Mercurial > repos > proteore > proteore_venn_diagram
changeset 7:98b7912a9ceb draft
planemo upload commit 89cd1b5f2ca7b135abfe2d9ed18bf2478a59e099-dirty
| author | proteore |
|---|---|
| date | Tue, 05 Mar 2019 11:25:31 -0500 |
| parents | d1fd04dcb13a |
| children | bca31ac678f1 |
| files | venn_diagram.xml |
| diffstat | 1 files changed, 38 insertions(+), 27 deletions(-) [+] |
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--- a/venn_diagram.xml Tue Dec 18 10:06:31 2018 -0500 +++ b/venn_diagram.xml Tue Mar 05 11:25:31 2019 -0500 @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="Jvenn" name="Venn diagram" version="2018.12.18"> +<tool id="Jvenn" name="Venn diagram" version="2019.02.21"> <description>[JVenn] </description> <command><![CDATA[ @@ -8,9 +8,9 @@ #for $i, $s in enumerate($series) --input #if $s.se.input == "file" - "$s.se.file" "$s.se.name" "file" "$s.se.header" "$s.se.ncol" + "$s.se.file" "$s.name" "file" "$s.se.header" "$s.se.ncol" #else - "$s.se.list" "$s.se.name" "list" + "$s.se.list" "$s.name" "list" #end if #end for --summary "$output_summary" @@ -19,30 +19,41 @@ <!-- Files --> <repeat name="series" title="List to compare" min="2" max="6" > <conditional name="se" > - <param type="select" name="input" label="Enter your list" help="Copy/paste or from a file (e.g. table)" > - <option value="list">Copy/paste list </option> - <option value="file" selected="true">Input file containing your list</option> - </param> - <when value="file"> - <param type="data" name="file" format="txt,tabular" label="Select your file" /> - <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" /> - <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' /> - <param type="text" name="name" value="" label="Enter the name of this list" help="This name will be displayed on venn diagram" /> - </when> - <when value="list"> - <param type="text" name="list" label="Copy/paste list" help='IDs must be separated by spaces into the form field, for example: P31946 P62258' > - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - </valid> - <mapping initial="none"> - <add source="'" target="__sq__"/> - </mapping> - </sanitizer> - </param> - <param type="text" name="name" value="" label="Enter the name of this list" help="This name will be displayed on venn diagram" /> - </when> - </conditional> + <param type="select" name="input" label="Enter your list" help="Copy/paste or from a file (e.g. table)" > + <option value="list">Copy/paste list </option> + <option value="file" selected="true">Input file containing your list</option> + </param> + <when value="file"> + <param type="data" name="file" format="txt,tabular" label="Select your file" /> + <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" /> + <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'> + <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator> + </param> + </when> + <when value="list"> + <param type="text" name="list" label="Copy/paste list" help='IDs must be separated by spaces into the form field, for example: P31946 P62258' > + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="/"/> + </valid> + <mapping initial="none"> + <add source="'" target="__sq__"/> + </mapping> + </sanitizer> + </param> + </when> + </conditional> + <param type="text" name="name" value="" label="Enter the name of this list" help="This name will be displayed on venn diagram"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping initial="none"> + <add source="'" target="__sq__"/> + </mapping> + </sanitizer> + </param> </repeat> </inputs> <outputs>