Mercurial > repos > proteore > proteore_pathview_mapping
changeset 11:6d5c0ff2b0bd draft
planemo upload commit 3cfb63ac3585431e7cdcc0a0bd11c33b946a6751-dirty
| author | proteore |
|---|---|
| date | Fri, 14 Sep 2018 09:52:28 -0400 |
| parents | e8d6e50f5d38 |
| children | 9fe4a861601b |
| files | Pathview.xml |
| diffstat | 1 files changed, 51 insertions(+), 51 deletions(-) [+] |
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--- a/Pathview.xml Thu Sep 13 03:25:04 2018 -0400 +++ b/Pathview.xml Fri Sep 14 09:52:28 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="Pathview" name="KEGG pathway mapping (pathview)" version="2018.09.13"> +<tool id="Pathview" name="KEGG pathway mapping (pathview)" version="2018.09.14"> <requirements> <requirement type="package" version="1.18.0">bioconductor-pathview</requirement> </requirements> @@ -38,56 +38,7 @@ ]]></command> <inputs> - <param name="id_type" type="select" label="Select your identifiers type :"> - <option value="uniprotID">Uniprot Accession number</option> - <option value="geneID">Entrez gene ID</option> - </param> - <conditional name="input" > - <param name="ids" type="select" label="Provide your identifiers" help="Copy/paste or ID list from a file (e.g. table)" > - <option value="text">Copy/paste your identifiers</option> - <option value="file" selected="true">Input file containing your identifiers</option> - </param> - <when value="text" > - <param name="txt" type="text" label="Copy/paste your identifiers" help='IDs must be separated by "," into the form field, for example: P31946,P62258' > - <sanitizer invalid_char=''> - <valid initial="string.printable"> - <remove value="'"/> - </valid> - <mapping initial="none"> - <add source="'" target="__sq__"/> - </mapping> - </sanitizer> - </param> - </when> - <when value="file" > - <param name="file" type="data" format="txt,tabular" label="Select a file that contains your list of IDs" help="" /> - <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contains a header?" /> - <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' /> - <conditional name="expression_values"> - <param name="nb_exp" type="select" label="How many expression values column in your file ?"> - <option value="0" >0</option> - <option value="1" >1</option> - <option value="2" >2</option> - <option value="3" >3</option> - </param> - <when value="0"> - </when> - <when value="1"> - <param name="e1" type="text" value="" label="First column number of your expression data" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on'/> - </when> - <when value="2"> - <param name="e1" type="text" value="" label="First column number of your expression data"/> - <param name="e2" type="text" value="" label="Second column number of your expression data"/> - </when> - <when value="3"> - <param name="e1" type="text" value="" label="First column number of your expression data"/> - <param name="e2" type="text" value="" label="Second column number of your expression data"/> - <param name="e3" type="text" value="" label="Third column number of your expression data"/> - </when> - </conditional> - </when> - </conditional> - <conditional name="species"> + <conditional name="species"> <param name="ref_file" type="select" label="Select species" > <option value="hsa">Human (hsa)</option> <option value="mmu">Mouse (mmu)</option> @@ -161,6 +112,55 @@ </conditional> </when> </conditional> + <param name="id_type" type="select" label="Select your identifiers type :"> + <option value="uniprotID">Uniprot Accession number</option> + <option value="geneID">Entrez gene ID</option> + </param> + <conditional name="input" > + <param name="ids" type="select" label="Provide your identifiers" help="Copy/paste or ID list from a file (e.g. table)" > + <option value="text">Copy/paste your identifiers</option> + <option value="file" selected="true">Input file containing your identifiers</option> + </param> + <when value="text" > + <param name="txt" type="text" label="Copy/paste your identifiers" help='IDs must be separated by "," into the form field, for example: P31946,P62258' > + <sanitizer invalid_char=''> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping initial="none"> + <add source="'" target="__sq__"/> + </mapping> + </sanitizer> + </param> + </when> + <when value="file" > + <param name="file" type="data" format="txt,tabular" label="Select a file that contains your list of IDs" help="" /> + <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contains a header?" /> + <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' /> + <conditional name="expression_values"> + <param name="nb_exp" type="select" label="How many expression values column in your file ?"> + <option value="0" >0</option> + <option value="1" >1</option> + <option value="2" >2</option> + <option value="3" >3</option> + </param> + <when value="0"> + </when> + <when value="1"> + <param name="e1" type="text" value="" label="First column number of your expression data" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on'/> + </when> + <when value="2"> + <param name="e1" type="text" value="" label="First column number of your expression data"/> + <param name="e2" type="text" value="" label="Second column number of your expression data"/> + </when> + <when value="3"> + <param name="e1" type="text" value="" label="First column number of your expression data"/> + <param name="e2" type="text" value="" label="Second column number of your expression data"/> + <param name="e3" type="text" value="" label="Third column number of your expression data"/> + </when> + </conditional> + </when> + </conditional> <param name="native" type="select" label="Choose the output graph format"> <option value="true">KEGG graph (.png)</option> <option value="false">Graphviz layout engine (.pdf)</option>