Mercurial > repos > proteore > proteore_retrieve_from_hpa

annotate Build_tissue-specific_expression_dataset.xml @ 1:cfcc7a780991 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
author proteore
date Thu, 13 Dec 2018 03:59:41 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
1 <tool id="retrieve_from_hpa" name="Build tissue-specific expression dataset" version="2018.12.12">
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
2 <description>[Human Protein Atlas](no input required)</description>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
3 <requirements>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
4 <requirement type="package" version="3.4.1">R</requirement>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
5 </requirements>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
6 <stdio>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
7 <exit_code range="1:" />
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
8 </stdio>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
9 <command interpreter="Rscript">
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
10 $__tool_directory__/Build_tissue-specific_expression_dataset.R
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
11 --data_source="$input.data_source"
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
12 #if $input.data_source == "immuno"
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
13 --hpa_ref="$__tool_directory__/normal_tissue.tsv"
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
14 --tissue="$input.normal_tissue"
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
15 --level="$input.level"
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
16 --reliability="$input.reliability"
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
17 #else if $input.data_source == "rnaseq"
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
18 --hpa_ref="$__tool_directory__/rna_tissue.tsv"
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
19 --sample="$input.sample"
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
20 #end if
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
21 --output="$output"
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
22 </command>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
23
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
24 <inputs>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
25 <conditional name="input">
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
26 <param name="data_source" type="select" label="Please choose experimental data source (antibody- or RNAseq-based)">
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
27 <option value="immuno">Expression profiles based on immunohistochemistry</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
28 <option value="rnaseq">RNA levels based on RNA-seq</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
29 </param>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
30 <when value="immuno">
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
31 <param name="normal_tissue" type="select" label="Select tissue by clicking the dropdown menu below" multiple="True" optional="False">
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
32 <option value="adrenal gland" >Adrenal gland</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
33 <option value="appendix" >Appendix</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
34 <option value="bone marrow" >Bone marrow</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
35 <option value="breast" >Breast</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
36 <option value="bronchus" >Bronchus</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
37 <option value="caudate" >Caudate</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
38 <option value="cerebellum" >Cerebellum</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
39 <option value="cerebral cortex" >Cerebral cortex</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
40 <option value="cervix" >Cervix</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
41 <option value="colon" >Colon</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
42 <option value="duodenum" >Duodenum</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
43 <option value="endometrium 1" >Endometrium 1</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
44 <option value="endometrium 2" >Endometrium 2</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
45 <option value="epididymis" >Epididymis</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
46 <option value="esophagus" >Esophagus</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
47 <option value="fallopian tube" >Fallopian tube</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
48 <option value="gallbladder" >Gallbladder</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
49 <option value="heart muscle" >Heart muscle</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
50 <option value="hippocampus" >Hippocampus</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
51 <option value="kidney" >Kidney</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
52 <option value="liver" >Liver</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
53 <option value="lung" >Lung</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
54 <option value="lymph node" >Lymph node</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
55 <option value="nasopharynx" >Nasopharynx</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
56 <option value="oral mucosa" >Oral mucosa</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
57 <option value="ovary" >Ovary</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
58 <option value="pancreas" >Pancreas</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
59 <option value="parathyroid gland" >Parathyroid gland</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
60 <option value="placenta" >Placenta</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
61 <option value="prostate" >Prostate</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
62 <option value="rectum" >Rectum</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
63 <option value="salivary gland" >Salivary gland</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
64 <option value="seminal vesicle" >Seminal vesicle</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
65 <option value="skeletal muscle" >Skeletal muscle</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
66 <option value="skin 1" >Skin 1</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
67 <option value="skin 2" >Skin 2</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
68 <option value="small intestine" >Small intestine</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
69 <option value="smooth muscle" >Smooth muscle</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
70 <option value="soft tissue 1" >Soft tissue 1</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
71 <option value="soft tissue 2" >Soft tissue 2</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
72 <option value="spleen" >Spleen</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
73 <option value="stomach 1" >Stomach 1</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
74 <option value="stomach 2" >Stomach 2</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
75 <option value="testis" >Testis</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
76 <option value="thyroid gland" >Thyroid gland</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
77 <option value="tonsil" >Tonsil</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
78 <option value="urinary bladder" >Urinary bladder</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
79 <option value="vagina" >Vagina</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
80 </param>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
81 <param name="level" type="select" label="Expression level" display="checkboxes" multiple="True" optional="False">
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
82 <option value="High" selected="true">High</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
83 <option value="Medium">Medium</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
84 <option value="Low">Low</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
85 <option value="Not detected">Not detected</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
86 </param>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
87 <param name="reliability" type="select" label="Reliability score" display="checkboxes" multiple="True" optional="False">
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
88 <option value="Enhanced" selected="true">Enhanced</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
89 <option value="Supported" selected="true">Supported</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
90 <option value="Approved">Approved</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
91 <option value="Uncertain">Uncertain</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
92
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
93 </param>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
94 </when>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
95 <when value="rnaseq">
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
96 <param name="sample" type="select" label="Keep and annotate genes present in the following tissue(s)" multiple="True" optional="False">
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
97 <option value="adipose tissue">Adipose tissue</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
98 <option value="adrenal gland">Adrenal gland</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
99 <option value="appendix">Appendix</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
100 <option value="bone marrow">Bone marrow</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
101 <option value="breast">Breast</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
102 <option value="cerebral cortex">Cerebral cortex</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
103 <option value="cervix, uterine">Cervix, uterine</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
