Mercurial > repos > proteore > proteore_reactome

comparison reactome_analysis.xml @ 4:878128362e33 draft

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planemo upload commit 34edf9c3db61650a03d5a0d548b9697a94ecde34-dirty
author proteore
date Tue, 03 Apr 2018 08:24:45 -0400
parents be06c14e543d
children 7fbd66f985b7
comparison
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3:be06c14e543d 4:878128362e33
19 <param name="input" type="select" label="Input identifiers (Uniprot accession number (e.g. P01023), Entrez gene ID (e.g.7157) or gene name (e.g. AQP7)" multiple="False" > 19 <param name="input" type="select" label="Input identifiers (Uniprot accession number (e.g. P01023), Entrez gene ID (e.g.7157) or gene name (e.g. AQP7)" multiple="False" >
20 <option value="text">Copy/paste your list of IDs </option> 20 <option value="text">Copy/paste your list of IDs </option>
21 <option value="file" selected="true">Input file containing your identifiers</option> 21 <option value="file" selected="true">Input file containing your identifiers</option>
22 </param> 22 </param>
23 <when value="text" > 23 <when value="text" >
24 <param name="list" type="text" label="Enter list of identifiers" /> 24 <param name="list" type="text" label="Enter list of identifiers" help="IDs must be separated by space into the form field, for example: P31946 P62258">
25 <sanitizer>
26 <valid initial="string.printable">
27 <remove value="&apos;"/>
28 </valid>
29 <mapping initial="none">
30 <add source="&apos;" target="__sq__"/>
31 </mapping>
32 </sanitizer>
33 </param>
25 </when> 34 </when>
26 <when value="file" > 35 <when value="file" >
27 <param name="file" type="data" format="txt, tabular" label="Input file containing your identifiers" help="Input file is a tab-delimited file containing different information of proteins, such as an output of MaxQuant software" /> 36 <param name="file" type="data" format="txt, tabular" label="Input file containing your identifiers" help="Input file is a tab-delimited file containing different information of proteins, such as an output of MaxQuant software" />
28 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" /> 37 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
29 <param type="text" name="ncol" value="c1" label="Please specify the column where you would like to apply the comparison" help ='For example, fill in "c1" if you want to filter the first column' /> 38 <param type="text" name="ncol" value="c1" label="Please specify the column where you would like to apply the comparison" help ='For example, fill in "c1" if you want to filter the first column' />
31 40
32 </conditional> 41 </conditional>
33 </inputs> 42 </inputs>
34 <outputs> 43 <outputs>
35 <data name="output" format="html" label="" /> 44 <data name="output" format="html" label="" />
36 <data name="trash" format="tabular" label="Invalid identifiers" /> 45 <data name="trash" format="tabular" hidden="true" label="Invalid id not send to reactome">
46 <discover_datasets pattern="(Reactome_Analysis_Tools_invalid_ID).txt" ext="txt" visible="false" assign_primary_output="false"/>
47 </data>
37 </outputs> 48 </outputs>
38 <tests> 49 <tests>
39 <test> 50 <test>
40 <conditional name="opt" > 51 <conditional name="opt" >
41 <param name="input" value="file" /> 52 <param name="input" value="file" />
42 <param name="file" value="ID_Converter_FKW_Lacombe_et_al_2017_OK.txt" /> 53 <param name="file" value="ID_Converter_FKW_Lacombe_et_al_2017_OK.txt" />
43 <param name="header" value="true" /> 54 <param name="header" value="true" />
44 <param name="ncol" value="c1" /> 55 <param name="ncol" value="c1" />
45 </conditional> 56 </conditional>
46 <output name="output" file="Reactome_Analysis_Tools.html" ftype="html" /> 57 <output name="output" file="Reactome_Analysis_Tools.html" ftype="html" />
47 <output name="trash" file="Reactome_Analysis_Tools_invalid_ID.txt" ftype="tab" /> 58 <!-- <output name="trash" file="Reactome_Analysis_Tools_invalid_ID.txt" ftype="tab" hidden="true" /> -->
48 </test> 59 </test>
49 </tests> 60 </tests>
50 <help><![CDATA[ 61 <help><![CDATA[
51 Reactome software provides service of creating diagram representing the relations between the biological processes. This tool allows linking to Reactome web service with pre-loaded data from a list of IDs, a file containing IDs or from a column of a complexed file. 62 Reactome software provides service of creating diagram representing the relations between the biological processes. This tool allows linking to Reactome web service with pre-loaded data from a list of IDs, a file containing IDs or from a column of a complexed file.
52 63