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comparison Pathview.xml @ 8:33c9bd75882a draft

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planemo upload commit 1953798eb28b6e45c78342ed4c6a6a978d096fca
author proteore
date Thu, 30 Aug 2018 06:12:51 -0400
parents b617d4bbebf8
children 560541195c3f
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7:b617d4bbebf8 8:33c9bd75882a
1 <tool id="Pathview" name="KEGG pathway mapping (pathview)" version="2018.08.27"> 1 <tool id="Pathview" name="KEGG pathway mapping (pathview)" version="2018.08.30">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="1.18.0">bioconductor-pathview</requirement> 3 <requirement type="package" version="1.18.0">bioconductor-pathview</requirement>
4 </requirements> 4 </requirements>
5 <command detect_errors="exit_code"><![CDATA[ 5 <command detect_errors="exit_code"><![CDATA[
6 Rscript $__tool_directory__/PathView.R 6 Rscript $__tool_directory__/PathView.R
9 #else 9 #else
10 --input="$input.file" 10 --input="$input.file"
11 --id_column="$input.ncol" 11 --id_column="$input.ncol"
12 --header="$input.header" 12 --header="$input.header"
13 #end if 13 #end if
14 #if $species.pathways.pathways_id == "pathways_ids" 14 #if $species.pathways.pathways_id != "pathways_file"
15 --pathways_id="$species.pathways.pids" 15 --pathways_id="$species.pathways.pids"
16 #else 16 #else
17 --pathways_id="$species.pathways.pids" 17 --pathways_input="$species.pathways.file"
18 --header2="$species.pathways.header2"
19 --pathway_col="$species.pathways.ncol2"
18 #end if 20 #end if
19 --id_type="$id_type" 21 --id_type="$id_type"
20 --native_kegg="$native" 22 --native_kegg="$native"
21 23
22 #if $input.ids=="file" 24 #if $input.ids=="file"
34 36
35 --species=${species.ref_file} 37 --species=${species.ref_file}
36 38
37 ]]></command> 39 ]]></command>
38 <inputs> 40 <inputs>
41 <param name="id_type" type="select" label="Select your identifiers type :">
42 <option value="uniprotID">Uniprot Accession number</option>
43 <option value="geneID">Entrez gene ID</option>
44 </param>
39 <conditional name="input" > 45 <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)" > 46 <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> 47 <option value="text">Copy/paste your identifiers</option>
42 <option value="file" selected="true">Input file containing your identifiers</option> 48 <option value="file" selected="true">Input file containing your identifiers</option>
43 </param> 49 </param>
53 </sanitizer> 59 </sanitizer>
54 </param> 60 </param>
55 </when> 61 </when>
56 <when value="file" > 62 <when value="file" >
57 <param name="file" type="data" format="txt,tabular" label="Select a file that contains your list of IDs" help="" /> 63 <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?" /> 64 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contains a 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' /> 65 <param name="ncol" type="text" value="c1" label="The column which contains your 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"> 66 <conditional name="expression_values">
61 <param name="nb_exp" type="select" label="How many expression values column in your file ?"> 67 <param name="nb_exp" type="select" label="How many expression values column in your file ?">
62 <option value="0" >0</option> 68 <option value="0" >0</option>
63 <option value="1" >1</option> 69 <option value="1" >1</option>
64 <option value="2" >2</option> 70 <option value="2" >2</option>
79 <param name="e3" type="text" value="" label="Third column number of your expression data"/> 85 <param name="e3" type="text" value="" label="Third column number of your expression data"/>
80 </when> 86 </when>
81 </conditional> 87 </conditional>
82 </when> 88 </when>
83 </conditional> 89 </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 <conditional name="species">
90 <param name="ref_file" type="select" label="Select species" > 91 <param name="ref_file" type="select" label="Select species" >
91 <option value="hsa">Human (hsa)</option> 92 <option value="hsa">Human (hsa)</option>
92 <option value="mmu">Mouse (mmu)</option> 93 <option value="mmu">Mouse (mmu)</option>
93 </param> 94 </param>
94 <when value="hsa"> 95 <when value="hsa">
95 <conditional name="pathways"> 96 <conditional name="pathways">
96 <param name="pathways_id" type="select" label="Provide your pathway(s)" help="Enter KEGG pathway name(s) or KEGG pathway id(s)"> 97 <param name="pathways_id" type="select" label="Provide your pathway(s)" help="Enter KEGG pathway name(s) or KEGG pathway id(s)">
97 <option value="pathways_names">KEGG pathway name(s)</option> 98 <option value="pathways_names">KEGG pathway name(s)</option>
98 <option value="pathways_ids">KEGG pathway id(s)</option> 99 <option value="pathways_ids">KEGG pathway id(s)</option>
100 <option value="pathways_file">KEGG pathway id(s) from file</option>
99 </param> 101 </param>
100 <when value="pathways_names"> 102 <when value="pathways_names">
101 <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 <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'>
102 <options from_data_table="hsa_pathways"> 104 <options from_data_table="hsa_pathways">
103 <filter type="sort_by" column="1"/> 105 <filter type="sort_by" column="1"/>
104 <validator type="no_options" message="No indexes are available for the selected input dataset"/> 106 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
105 </options> 107 </options>
106 </param> 108 </param>
107 </when> 109 </when>