104 <option value="colon">Colon</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
105 <option value="duodenum">Duodenum</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
106 <option value="endometrium">Endometrium</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
107 <option value="epididymis">Epididymis</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
108 <option value="esophagus">Esophagus</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
109 <option value="fallopian tube">Fallopian tube</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
110 <option value="gallbladder">Gallbladder</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
111 <option value="heart muscle">Heart muscle</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
112 <option value="kidney">Kidney</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
113 <option value="liver">Liver</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
114 <option value="lung">Lung</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
115 <option value="lymph node">Lymph node</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
116 <option value="ovary">Ovary</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
117 <option value="pancreas">Pancreas</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
118 <option value="parathyroid gland">Parathyroid gland</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
119 <option value="placenta">Placenta</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
120 <option value="prostate">Prostate</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
121 <option value="rectum">Rectum</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
122 <option value="salivary gland">Salivary gland</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
123 <option value="seminal vesicle">Seminal vesicle</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
124 <option value="skeletal muscle">Skeletal muscle</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
125 <option value="skin">Skin</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
126 <option value="small intestine">Small intestine</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
127 <option value="smooth muscle">Smooth muscle</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
128 <option value="spleen">Spleen</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
129 <option value="stomach">Stomach</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
130 <option value="testis">Testis</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
131 <option value="thyroid gland">Thyroid gland</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
132 <option value="tonsil">Tonsil</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
133 <option value="rinary bladder">Urinary bladder</option>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
134 </param>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
135 </when>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
136 </conditional>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
137 </inputs>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
138
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
139 <outputs>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
140 <data name="output" format="tsv" label=""/>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
141 </outputs>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
142
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
143 <tests>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
144 <test>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
145 <conditional name="input">
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
146 <param name="data_source" value="immuno"/>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
147 <param name="normal_tissue" value="lung,ovary"/>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
148 <param name="level" value="High"/>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
149 <param name="reliability" value="Approved,Supported"/>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
150 </conditional>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
151 <output name="output" file="test.txt"/>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
152 </test>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
153 </tests>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
154
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
155 <help><![CDATA[
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
156
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
157 This tool allows to retrieve information from Human Protein Atlas (https://www.proteinatlas.org/)
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
158 regarding the expression profiles of human genes both at the mRNA and protein levels
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
159 without any input required. It could be used to:
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
160
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
161 * Select a list of proteins highly expressed in a given tissue for data mining or comparison purpose in terms of expected protein content from one tissue to another
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
162
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
163 * Build a "reference" proteome restricted to a given tissue (for instance for GO analysis as a reference background restricted to a biological sample)
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
164
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
165 The resources from Human Protein Atlas that can be queried are the following:
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
166
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
167 1. Human normal tissue data: expression profiles for proteins in human tissues based on immunohistochemisty using tissue micro arrays measured in 58 tissues and 82 cell types.
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
168
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
169 The tab-separated file includes Ensembl gene identifier ("Gene"), tissue name ("Tissue"), annotated cell type ("Cell type"), expression value ("Level"), and the gene reliability of the expression value ("Reliability score").
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
170
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
171 The reliability score is divided into Enhanced, Supported, Approved, or Uncertain with the following definitions:
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
172
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
173 * Enhanced: One or several antibodies with non-overlapping epitopes targeting the same gene have obtained enhanced validation based on orthogonal or independent antibody validation method.
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
174
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
175 * Supported: Consistency with RNA-seq and/or protein/gene characterization data, in combination with similar staining pattern if independent antibodies are available.
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
176
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
177 * Approved: Consistency with RNA-seq data in combination with inconsistency with, or lack of, protein/gene characterization data. Alternatively, consistency with protein/gene characterization data in combination with inconsistency with RNA-seq data. If independent antibodies are available, the staining pattern is partly similar or dissimilar.
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
178
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
179 * Uncertain:
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
180
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
181 Inconsistency with, or lack of, RNA-seq and/or protein/gene characterization data, in combination with dissimilar staining pattern if independent antibodies are available.
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
182
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
183 The data is based on The Human Protein Atlas version 18 and Ensembl version 88.38.
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
184
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
185 2. RNA levels based on RNA-seq data: RNA levels measured in 64 cell lines and 37 tissues based on RNA-seq experiments. The tab-separated file includes Ensembl gene identifier ("Gene"), analysed sample ("Sample") and transcripts per million ("Value" and "Unit").
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
186
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
187 The data is based on The Human Protein Atlas version 18 and Ensembl version 88.38.
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
188
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
189 For more information: https://www.proteinatlas.org/about/help
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
190
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
191 -----
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
192
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
193 .. class:: infomark
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
194
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
195 **Authors**
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
196
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
197 T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
198
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
199 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
200
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
201 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
202
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
203 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
204
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
205 ]]></help>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
206
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
207 <citations>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
208 </citations>
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
209
cfcc7a780991 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents:
diff changeset
210 </tool>