirements>

          <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>

  <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>