Mercurial > repos > proteore > proteore_maps_visualization

comparison kegg_maps_visualization.xml @ 5:f4e02d20546b draft

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planemo upload commit c6b2e31fccac66c2caa687b375cbf9947f7ba88e-dirty
author proteore
date Tue, 14 May 2019 09:28:50 -0400
parents 4cc2265d1294
children 005221a20848
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4:4cc2265d1294 5:f4e02d20546b
1 <tool id="kegg_maps_visualization" name="KEGG maps visualization" version="2019.01.31"> 1 <tool id="kegg_maps_visualization" name="Pathways visualization" version="2019.05.14">
2 <description>of (differentially expressed) genes/proteins</description> 2 <description>of (differentially expressed) genes/proteins [KEGG]</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.18.0">bioconductor-pathview</requirement> 4 <requirement type="package" version="1.18.0">bioconductor-pathview</requirement>
5 <requirement type="package" version="1.18.0">bioconductor-keggrest</requirement> 5 <requirement type="package" version="1.18.0">bioconductor-keggrest</requirement>
6 </requirements> 6 </requirements>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
67 </valid> 67 </valid>
68 <mapping> 68 <mapping>
69 <add source="&#x20;" target=""/> 69 <add source="&#x20;" target=""/>
70 </mapping> 70 </mapping>
71 </sanitizer> 71 </sanitizer>
72 <validator type="regex" message="Please enter correct pathway id(s)">([a-z]{3}[0-9]{5}[\s]*)+</validator>
72 </param> 73 </param>
73 </when> 74 </when>
74 <when value="pathways_file"> 75 <when value="pathways_file">
75 <param name="file" type="data" format="txt,tabular" label="Select your file" help="Pathway id format : 'path:hsa00010' or 'hsa00010' or '00010'" /> 76 <param name="file" type="data" format="txt,tabular" label="Select your file" help="Pathway id format : 'path:hsa00010' or 'hsa00010' or '00010'" />
76 <param name="header2" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" /> 77 <param name="header2" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
77 <param name="ncol2" type="text" value="c1" label="Column of pathways IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' /> 78 <param name="ncol2" type="text" value="c1" label="Column of pathways IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on'>
79 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
80 </param>
78 </when> 81 </when>
79 </conditional> 82 </conditional>
80 </when> 83 </when>
81 <when value="mmu"> 84 <when value="mmu">
82 <conditional name="pathways"> 85 <conditional name="pathways">
101 </valid> 104 </valid>
102 <mapping> 105 <mapping>
103 <add source="&#x20;" target=""/> 106 <add source="&#x20;" target=""/>
104 </mapping> 107 </mapping>
105 </sanitizer> 108 </sanitizer>
109 <validator type="regex" message="Please enter correct pathway id(s)">([a-z]{3}[0-9]{5}[\s]*)+</validator>
106 </param> 110 </param>
107 </when> 111 </when>
108 <when value="pathways_file"> 112 <when value="pathways_file">
109 <param name="file" type="data" format="txt,tabular" label="Enter your file" help="Pathway id format : 'path:mmu00053' or 'mmu00053' or '00053'" /> 113 <param name="file" type="data" format="txt,tabular" label="Enter your file" help="Pathway id format : 'path:mmu00053' or 'mmu00053' or '00053'" />
110 <param name="header2" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" /> 114 <param name="header2" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
111 <param name="ncol2" type="text" value="c1" label="Column of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' /> 115 <param name="ncol2" type="text" value="c1" label="Column of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on'>
116 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
117 </param>
112 </when> 118 </when>
113 </conditional> 119 </conditional>
114 </when> 120 </when>
115 <when value="rno"> 121 <when value="rno">
116 <conditional name="pathways"> 122 <conditional name="pathways">
135 </valid> 141 </valid>
136 <mapping> 142 <mapping>
137 <add source="&#x20;" target=""/> 143 <add source="&#x20;" target=""/>
138 </mapping> 144 </mapping>
139 </sanitizer> 145 </sanitizer>
146 <validator type="regex" message="Please enter correct pathway id(s)">([a-z]{3}[0-9]{5}[\s]*)+</validator>
140 </param> 147 </param>
141 </when> 148 </when>
142 <when value="pathways_file"> 149 <when value="pathways_file">
143 <param name="file" type="data" format="txt,tabular" label="Select your file" help="Pathway id format : 'path:hsa00010' or 'hsa00010' or '00010'" /> 150 <param name="file" type="data" format="txt,tabular" label="Select your file" help="Pathway id format : 'path:hsa00010' or 'hsa00010' or '00010'" />
144 <param name="header2" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" /> 151 <param name="header2" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
145 <param name="ncol2" type="text" value="c1" label="Column of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' /> 152 <param name="ncol2" type="text" value="c1" label="Column of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on'>
153 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
154 </param>
146 </when> 155 </when>
147 </conditional> 156 </conditional>
148 </when> 157 </when>
149 </conditional> 158 </conditional>
150 <!--/section--> 159 <!--/section-->
172 </param> 181 </param>
173 </when> 182 </when>
174 <when value="file" > 183 <when value="file" >
175 <param name="file" type="data" format="txt,tabular" label="Select your file" help="" /> 184 <param name="file" type="data" format="txt,tabular" label="Select your file" help="" />
176 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" /> 185 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
177 <param name="ncol" type="text" value="c1" label="Column if 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' /> 186 <param name="ncol" type="text" value="c1" label="Column if 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'>
187 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
188 </param>
178 <conditional name="foldchange" > 189 <conditional name="foldchange" >
179 <param name="fc" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Map quantitative data on the pathway?"/> 190 <param name="fc" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Map quantitative data on the pathway?"/>
180 <when value="true"> 191 <when value="true">
181 <param name="fc_col" type="text" label="Column(s) number of quantitative data (separated by ','. 3 columns max)" help="For example : c1,c3,c4"/> 192 <param name="fc_col" type="text" label="Column(s) number of quantitative data (separated by ','. 3 columns max)" help="For example : c1,c3,c4">
193 <validator type="regex" message="Please enter column numbers, for example: 'c1,c3' for first and third columns">([c]{0,1}[0-9]+[,]*){1,3}</validator>
194 </param>
182 </when> 195 </when>
183 <when value="false"/> 196 <when value="false"/>
184 </conditional> 197 </conditional>
185 </when> 198 </when>
186 </conditional> 199 </conditional>