Mercurial > repos > proteore > proteore_expression_levels_by_tissue
comparison get_expression_profiles.xml @ 9:0a0f6c37f05e draft
planemo upload commit 47b21d3d533a6729de0269f70b033f976419368c-dirty
author | proteore |
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date | Wed, 13 Mar 2019 09:15:52 -0400 |
parents | 2c0bab71a436 |
children | 6e85f07c20ee |
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8:2c0bab71a436 | 9:0a0f6c37f05e |
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1 <tool id="sel_ann_hpa" name="Get expression profiles" version="2018.12.17"> | 1 <tool id="sel_ann_hpa" name="Get expression profiles" version="2019.03.06"> |
2 <description>by (normal or tumor) tissue/cell type [Human Protein Atlas] | 2 <description>by (normal or tumor) tissue/cell type [Human Protein Atlas] |
3 </description> | 3 </description> |
4 <requirements> | 4 <requirements> |
5 </requirements> | 5 </requirements> |
6 <stdio> | 6 <stdio> |
7 <exit_code range="1:" /> | 7 <exit_code range="1:" /> |
8 </stdio> | 8 </stdio> |
9 <command interpreter="Rscript"> | 9 <command interpreter="Rscript"> |
10 $__tool_directory__/get_expression_profiles.R | 10 $__tool_directory__/get_expression_profiles.R |
11 --ref_file="$__tool_directory__/$options.proteinatlas" | 11 |
12 #if "protein_atlas" in str($options.proteinatlas).split("/") | |
13 --ref_file="$options.proteinatlas" | |
14 #else | |
15 --ref_file="$__tool_directory__/$options.proteinatlas" | |
16 #end if | |
17 | |
12 --input_type="$input.ids" | 18 --input_type="$input.ids" |
13 #if $input.ids == "list" | 19 #if $input.ids == "list" |
14 --input="$input.list" | 20 --input="$input.list" |
15 #else | 21 #else |
16 --input="$input.file" | 22 --input="$input.file" |
49 </param> | 55 </param> |
50 </when> | 56 </when> |
51 <when value="file" > | 57 <when value="file" > |
52 <param name="file" type="data" format="txt,tabular" label="" help="" /> | 58 <param name="file" type="data" format="txt,tabular" label="" help="" /> |
53 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" /> | 59 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" /> |
54 <param name="ncol" type="text" value="c1" label="Column number of IDs to map" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' /> | 60 <param name="ncol" type="text" value="c1" label="Column number of IDs to map" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on'> |
61 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator> | |
62 </param> | |
55 </when> | 63 </when> |
56 </conditional> | 64 </conditional> |
57 <conditional name="options"> | 65 <conditional name="options"> |
58 <param name="database" type="select" label="Human Protein Atlas (normal or tumor tissue)"> | 66 <param name="database" type="select" label="Human Protein Atlas (normal or tumor tissue)"> |
59 <option value="normal">Human Normal Tissue</option> | 67 <option value="normal">Human Normal Tissue</option> |
60 <option value="tumor">Human Tumor Tissue</option> | 68 <option value="tumor">Human Tumor Tissue</option> |
61 </param> | 69 </param> |
62 <when value="normal"> | 70 <when value="normal"> |
63 <param name="proteinatlas" type="select" label="Normal tissue HPA version" > | 71 <param name="proteinatlas" type="select" label="Normal tissue HPA version" > |
64 <!--options from_file="proteinatlas.loc" > | 72 <options from_data_table="proteore_protein_atlas_normal_tissue"/> |
65 <column name="name" index="1"/> | |
66 <column name="value" index="2"/> | |
67 <filter type="remove_value" key="name" value="Full Human Protein Atlas (23/10/18)"/> | |
68 <filter type="remove_value" key="name" value="HPA Tumor Tissue (23/10/18)"/> | |
69 </options--> | |
70 <option value="tool-data/HPA_normal_tissue_23-10-2018.tsv">HPA Normal Tissue (23/10/18)</option> | |
71 </param> | 73 </param> |
72 <param name="normal_tissue" type="select" label="Select tissue(s)" multiple="True" display="checkboxes" optional="False"> | 74 <param name="normal_tissue" type="select" label="Select tissue(s)" multiple="True" display="checkboxes" optional="False"> |
73 <option value="adrenal gland" >Adrenal gland</option> | 75 <option value="adrenal gland" >Adrenal gland</option> |
74 <option value="appendix" >Appendix</option> | 76 <option value="appendix" >Appendix</option> |
75 <option value="bone marrow" >Bone marrow</option> | 77 <option value="bone marrow" >Bone marrow</option> |
132 <option value="Uncertain">Uncertain</option> | 134 <option value="Uncertain">Uncertain</option> |
133 </param> | 135 </param> |
134 </when> | 136 </when> |
135 <when value="tumor"> | 137 <when value="tumor"> |
136 <param name="proteinatlas" type="select" label="Tumor tissue HPA version" > | 138 <param name="proteinatlas" type="select" label="Tumor tissue HPA version" > |
137 <!--options from_file="proteinatlas.loc" > | 139 <options from_data_table="proteore_protein_atlas_tumor_tissue"/> |
138 <column name="name" index="1" /> | |
139 <column name="value" index="2" /> | |
140 <filter type="remove_value" meta_ref="proteinatlas" key="name" value="Full Human Protein Atlas (23/10/18)" /> | |
141 <filter type="remove_value" meta_ref="proteinatlas" key="name" value="HPA Normal Tissue (23/10/18)" /> | |
142 </options--> | |
143 <option value="tool-data/HPA_pathology_23-10-2018.tsv">HPA Tumor Tissue (23/10/18)</option> | |
144 </param> | 140 </param> |
145 <param name="cancer_tissue" type="select" label="Select cancer tissue(s)" multiple="True" display="checkboxes" optional="False"> | 141 <param name="cancer_tissue" type="select" label="Select cancer tissue(s)" multiple="True" display="checkboxes" optional="False"> |
146 <option value="breast cancer" >Breast cancer</option> | 142 <option value="breast cancer" >Breast cancer</option> |
147 <option value="carcinoid" >Carcinoid</option> | 143 <option value="carcinoid" >Carcinoid</option> |
148 <option value="cervical cancer" >Cervical cancer</option> | 144 <option value="cervical cancer" >Cervical cancer</option> |
242 | 238 |
243 .. class:: infomark | 239 .. class:: infomark |
244 | 240 |
245 **Authors** | 241 **Authors** |
246 | 242 |
247 T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR | 243 David Christiany, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR |
248 | 244 |
249 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR | 245 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR |
250 | 246 |
251 This work has been partially funded through the French National Agency for Research (ANR) IFB project. | 247 This work has been partially funded through the French National Agency for Research (ANR) IFB project. |
252 | 248 |