Mercurial > repos > proteore > proteore_expression_rnaseq_abbased

comparison add_expression_data.xml @ 8:c9e48832420b draft

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"planemo upload commit 330a2527c7e20c4d189a0f1b7a184a8c4610b4b6-dirty"
author proteore
date Wed, 22 Jan 2020 15:11:58 +0000
parents fda784211e3a
children 28d51adf8292
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7:fda784211e3a 8:c9e48832420b
1 <tool id="rna_abbased_data" name="Add expression data" version="2020.01.22"> 1 <tool id="rna_abbased_data" name="Add expression data" version="2020.01.22.1">
2 <description> (RNAseq or Immuno-assays)[Human Protein Atlas] 2 <description> (RNAseq or Immuno-assays)[Human Protein Atlas]
3 </description> 3 </description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="3.4.1">R</requirement> 5 <requirement type="package" version="3.4.1">R</requirement>
6 </requirements> 6 </requirements>
20 --inputtype="tabfile" 20 --inputtype="tabfile"
21 --header='$inputtype.header' 21 --header='$inputtype.header'
22 --column='$inputtype.column' 22 --column='$inputtype.column'
23 #end if 23 #end if
24 24
25 #if "protein_atlas" in str($input.ref_file).split("/") 25 #if "protein_atlas" in str($ref_file).split("/")
26 --hpa_ref="$input.ref_file" 26 --hpa_ref="$ref_file"
27 #else 27 #else
28 --hpa_ref="$__tool_directory__/$input.ref_file" 28 --hpa_ref="$__tool_directory__/$ref_file"
29 #end if 29 #end if
30 30
31 ]]></command> 31 ]]></command>
32 32
33 <inputs> 33 <inputs>
34 <param name="ref_file" type="select" label="HPA source file version" >
35 <options from_data_table="proteore_protein_full_atlas">
36 <filter type="sort_by" column="0"/>
37 </options>
38 </param>
34 <conditional name="inputtype"> 39 <conditional name="inputtype">
35 <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)"> 40 <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)">
36 <option value="file_all" selected="true">Input file containing your IDs</option> 41 <option value="file_all" selected="true">Input file containing your IDs</option>
37 <option value="copy_paste">Copy/paste your list of IDs</option> 42 <option value="copy_paste">Copy/paste your list of IDs</option>
38 </param> 43 </param>