Mercurial > repos > proteore > proteore_expression_rnaseq_abbased

comparison expression_rnaseq_abbased.xml @ 5:f15cdeeba4b4 draft

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planemo upload commit 4af7ac25de19ca10b1654820e909c647a2d337b2-dirty
author proteore
date Mon, 19 Mar 2018 10:07:38 -0400
parents 2f95774977ff
children c9943f867413
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4:2f95774977ff 5:f15cdeeba4b4
10 </stdio> 10 </stdio>
11 <command><![CDATA[ 11 <command><![CDATA[
12 12
13 #if $inputtype.filetype == "copy_paste": 13 #if $inputtype.filetype == "copy_paste":
14 14
15 Rscript --vanilla $__tool_directory__/get_data_HPA_v2.R --inputtype copypaste --input '$inputtype.genelist' --header FALSE --proteinatlas $__tool_directory__/proteinatlas.csv --column c1 --select '$options.hpaparams' --output '$output' 15 Rscript $__tool_directory__/add_expression_HPA.R --inputtype="copypaste" --input='$inputtype.genelist' --atlas="$__tool_directory__/proteinatlas.csv" --select='$options.hpaparams' --output='$output'
16 16
17 #else 17 #else
18 18
19 Rscript --vanilla $__tool_directory__/get_data_HPA_v2.R --inputtype tabfile --input '$inputtype.genelist' --header '$inputtype.header' --proteinatlas $__tool_directory__/proteinatlas.csv --column '$inputtype.column' --select '$options.hpaparams' --output '$output' 19 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'
20 20
21 #end if 21 #end if
22 22
23 23
24 ]]></command> 24 ]]></command>
34 </when> 34 </when>
35 <when value="file_all"> 35 <when value="file_all">
36 <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."/> 36 <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."/>
37 <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"/> 37 <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"/>
38 <param name="header" type="select" label="Does your file have a header?" multiple="false" optional="false"> 38 <param name="header" type="select" label="Does your file have a header?" multiple="false" optional="false">
39 <option value="TRUE" selected="true">Yes</option> 39 <option value="true" selected="true">Yes</option>
40 <option value="FALSE" selected="false">No</option> 40 <option value="false" selected="false">No</option>
41 </param> 41 </param>
42 </when> 42 </when>
43 </conditional> 43 </conditional>
44 <section name="options" title="RNAseq/Ab-based expression data" expanded="True"> 44 <section name="options" title="RNAseq/Ab-based expression data" expanded="True">
45 <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"> 45 <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">
46 <option value="Gene" selected="true">Gene name</option> 46 <option value="Gene" selected="true">Gene name</option>
47 <option value="Gene.description" selected="false">Gene description</option> 47 <option value="Gene description" selected="false">Gene description</option>
48 <option value="Evidence">Evidence (at protein level, at transcript level or no evidence)</option> 48 <option value="Evidence">Evidence (at protein level, at transcript level or no evidence)</option>
49 <option value="Antibody">Antibody reference</option> 49 <option value="Antibody">Antibody reference</option>
50 <option value="RNA.tissue.category">RNA tissue category</option> 50 <option value="RNA tissue category">RNA tissue category</option>
51 <option value="Reliability.IH">IH detection level</option> 51 <option value="Reliability (IH)">IH detection level</option>
52 <option value="Reliability.IF">IF detection level</option> 52 <option value="Reliability (IF)">IF detection level</option>
53 <option value="Subcellular.location">Subcellular location</option> 53 <option value="Subcellular location">Subcellular location</option>
54 <option value="RNA.TS.TPM">RNA tissue specificity abundance in 'Transcript Per Million'</option> 54 <option value="RNA TS TPM">RNA tissue specificity abundance in 'Transcript Per Million'</option>
55 <option value="TPM.max.in.non.specific">RNA non-specific tissue abundance in 'Transcript Per Million'</option> 55 <option value="TPM max in non-specific">RNA non-specific tissue abundance in 'Transcript Per Million'</option>
56 </param> 56 </param>
57 </section> 57 </section>
58 58
59 </inputs> 59 </inputs>
60 60