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comparison get_expression_profiles.xml @ 9:0a0f6c37f05e draft

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planemo upload commit 47b21d3d533a6729de0269f70b033f976419368c-dirty
author proteore
date Wed, 13 Mar 2019 09:15:52 -0400
parents 2c0bab71a436
children 6e85f07c20ee
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8:2c0bab71a436 9:0a0f6c37f05e
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