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comparison Pathview.xml @ 0:097bb3ed2b4d draft

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author proteore
date Wed, 22 Aug 2018 11:30:23 -0400
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1 <tool id="Pathview" name="KEGG pathway mapping (pathview)" version="2018.08.22">
2 <requirements>
3 <requirement type="package" version="1.18.0">bioconductor-pathview</requirement>
4 </requirements>
5 <command detect_errors="exit_code"><![CDATA[
6 Rscript $__tool_directory__/PathView.R
7 #if $input.ids == "text"
8 --id_list="$input.txt"
9 #else
10 --input="$input.file"
11 --id_column="$input.ncol"
12 --header="$input.header"
13 #end if
14 #if $species.pathways.pathways_id == "pathways_ids"
15 --pathways_id="$species.pathways.pids"
16 #else
17 --pathways_id="$species.pathways.pids"
18 #end if
19 --id_type="$id_type"
20 --native_kegg="$native"
21
22 #if $input.ids=="file"
23 #if $input.expression_values.nb_exp =="1"
24 --expression_values1="$input.expression_values.e1"
25 #else if $input.expression_values.nb_exp =="2"
26 --expression_values1="$input.expression_values.e1"
27 --expression_values2="$input.expression_values.e2"
28 #else if $input.expression_values.nb_exp =="3"
29 --expression_values1="$input.expression_values.e1"
30 --expression_values2="$input.expression_values.e2"
31 --expression_values3="$input.expression_values.e3"
32 #end if
33 #end if
34
35 --species=${species.ref_file}
36
37 ]]></command>
38 <inputs>
39 <conditional name="input" >
40 <param name="ids" type="select" label="Provide your identifiers" help="Copy/paste or ID list from a file (e.g. table)" >
41 <option value="text">Copy/paste your identifiers</option>
42 <option value="file" selected="true">Input file containing your identifiers</option>
43 </param>
44 <when value="text" >
45 <param name="txt" type="text" label="Copy/paste your identifiers" help='IDs must be separated by "," into the form field, for example: P31946,P62258' >
46 <sanitizer invalid_char=''>
47 <valid initial="string.printable">
48 <remove value="&apos;"/>
49 </valid>
50 <mapping initial="none">
51 <add source="&apos;" target="__sq__"/>
52 </mapping>
53 </sanitizer>
54 </param>
55 </when>
56 <when value="file" >
57 <param name="file" type="data" format="txt,tabular" label="Select a file that contains your list of IDs" help="" />
58 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
59 <param name="ncol" type="text" value="c1" label="The 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 <conditional name="expression_values">
61 <param name="nb_exp" type="select" label="How many expression values column in your file ?">
62 <option value="0" >0</option>
63 <option value="1" >1</option>
64 <option value="2" >2</option>
65 <option value="3" >3</option>
66 </param>
67 <when value="0">
68 </when>
69 <when value="1">
70 <param name="e1" type="text" value="" label="First column number of your expression data" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on'/>
71 </when>
72 <when value="2">
73 <param name="e1" type="text" value="" label="First column number of your expression data"/>
74 <param name="e2" type="text" value="" label="Second column number of your expression data"/>
75 </when>
76 <when value="3">
77 <param name="e1" type="text" value="" label="First column number of your expression data"/>
78 <param name="e2" type="text" value="" label="Second column number of your expression data"/>
79 <param name="e3" type="text" value="" label="Third column number of your expression data"/>
80 </when>
81 </conditional>
82 </when>
83 </conditional>
84 <param name="id_type" type="select" label="select your identifiers type :">
85 <option value="uniprotID">Uniprot Accession number</option>
86 <option value="geneID">Entrez gene ID</option>
87 </param>
88
89 <conditional name="species">
90 <param name="ref_file" type="select" label="Select species" >
91 <options from_data_table="kegg_pathways"/>
92 <option value="hsa"/>
93 <option value="mmu"/>
94 </param>
95 <when value="hsa">
96 <conditional name="pathways">
97 <param name="pathways_id" type="select" label="Provide your pathway(s)" help="Enter KEGG pathway name(s) or KEGG pathway id(s)">
98 <option value="pathways_names">KEGG pathway name(s)</option>
99 <option value="pathways_ids">KEGG pathway id(s)</option>
100 </param>
101 <when value="pathways_names">
102 <param name="pids" type="select" label="Select pathway(s)" multiple="true" help='You can select one or several pathway(s), you can write the beginning of your pathways to search using autocomplete'>
103 <options from_data_table="hsa_pathways">
104 <filter type="sort_by" column="1"/>
105 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
106 </options>
107 </param>
108 </when>
109 <when value="pathways_ids">
110 <param name="pids" type="text" label="Copy/paste your pathway id(s)" help='IDs must be separated by "," into the form field, for example: "00010,05412" or "hsa00010,hsa05412"'>
111 <sanitizer invalid_char=''>
