diff cmstat.xml @ 13:ffa96097e5b2 draft

Uploaded

--- a/cmstat.xml	Fri Nov 08 10:48:11 2013 -0500
+++ b/cmstat.xml	Fri Feb 13 03:12:04 2015 -0500
@@ -3,9 +3,10 @@
     <requirements>
         <requirement type="package">infernal</requirement>
         <requirement type="package" version="1.1">infernal</requirement>
-        <requirement type="package" version="8.21">gnu_coreutils</requirement>
+        <requirement type="package" version="8.22">gnu_coreutils</requirement>
     </requirements>
     <command>
+<![CDATA[
         ## a temp file is needed, because the standard tabular output from infernal is not usefull in Galaxy
         ## it will be converted to a tab delimited file and piped to Galaxy
         temp_tabular_output=\$(mktemp);
@@ -25,6 +26,7 @@
             ## 2. replace the first 18 spaces with tabs, 18th field is a free text field (can contain spaces)
             sed -e 's/#.*$//' -e '/^$/d' -e 's/ /\t/g' -e 's/\t/ /18g' \$temp_tabular_output > $outfile
 
+]]>
     </command>
         <inputs>
             <conditional name="cm_opts">
@@ -50,6 +52,7 @@
         <data format="tabular" name="outfile" label="cmstat on ${on_string}"/>
     </outputs>
     <help>
+<![CDATA[
 
 
 **What it does**
@@ -61,7 +64,7 @@
 -------------
 
 By default, cmstat prints general statistics of the model and the alignment it was built from, one line per model in a
-tabular format. 
+tabular format.
 
 The columns are:
 
@@ -91,14 +94,12 @@
 How do I cite Infernal?
 -----------------------
 
-The Infernal 1.0 paper (Nawrocki et al., 2009) is the best paper to reference. 
-If you’re writing for an enlightened (url-friendly) journal, you may want to cite the webpage
-http://infernal.janelia.org/ because it is kept up-to-date. We hope to publish a paper related to
-Infernal version 1.1 soon.
+The recommended citation for using Infernal 1.1 is E. P. Nawrocki and S. R. Eddy, Infernal 1.1: 100-fold faster RNA homology searches , Bioinformatics 29:2933-2935 (2013).
 
 **Galaxy Wrapper Author**::
 
     *  Bjoern Gruening, University of Freiburg
 
+]]>
     </help>
 </tool>