Mercurial > repos > proteore > proteore_venn_diagram

comparison venn_diagram.xml @ 7:98b7912a9ceb draft

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planemo upload commit 89cd1b5f2ca7b135abfe2d9ed18bf2478a59e099-dirty
author proteore
date Tue, 05 Mar 2019 11:25:31 -0500
parents d1fd04dcb13a
children bca31ac678f1
comparison
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6:d1fd04dcb13a 7:98b7912a9ceb
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="Jvenn" name="Venn diagram" version="2018.12.18"> 2 <tool id="Jvenn" name="Venn diagram" version="2019.02.21">
3 <description>[JVenn] 3 <description>[JVenn]
4 </description> 4 </description>
5 <command><![CDATA[ 5 <command><![CDATA[
6 python $__tool_directory__/venn_diagram.py 6 python $__tool_directory__/venn_diagram.py
7 7
8 #for $i, $s in enumerate($series) 8 #for $i, $s in enumerate($series)
9 --input 9 --input
10 #if $s.se.input == "file" 10 #if $s.se.input == "file"
11 "$s.se.file" "$s.se.name" "file" "$s.se.header" "$s.se.ncol" 11 "$s.se.file" "$s.name" "file" "$s.se.header" "$s.se.ncol"
12 #else 12 #else
13 "$s.se.list" "$s.se.name" "list" 13 "$s.se.list" "$s.name" "list"
14 #end if 14 #end if
15 #end for 15 #end for
16 --summary "$output_summary" 16 --summary "$output_summary"
17 ]]></command> 17 ]]></command>
18 <inputs> 18 <inputs>
19 <!-- Files --> 19 <!-- Files -->
20 <repeat name="series" title="List to compare" min="2" max="6" > 20 <repeat name="series" title="List to compare" min="2" max="6" >
21 <conditional name="se" > 21 <conditional name="se" >
22 <param type="select" name="input" label="Enter your list" help="Copy/paste or from a file (e.g. table)" > 22 <param type="select" name="input" label="Enter your list" help="Copy/paste or from a file (e.g. table)" >
23 <option value="list">Copy/paste list </option> 23 <option value="list">Copy/paste list </option>
24 <option value="file" selected="true">Input file containing your list</option> 24 <option value="file" selected="true">Input file containing your list</option>
25 </param> 25 </param>
26 <when value="file"> 26 <when value="file">
27 <param type="data" name="file" format="txt,tabular" label="Select your file" /> 27 <param type="data" name="file" format="txt,tabular" label="Select your file" />
28 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" /> 28 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
29 <param type="text" name="ncol" value="c1" label="Column number on which apply the comparison" help ='For example, fill in "c1" if you want to filter the first column' /> 29 <param type="text" name="ncol" value="c1" label="Column number on which apply the comparison" help ='For example, fill in "c1" if you want to filter the first column'>
30 <param type="text" name="name" value="" label="Enter the name of this list" help="This name will be displayed on venn diagram" /> 30 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
31 </when> 31 </param>
32 <when value="list"> 32 </when>
33 <param type="text" name="list" label="Copy/paste list" help='IDs must be separated by spaces into the form field, for example: P31946 P62258' > 33 <when value="list">
34 <sanitizer> 34 <param type="text" name="list" label="Copy/paste list" help='IDs must be separated by spaces into the form field, for example: P31946 P62258' >
35 <valid initial="string.printable"> 35 <sanitizer>
36 <remove value="&apos;"/> 36 <valid initial="string.printable">
37 </valid> 37 <remove value="&apos;"/>
38 <mapping initial="none"> 38 <remove value="/"/>
39 <add source="&apos;" target="__sq__"/> 39 </valid>
40 </mapping> 40 <mapping initial="none">
41 </sanitizer> 41 <add source="&apos;" target="__sq__"/>
42 </param> 42 </mapping>
43 <param type="text" name="name" value="" label="Enter the name of this list" help="This name will be displayed on venn diagram" /> 43 </sanitizer>
44 </when> 44 </param>
45 </conditional> 45 </when>
46 </conditional>
47 <param type="text" name="name" value="" label="Enter the name of this list" help="This name will be displayed on venn diagram">
48 <sanitizer>
49 <valid initial="string.printable">
50 <remove value="&apos;"/>
51 </valid>
52 <mapping initial="none">
53 <add source="&apos;" target="__sq__"/>
54 </mapping>
55 </sanitizer>
56 </param>
46 </repeat> 57 </repeat>
47 </inputs> 58 </inputs>
48 <outputs> 59 <outputs>
49 <data format="html" name="output_summary" label="Venn diagram" from_work_dir="venn_diagram_summary.html" /> 60 <data format="html" name="output_summary" label="Venn diagram" from_work_dir="venn_diagram_summary.html" />
50 <data format="tsv" name="output_text" label="Venn diagram text output" from_work_dir="venn_diagram_text_output.tsv" /> 61 <data format="tsv" name="output_text" label="Venn diagram text output" from_work_dir="venn_diagram_text_output.tsv" />