112 <valid initial="string.printable">
113 <remove value="&apos;"/>
114 </valid>
115 <mapping>
116 <add source="&#x20;" target=""/>
117 </mapping>
118 </sanitizer>
119 </param>
120 </when>
121 </conditional>
122 </when>
123 <when value="mmu">
124 <conditional name="pathways">
125 <param name="pathways_id" type="select" label="Provide your pathway(s)" help="Enter KEGG pathway name(s) or KEGG pathway id(s)">
126 <option value="pathways_names">KEGG pathway name(s)</option>
127 <option value="pathways_ids">KEGG pathway id(s)</option>
128 </param>
129 <when value="pathways_names">
130 <param name="pids" type="select" label="Select pathway(s)" multiple="true" help='You can select one or several pathway(s), you can write the beginning of your pathways to search using autocomplete'>
131 <options from_data_table="mmu_pathways">
132 <filter type="sort_by" column="1"/>
133 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
134 </options>
135 </param>
136 </when>
137 <when value="pathways_ids">
138 <param name="pids" type="text" label="Copy/paste your pathway id(s)" help='IDs must be separated by "," into the form field, for example: "00010,05412" or "hsa00010,hsa05412"'>
139 <sanitizer invalid_char=''>
140 <valid initial="string.printable">
141 <remove value="&apos;"/>
142 </valid>
143 <mapping>
144 <add source="&#x20;" target=""/>
145 </mapping>
146 </sanitizer>
147 </param>
148 </when>
149 </conditional>
150 </when>
151 </conditional>
152 <param name="native" type="select" label="Choose the output graph format">
153 <option value="true">KEGG graph (.png)</option>
154 <option value="false">Graphviz layout engine (.pdf)</option>
155 </param>
156 </inputs>
157 <outputs>
158 <data name="graphviz_from_file" format="pdf" label="KEGG mapping with ${input.file.name}">
159 <filter>native=="false" and input["ids"] == "file"</filter>
160 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.pathview.*\.pdf" ext="pdf" visible="true" assign_primary_output="true"/>
161 </data>
162 <data name="kegg_from_file" format="png" label="KEGG mapping with ${input.file.name}">
163 <filter>native=="true" and input["ids"] == "file"</filter>
164 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.pathview.*\.png" ext="png" visible="true" assign_primary_output="true"/>
165 </data>
166 <data name="graphviz_from_list" format="pdf" label="KEGG mapping with given ids">
167 <filter>native=="false" and input["ids"] == "text"</filter>
168 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.pathview.*\.pdf" ext="pdf" visible="true" assign_primary_output="true"/>
169 </data>
170 <data name="kegg_from_list" format="png" label="KEGG mapping with given ids">
171 <filter>native=="true" and input["ids"] == "text"</filter>
172 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.pathview.*\.png" ext="png" visible="true" assign_primary_output="true"/>
173 </data>
174 </outputs>
175 <tests>
176 <test>
177 <conditional name="input">
178 <param name="ids" value="file"/>
179 <param name="file" value="Lacombe_et_al_2017_OK.txt"/>
180 <param name="header" value="true"/>
181 <param name="ncol" value="c1"/>
182 </conditional>
183 <conditional name="pathways">
184 <param name="pathways_id" value="pathways_ids"/>
185 <param name="pids" value="04514,05167,00010"/>
186 </conditional>
187 <param name="id_type" value="uniprotID"/>
188 <param name="species" value="hsa"/>
189 <param name="native" value="true"/>
190 <output name="kegg_from_file" file="hsa04514.pathview.png" compare="sim_size"/>
191 <output name="kegg_from_file" file="hsa05167.pathview.png" compare="sim_size"/>
192 <output name="kegg_from_file" file="hsa00010.pathview.png" compare="sim_size"/>
193 </test>
194 </tests>
195 <help><![CDATA[
196 This tool map a list of Uniprot Accession number or Entrez gene ID to KEGG pathway with pathview R package.
197
198 Select an input file containing ids in a column, set header and column number or copy/paste your ids.
199
200 Select your identifier type and a species of interest (for now only human available).
201
202 Select one or several pathways of interest from the dropdown menu or copy/paste KEGG pathway id(s)
203
204 Select the graph format : KEGG or graphviz
205
206 Uniprot accession number converted to Entrez geneID or Entrez geneID are mapped to each selected pathways.
207
208 Output : One file (png or pdf) for each selected pathway.
209
210 -----
211
212 .. class:: infomark
213
214 **Authors**
215
216 David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
217
218 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
219
220 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
221
222 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
223 ]]></help>
224 <citations>
225 <citation type="doi">10.1093/nar/gkx372</citation>
226 <citation type="bibtex">
227 @misc{renameTODO,
228 author = {Weijun Luo},
229 year = {2013},
230 title = {pathview},
231 url = {https://bioconductor.org/packages/release/bioc/html/pathview.html},
232 }</citation>
233 </citations>
234 </tool>