Mercurial > repos > proteore > proteore_expression_rnaseq_abbased

annotate add_expression_data.xml @ 12:f8d3a8a2f2e5 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 58e072579a4be282c00b54ebb88fbc59e189a7ed-dirty"
author proteore
date Thu, 23 Jan 2020 10:44:39 +0000
parents 4c27466a4e15
children 8ee4cfdc1a92
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
12
f8d3a8a2f2e5 "planemo upload commit 58e072579a4be282c00b54ebb88fbc59e189a7ed-dirty"
proteore
parents: 11
diff changeset
1 <tool id="rna_abbased_data" name="Add expression data" version="2020.01.23">
4
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
2 <description> (RNAseq or Immuno-assays)[Human Protein Atlas]
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
3 </description>
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
4 <requirements>
11
4c27466a4e15 "planemo upload commit 330a2527c7e20c4d189a0f1b7a184a8c4610b4b6-dirty"
proteore
parents: 10
diff changeset
5 <requirement type="package" version="3.4.4">R</requirement>
4
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
6 </requirements>
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
7 <stdio>
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
8 <exit_code range="1:" />
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
9 </stdio>
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
10 <command><![CDATA[
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
11
7
fda784211e3a "planemo upload commit 330a2527c7e20c4d189a0f1b7a184a8c4610b4b6-dirty"
proteore
parents: 6
diff changeset
12 Rscript $__tool_directory__/add_expression_HPA.R
fda784211e3a "planemo upload commit 330a2527c7e20c4d189a0f1b7a184a8c4610b4b6-dirty"
proteore
parents: 6
diff changeset
13 --input='$inputtype.genelist'
fda784211e3a "planemo upload commit 330a2527c7e20c4d189a0f1b7a184a8c4610b4b6-dirty"
proteore
parents: 6
diff changeset
14 --select='$options.hpaparams'
fda784211e3a "planemo upload commit 330a2527c7e20c4d189a0f1b7a184a8c4610b4b6-dirty"
proteore
parents: 6
diff changeset
15 --output='$output'
fda784211e3a "planemo upload commit 330a2527c7e20c4d189a0f1b7a184a8c4610b4b6-dirty"
proteore
parents: 6
diff changeset
16
fda784211e3a "planemo upload commit 330a2527c7e20c4d189a0f1b7a184a8c4610b4b6-dirty"
proteore
parents: 6
diff changeset
17 #if $inputtype.filetype == "copy_paste":
fda784211e3a "planemo upload commit 330a2527c7e20c4d189a0f1b7a184a8c4610b4b6-dirty"
proteore
parents: 6
diff changeset
18 --inputtype="copypaste"
fda784211e3a "planemo upload commit 330a2527c7e20c4d189a0f1b7a184a8c4610b4b6-dirty"
proteore
parents: 6
diff changeset
19 #else
fda784211e3a "planemo upload commit 330a2527c7e20c4d189a0f1b7a184a8c4610b4b6-dirty"
proteore
parents: 6
diff changeset
20 --inputtype="tabfile"
fda784211e3a "planemo upload commit 330a2527c7e20c4d189a0f1b7a184a8c4610b4b6-dirty"
proteore
parents: 6
diff changeset
21 --header='$inputtype.header'
fda784211e3a "planemo upload commit 330a2527c7e20c4d189a0f1b7a184a8c4610b4b6-dirty"
proteore
parents: 6
diff changeset
22 --column='$inputtype.column'
fda784211e3a "planemo upload commit 330a2527c7e20c4d189a0f1b7a184a8c4610b4b6-dirty"
proteore
parents: 6
diff changeset
23 #end if
4
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
24
8
c9e48832420b "planemo upload commit 330a2527c7e20c4d189a0f1b7a184a8c4610b4b6-dirty"
proteore
parents: 7
diff changeset
25 #if "protein_atlas" in str($ref_file).split("/")
12
f8d3a8a2f2e5 "planemo upload commit 58e072579a4be282c00b54ebb88fbc59e189a7ed-dirty"
proteore
parents: 11
diff changeset
26 --atlas="$ref_file"
7
fda784211e3a "planemo upload commit 330a2527c7e20c4d189a0f1b7a184a8c4610b4b6-dirty"
proteore
parents: 6
diff changeset
27 #else
12
f8d3a8a2f2e5 "planemo upload commit 58e072579a4be282c00b54ebb88fbc59e189a7ed-dirty"
proteore
parents: 11
diff changeset
28 --atlasf="$__tool_directory__/$ref_file"
7
fda784211e3a "planemo upload commit 330a2527c7e20c4d189a0f1b7a184a8c4610b4b6-dirty"
proteore
parents: 6
diff changeset
29 #end if
4
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
30
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
31 ]]></command>
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
32
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
33 <inputs>
8
c9e48832420b "planemo upload commit 330a2527c7e20c4d189a0f1b7a184a8c4610b4b6-dirty"
proteore
parents: 7
diff changeset
34 <param name="ref_file" type="select" label="HPA source file version" >
c9e48832420b "planemo upload commit 330a2527c7e20c4d189a0f1b7a184a8c4610b4b6-dirty"
proteore
parents: 7
diff changeset