108 <when value="pathways_ids"> 110 <when value="pathways_ids">
109 <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 <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" or "path:hsa00010"'>
110 <sanitizer invalid_char=''> 112 <sanitizer invalid_char=''>
111 <valid initial="string.printable"> 113 <valid initial="string.printable">
112 <remove value="&apos;"/> 114 <remove value="&apos;"/>
113 </valid> 115 </valid>
114 <mapping> 116 <mapping>
115 <add source="&#x20;" target=""/> 117 <add source="&#x20;" target=""/>
116 </mapping> 118 </mapping>
117 </sanitizer> 119 </sanitizer>
118 </param> 120 </param>
119 </when> 121 </when>
122 <when value="pathways_file">
123 <param name="file" type="data" format="txt,tabular" label="Select a file with a column of pathways id" help="Pathway id format : 'path:hsa00010' or 'hsa00010' or '00010'" />
124 <param name="header2" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contains a header?" />
125 <param name="ncol2" type="text" value="c1" label="The column which contains your pathways ids" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />
126 </when>
120 </conditional> 127 </conditional>
121 </when> 128 </when>
122 <when value="mmu"> 129 <when value="mmu">
123 <conditional name="pathways"> 130 <conditional name="pathways">
124 <param name="pathways_id" type="select" label="Provide your pathway(s)" help="Enter KEGG pathway name(s) or KEGG pathway id(s)"> 131 <param name="pathways_id" type="select" label="Provide your pathway(s)" help="Enter KEGG pathway name(s) or KEGG pathway id(s)">
125 <option value="pathways_names">KEGG pathway name(s)</option> 132 <option value="pathways_names">KEGG pathway name(s)</option>
126 <option value="pathways_ids">KEGG pathway id(s)</option> 133 <option value="pathways_ids">KEGG pathway id(s)</option>
134 <option value="pathways_file">KEGG pathway id(s) from file</option>
127 </param> 135 </param>
128 <when value="pathways_names"> 136 <when value="pathways_names">
129 <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'> 137 <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'>
130 <options from_data_table="mmu_pathways"> 138 <options from_data_table="mmu_pathways">
131 <filter type="sort_by" column="1"/> 139 <filter type="sort_by" column="1"/>
132 <validator type="no_options" message="No indexes are available for the selected input dataset"/> 140 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
133 </options> 141 </options>
134 </param> 142 </param>
135 </when> 143 </when>
136 <when value="pathways_ids"> 144 <when value="pathways_ids">
137 <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"'> 145 <param name="pids" type="text" label="Copy/paste your pathway id(s)" help='IDs must be separated by "," into the form field, for example: "path:mmu00053" or "mmu00053,mmu00340" or "00053"'>
138 <sanitizer invalid_char=''> 146 <sanitizer invalid_char=''>
139 <valid initial="string.printable"> 147 <valid initial="string.printable">
140 <remove value="&apos;"/> 148 <remove value="&apos;"/>
141 </valid> 149 </valid>
142 <mapping> 150 <mapping>
143 <add source="&#x20;" target=""/> 151 <add source="&#x20;" target=""/>
144 </mapping> 152 </mapping>
145 </sanitizer> 153 </sanitizer>
146 </param> 154 </param>
155 </when>
156 <when value="pathways_file">
157 <param name="file" type="data" format="txt,tabular" label="Select a file with a column of pathways id " help="Pathway id format : 'path:mmu00053' or 'mmu00053' or '00053'" />
158 <param name="header2" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
159 <param name="ncol2" type="text" value="c1" label="The column which contains your pathways ids" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />
147 </when> 160 </when>
148 </conditional> 161 </conditional>
149 </when> 162 </when>
150 </conditional> 163 </conditional>
151 <param name="native" type="select" label="Choose the output graph format"> 164 <param name="native" type="select" label="Choose the output graph format">
192 </test> 205 </test>
193 </tests> 206 </tests>
194 <help><![CDATA[ 207 <help><![CDATA[
195 This tool map a list of Uniprot Accession number or Entrez gene ID to KEGG pathway with pathview R package. 208 This tool map a list of Uniprot Accession number or Entrez gene ID to KEGG pathway with pathview R package.
196 209
210 Select your identifier type : UniprotAC or Entrez gene ID
211
197 Select an input file containing ids in a column, set header and column number or copy/paste your ids. 212 Select an input file containing ids in a column, set header and column number or copy/paste your ids.
198 213
199 Select your identifier type and a species of interest (for now only human available). 214 You can import 1 to 3 column(s) of expression values if you are importing ids from a file.
200 215
201 Select one or several pathways of interest from the dropdown menu or copy/paste KEGG pathway id(s) 216 Select a species of interest.
202 217
203 Select the graph format : KEGG or graphviz 218 Select one or several pathways of interest from the dropdown menu or copy/paste KEGG pathway id(s) or import it from a file.
219
220 Select the graph format : KEGG (jpg) or graphviz (pdf)
204 221
205 Uniprot accession number converted to Entrez geneID or Entrez geneID are mapped to each selected pathways. 222 Uniprot accession number converted to Entrez geneID or Entrez geneID are mapped to each selected pathways.
206 223
207 Output : One file (png or pdf) for each selected pathway. 224 Output : One file (png or pdf) for each selected pathway.
208 225