Mercurial > repos > proteore > proteore_kegg_pathways_coverage

changeset 2:179bfc3c7938 draft

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planemo upload commit 170560760f17fd1b77efe8bb95fedf3eb2433f0b-dirty
author proteore
date Thu, 22 Nov 2018 04:38:42 -0500
parents 7004924a3686
children e7b3609160c5
files compute_kegg_pathways.xml
diffstat 1 files changed, 11 insertions(+), 11 deletions(-) [+]
line wrap: on
line diff
--- a/compute_kegg_pathways.xml	Wed Nov 14 05:46:35 2018 -0500
+++ b/compute_kegg_pathways.xml	Thu Nov 22 04:38:42 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="compute_kegg_pathways" name="KEGG pathways" version="2018.11.14">
+<tool id="compute_kegg_pathways" name="KEGG pathways" version="2018.11.22">
     <description>identification and coverage</description>
     <requirements>
         <requirement type="package" version="1.18.0">bioconductor-keggrest</requirement>
@@ -22,12 +22,12 @@
     ]]></command>
     <inputs>
         <conditional name="input" >
-            <param name="ids" type="select" label="Enter your identifiers (KEGG genes ID)" help="Copy/paste or ID list from a file (e.g. table)" >
+            <param name="ids" type="select" label="Enter your list of 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 KEGG genes IDs</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 tab,space or carriage return into the form field, for example: hsa:3306 hsa:22948' >
+                <param name="txt" type="text" label="Copy/paste your identifiers" help='IDs must be separated by tab, space or carriage return into the form field, for example: hsa:3306 hsa:22948' >
                     <sanitizer invalid_char=''>
                         <valid initial="string.printable">
                             <remove value="&apos;"/>
@@ -39,14 +39,14 @@
                 </param>
             </when>
             <when value="file" >
-                <param name="file" type="data" format="txt,tabular,tsv" label="Select a file that contains your list of KEGG gene IDs" help="" />
-                <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
-                <param name="ncol" type="text" value="c1" label="The column number of KEGG genes 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' />
+                <param name="file" type="data" format="txt,tabular,tsv" label="Select a file that contains your list of identifiers" help="" />
+                <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain a header?" />
+                <param name="ncol" type="text" value="c1" label="The column number of your identifiers to map" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />
             </when>
         </conditional>
-        <param name="id_type" type="select" label="select your identifiers type :">
-            <option value="ncbi-geneid" selected="true">Entrez gene ID</option>
-            <option value="kegg-id">KEGG ID (genes)</option>
+        <param name="id_type" type="select" label="select your identifiers type :" >
+            <option value="ncbi-geneid" selected="true">Entrez genes ID</option>
+            <option value="kegg-id">KEGG genes ID</option>
             <option value="uniprot">Uniprot Accession number</option>
             
         </param>
@@ -76,7 +76,7 @@
     </tests>
     <help><![CDATA[
 
-This tool maps a list of KEGG gene IDs to KEGG pathway and return a list of KEGG pathways ranked by the percentage of coverage for each pathway; this is done by computing the number of KEGG genes IDs from your list divided by the total number of KEGG genes present in the considered species for each KEGG pathway. 
+This tool maps a list of identifiers to KEGG pathway and return a list of KEGG pathways ranked by the percentage of coverage for each pathway. This is done by computing the number of KEGG genes IDs from your list divided by the total number of KEGG genes present in the considered species for each KEGG pathway. 
 
 It allows you to directly identify the signaling pathways that are the most covered by your proteomics dataset.