35 <options from_data_table="proteore_protein_full_atlas">
c9e48832420b "planemo upload commit 330a2527c7e20c4d189a0f1b7a184a8c4610b4b6-dirty"
proteore
parents: 7
diff changeset
36 <filter type="sort_by" column="0"/>
c9e48832420b "planemo upload commit 330a2527c7e20c4d189a0f1b7a184a8c4610b4b6-dirty"
proteore
parents: 7
diff changeset
37 </options>
c9e48832420b "planemo upload commit 330a2527c7e20c4d189a0f1b7a184a8c4610b4b6-dirty"
proteore
parents: 7
diff changeset
38 </param>
4
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
39 <conditional name="inputtype">
6
ea59f5750c51 planemo upload commit fb27a6b5de5cd7b269a41be3c85c593b77aa1b18-dirty
proteore
parents: 5
diff changeset
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)">
4
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
41 <option value="file_all" selected="true">Input file containing your IDs</option>
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
42 <option value="copy_paste">Copy/paste your list of IDs</option>
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
43 </param>
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
44 <when value="copy_paste">
5
e919b55188ab planemo upload commit e51bfb0f336c151fefcccf97e0c34be60283fb3b-dirty
proteore
parents: 4
diff changeset
45 <param name="genelist" type="text" label="Enter a list of IDs">
4
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
46 <sanitizer>
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
47 <valid initial="string.printable">
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
48 <remove value="&apos;"/>
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
49 </valid>
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
50 <mapping initial="none">
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
51 <add source="&apos;" target="__sq__"/>
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
52 </mapping>
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
53 </sanitizer>
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
54 </param>
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
55 </when>
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
56 <when value="file_all">
5
e919b55188ab planemo upload commit e51bfb0f336c151fefcccf97e0c34be60283fb3b-dirty
proteore
parents: 4
diff changeset
57 <param name="genelist" type="data" format="txt,tabular" label="Select your file" help=""/>
6
ea59f5750c51 planemo upload commit fb27a6b5de5cd7b269a41be3c85c593b77aa1b18-dirty
proteore
parents: 5
diff changeset
58 <param name="column" type="text" label="Column IDs (e.g : Enter c1 if ENSG ID are in column n°1)" value="c1">
ea59f5750c51 planemo upload commit fb27a6b5de5cd7b269a41be3c85c593b77aa1b18-dirty
proteore
parents: 5
diff changeset
59 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
4
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
60 </param>
6
ea59f5750c51 planemo upload commit fb27a6b5de5cd7b269a41be3c85c593b77aa1b18-dirty
proteore
parents: 5
diff changeset
61 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?"/>
4
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
62 </when>
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
63 </conditional>
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
64 <section name="options" title="RNAseq/Ab-based expression data" expanded="True">
5
e919b55188ab planemo upload commit e51bfb0f336c151fefcccf97e0c34be60283fb3b-dirty
proteore
parents: 4
diff changeset
65 <param name="hpaparams" type="select" label="Select information to add to your list" multiple="True" display="checkboxes" optional="false" >
4
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
66 <option value="Gene" selected="true">Gene name</option>
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
67 <option value="Gene description" selected="false">Gene description</option>
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
68 <option value="Evidence">Evidence (at protein level, at transcript level or no evidence)</option>
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
69 <option value="Antibody">Antibody reference</option>
12
f8d3a8a2f2e5 "planemo upload commit 58e072579a4be282c00b54ebb88fbc59e189a7ed-dirty"
proteore
parents: 11
diff changeset
70 <option value="RNA tissue specificity">RNA tissue category</option>
f8d3a8a2f2e5 "planemo upload commit 58e072579a4be282c00b54ebb88fbc59e189a7ed-dirty"
proteore
parents: 11
diff changeset
71 <option value="Reliability (IH)">IH detection level</option>
4
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
72 <option value="Reliability (IF)">IF detection level</option>
