Mercurial > repos > proteore > proteore_expression_rnaseq_abbased

comparison add_expression_data.xml @ 7:fda784211e3a draft

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"planemo upload commit 330a2527c7e20c4d189a0f1b7a184a8c4610b4b6-dirty"
author proteore
date Wed, 22 Jan 2020 14:59:04 +0000
parents ea59f5750c51
children c9e48832420b
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6:ea59f5750c51 7:fda784211e3a
1 <tool id="rna_abbased_data" name="Add expression data" version="2019.06.27"> 1 <tool id="rna_abbased_data" name="Add expression data" version="2020.01.22">
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>
7 <stdio> 7 <stdio>
8 <exit_code range="1:" /> 8 <exit_code range="1:" />
9 </stdio> 9 </stdio>
10 <command><![CDATA[ 10 <command><![CDATA[
11 11
12 #if $inputtype.filetype == "copy_paste": 12 Rscript $__tool_directory__/add_expression_HPA.R
13 13 --input='$inputtype.genelist'
14 Rscript $__tool_directory__/add_expression_HPA.R --inputtype="copypaste" --input='$inputtype.genelist' --atlas="$__tool_directory__/proteinatlas.csv" --select='$options.hpaparams' --output='$output' 14 --select='$options.hpaparams'
15 --output='$output'
16
17 #if $inputtype.filetype == "copy_paste":
18 --inputtype="copypaste"
19 #else
20 --inputtype="tabfile"
21 --header='$inputtype.header'
22 --column='$inputtype.column'
23 #end if
15 24
16 #else 25 #if "protein_atlas" in str($input.ref_file).split("/")
17 26 --hpa_ref="$input.ref_file"
18 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='$output' 27 #else
19 28 --hpa_ref="$__tool_directory__/$input.ref_file"
20 #end if 29 #end if
21
22 30
23 ]]></command> 31 ]]></command>
24 32
25 <inputs> 33 <inputs>
26 <conditional name="inputtype"> 34 <conditional name="inputtype">