diff metaquantome_sample.xml @ 8:a1df90e6e7d4 draft default tip

planemo upload

--- a/metaquantome_sample.xml	Thu Feb 07 19:42:40 2019 -0500
+++ b/metaquantome_sample.xml	Fri Feb 08 10:36:53 2019 -0500
@@ -1,6 +1,6 @@
 <?xml version='1.0' encoding='utf-8'?>
 <tool id="sample" name="metaQuantome: create samples file" version="@VERSION@.3">
-    <description></description>
+    <description> by specifying the experiment's groups and associated column names</description>
     <macros>
         <token name="@VERSION@">1.1.2</token>
     </macros>
@@ -77,12 +77,11 @@
     </tests>
     <help><![CDATA[
 metaQuantome: create samples file
-===================
+=================================
 
-The *create samples file* module is used to generate the *samples file* input file for the metaQuantome workflow. This input file is used to specify which column names are affilated with which experimental groups. 
+The *create samples file* module is used to generate the *samples file* input file for the metaQuantome workflow. This input file is used to specify the column names used for each experimental group. These column names are referenced when handling the input data and performing statistical analysis. An example file is shown below.
 
 *Create samples file*
-
     =====  ====================
     group  colnames   
     =====  ====================
@@ -95,15 +94,16 @@
 
 1. **Specify Samples** You may specify the samples by providing the group names (ex: NS *no sucrose* and WS *with sucrose*) and each of their affilated column names (ex: X737WS, X737NS, etc...) from the input files (e.g., peptide intensity *int.tab*). 
 
-2. **Select samples from existing file's header** Alternatively, you can indicate the column indices of the selected headers for each experimental group (ex: columns 1, 3, and 5 for NS; columns 2, 4, and 6 for WS). You need to specify which file from the history you are referencing. An example is shown below.
+
+2. **Select samples from existing file's header** Alternatively, you can indicate the column indices of the selected headers for each experimental group (ex: columns 3, 5, and 7 for NS; columns 2, 4, and 6 for WS). You need to specify which file from the history you are referencing. An example is shown below.
 
-*Example int.tab file*
-============ ====== ======  ======  ======  ======  ====== 
-peptide      X737WS X737NS  X852WS  X852NS  X867WS  X867NS
-============ ====== ======  ======  ======  ======  ======
-LPGQQHGTPSAK 1      2       3       4       5       6
-ELPGLAALTDK  7      8       9       10      11      12
-============ ====== ======  ======  ======  ======  ======
+*int.tab file*
+    ============ ====== ======  ======  ======  ======  ====== 
+    peptide      X737WS X737NS  X852WS  X852NS  X867WS  X867NS
+    ============ ====== ======  ======  ======  ======  ======
+    LPGQQHGTPSAK 1      2       3       4       5       6
+    ELPGLAALTDK  7      8       9       10      11      12
+    ============ ====== ======  ======  ======  ======  ======
 
 
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