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
73 <option value="Subcellular location">Subcellular location</option>
12
f8d3a8a2f2e5 "planemo upload commit 58e072579a4be282c00b54ebb88fbc59e189a7ed-dirty"
proteore
parents: 11
diff changeset
74 <option value="RNA tissue specific NX">RNA tissue specificity abundance in 'Transcript Per Million'</option>
f8d3a8a2f2e5 "planemo upload commit 58e072579a4be282c00b54ebb88fbc59e189a7ed-dirty"
proteore
parents: 11
diff changeset
75 <option value="TPM max in non-specific">RNA non-specific tissue abundance in 'Transcript Per Million' (only for 23/10/2018 release)</option>
4
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
76 </param>
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
77 </section>
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
78
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
79 </inputs>
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
80
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
81
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
82 <outputs>
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
83 <data name="output" format="tsv" label=""/>
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
84 </outputs>
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
85
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
86 <tests>
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
87 <test>
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
88 <conditional name="inputtype">
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
89 <param name="filetype " value="file_all"/>
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
90 <param name="genelist" value="ID_Converter_Lacombe_et_al_2017_OK.txt"/>
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
91 <param name="column" value="c8"/>
5
e919b55188ab planemo upload commit e51bfb0f336c151fefcccf97e0c34be60283fb3b-dirty
proteore
parents: 4
diff changeset
92 <param name="header" value="true"/>
4
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
93 </conditional>
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
94 <section name="options">
5
e919b55188ab planemo upload commit e51bfb0f336c151fefcccf97e0c34be60283fb3b-dirty
proteore
parents: 4
diff changeset
95 <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"/>
4
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
96 </section>
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
97 <output name="output" file="Get_annotation_RNAseq.txt"/>
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
98 </test>
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
99 </tests>
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
100
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
101 <help><![CDATA[
5
e919b55188ab planemo upload commit e51bfb0f336c151fefcccf97e0c34be60283fb3b-dirty
proteore
parents: 4
diff changeset
102 **Description**
4
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
103
5
e919b55188ab planemo upload commit e51bfb0f336c151fefcccf97e0c34be60283fb3b-dirty
proteore
parents: 4
diff changeset
104 This tool adds expression annotation (RNAseq- or antibody-based experimental data - see "Parameters" below) from the Human Protein Atlas (HPA) database (https://www.proteinatlas.org/) to your gene/protein list.
e919b55188ab planemo upload commit e51bfb0f336c151fefcccf97e0c34be60283fb3b-dirty
proteore
parents: 4
diff changeset
105
e919b55188ab planemo upload commit e51bfb0f336c151fefcccf97e0c34be60283fb3b-dirty
proteore
parents: 4
diff changeset
106 -----
4
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
107
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
108 **Input**
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
109
6
ea59f5750c51 planemo upload commit fb27a6b5de5cd7b269a41be3c85c593b77aa1b18-dirty
proteore
parents: 5
diff changeset
110 Input can be either a list of Ensembl gene (ENSG) IDs (copy/paste mode) or a file containing multiple fields with at least one column of Ensembl gene IDs. If your input file contains other type of IDs, please use the ID_Converter tool to create a column of Ensembl gene IDs.
ea59f5750c51 planemo upload commit fb27a6b5de5cd7b269a41be3c85c593b77aa1b18-dirty
proteore
parents: 5
diff changeset
111
ea59f5750c51 planemo upload commit fb27a6b5de5cd7b269a41be3c85c593b77aa1b18-dirty
proteore
parents: 5
diff changeset
112 .. class:: warningmark
ea59f5750c51 planemo upload commit fb27a6b5de5cd7b269a41be3c85c593b77aa1b18-dirty
proteore
parents: 5
diff changeset
113
ea59f5750c51 planemo upload commit fb27a6b5de5cd7b269a41be3c85c593b77aa1b18-dirty
proteore
parents: 5
diff changeset
114 In copy/paste mode, the number of IDs considered in input is limited to 5000.
4
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
115
5
e919b55188ab planemo upload commit e51bfb0f336c151fefcccf97e0c34be60283fb3b-dirty
proteore
parents: 4
diff changeset
116 -----
4
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
117
5
e919b55188ab planemo upload commit e51bfb0f336c151fefcccf97e0c34be60283fb3b-dirty
proteore
parents: 4
diff changeset
118 **Parameters**
4
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
119
5
e919b55188ab planemo upload commit e51bfb0f336c151fefcccf97e0c34be60283fb3b-dirty
proteore
parents: 4
diff changeset
120 "Select information to add to your list": choose by clicking the following information:
4
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
121
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
122 - Gene name: according to the HGNC (Hugo Gene Nomenclature Committee)
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
123
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
124 - Gene description: entry description (full text)
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
125
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
126 - Evidence: at protein level, at transcript level or no evidence
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
127
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
128 - Antibody reference: reference of the HPA antibody used for immunohistochemistry and immunocytochemistry/IF
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
129
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
130 - RNA tissue category: categories based on RNA-Seq data to estimate the transcript abundance of each protein-coding gene in tissues. For more information, please refer to http://www.proteinatlas.org/about/assays+annotation#rna .
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
131
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
132 - IH detection level: level of detection of the protein associated to the coding gene tissues based on immunofluorescency. For more information, please refer to http://www.proteinatlas.org/about/assays+annotation#if .
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
133
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
134 - IF detection level:level of detection of the protein associated to the coding gene tissues based on immunohistochemistry. For more information, please refer to http://www.proteinatlas.org/about/assays+annotation#ih .
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
135
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
136 - Subcellular location:according to HPA data. For more information, please refer to https://www.proteinatlas.org/about/assays+annotation#ifa
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
137
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
138 - 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.
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
139
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
140 - RNA non-specific tissue abundance in 'Transcript Per Million': please refer to http://www.proteinatlas.org/about/assays+annotation#rna.
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
141
5
e919b55188ab planemo upload commit e51bfb0f336c151fefcccf97e0c34be60283fb3b-dirty
proteore
parents: 4
diff changeset
142 -----
e919b55188ab planemo upload commit e51bfb0f336c151fefcccf97e0c34be60283fb3b-dirty
proteore
parents: 4
diff changeset
143
e919b55188ab planemo upload commit e51bfb0f336c151fefcccf97e0c34be60283fb3b-dirty
proteore
parents: 4
diff changeset
144 **Output**
e919b55188ab planemo upload commit e51bfb0f336c151fefcccf97e0c34be60283fb3b-dirty
proteore
parents: 4
diff changeset
145
6
ea59f5750c51 planemo upload commit fb27a6b5de5cd7b269a41be3c85c593b77aa1b18-dirty
proteore
parents: 5
diff changeset
146 The output is a tabular file containing initial columns and new columns with annotation from HPA.
4
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
147
5
e919b55188ab planemo upload commit e51bfb0f336c151fefcccf97e0c34be60283fb3b-dirty
proteore
parents: 4
diff changeset
148 -----
e919b55188ab planemo upload commit e51bfb0f336c151fefcccf97e0c34be60283fb3b-dirty
proteore
parents: 4
diff changeset
149
e919b55188ab planemo upload commit e51bfb0f336c151fefcccf97e0c34be60283fb3b-dirty
proteore
parents: 4
diff changeset
150 **Data sources (release date)**
e919b55188ab planemo upload commit e51bfb0f336c151fefcccf97e0c34be60283fb3b-dirty
proteore
parents: 4
diff changeset
151
6
ea59f5750c51 planemo upload commit fb27a6b5de5cd7b269a41be3c85c593b77aa1b18-dirty
proteore
parents: 5
diff changeset
152 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
4
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
153
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
154 -----
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
155
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
156 .. class:: infomark
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
157
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
158 **Authors**
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
159
6
ea59f5750c51 planemo upload commit fb27a6b5de5cd7b269a41be3c85c593b77aa1b18-dirty
proteore
parents: 5
diff changeset
160 Lisa Perus, David Christiany, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
4
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
161
5
e919b55188ab planemo upload commit e51bfb0f336c151fefcccf97e0c34be60283fb3b-dirty
proteore
parents: 4
diff changeset
162 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux - INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR
4
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
163
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
164 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
165
6
ea59f5750c51 planemo upload commit fb27a6b5de5cd7b269a41be3c85c593b77aa1b18-dirty
proteore
parents: 5
diff changeset
166 Help: contact@proteore.org for any questions or concerns about this tool.
4
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
167
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
168 ]]></help>
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
169
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
170 <citations>
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
171 </citations>
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
172
3f9057cdfdde planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
173 </tool>