diff cmbuild.xml @ 13:ffa96097e5b2 draft

Uploaded

--- a/cmbuild.xml	Fri Nov 08 10:48:11 2013 -0500
+++ b/cmbuild.xml	Fri Feb 13 03:12:04 2015 -0500
@@ -4,14 +4,15 @@
     <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>
-        cmbuild 
+<![CDATA[
+        cmbuild
             #if $is_summery_output:
                 -o $summary_outfile
             #end if
-            
+
             ## to many outputs, is that one really needed?
             ##-O $annotated_source_alignment_outfile
 
@@ -55,10 +56,11 @@
 
             $cmfile_outfile
             $alignment_infile
-            
+
+]]>
     </command>
         <inputs>
-            <!-- Stockholm or SELEX 
+            <!-- Stockholm or SELEX
             SELEX is defined in EMBOSS datatypes
             -->
             <param name="alignment_infile" type="data" format="stockholm,selex" label="Sequence database"/>
@@ -69,13 +71,13 @@
                     <option value="--hand">user defined (--hand)</option>
                 </param>
                 <when value="--fast">
-                    <param name="symfrac" type="float" value="0.5" size="5" 
+                    <param name="symfrac" type="float" value="0.5" size="5"
                         label="Define the residue fraction threshold necessary to define a consensus (--symfrac)" help=""/>
                 </when>
                 <when value="--hand"/>
             </conditional>
 
-            <param name="noss" truevalue="--noss" falsevalue="" checked="False" type="boolean" 
+            <param name="noss" truevalue="--noss" falsevalue="" checked="False" type="boolean"
                 label="Ignore the secondary structure annotation, if any, in your multiple alignment file (--noss)" help=""/>
 
             <conditional name="relative_weights_opts">
@@ -91,7 +93,7 @@
                 <when value="--wnone"/>
                 <when value="--wgiven"/>
                 <when value="--wblosum">
-                    <param name="wid" type="float" value="0.5" size="5" 
+                    <param name="wid" type="float" value="0.5" size="5"
                         label="Percent identity for clustering the alignment (--wid)" help=""/>
                 </when>
             </conditional>
@@ -104,16 +106,16 @@
                 </param>
                 <when value="--enone"/>
                 <when value="--eent">
-                    <param name="ere" type="float" value="0.59" size="5" 
+                    <param name="ere" type="float" value="0.59" size="5"
                         label="Set the target mean match state relative entropy (--ere)" help=""/>
 
-                    <param name="eminseq" type="integer" value="" size="5" 
+                    <param name="eminseq" type="integer" value="" size="5"
                         label="Define the minimum allowed effective sequence number (--eminseq)" help=""/>
 
-                    <param name="ehmmre" type="float" value="" size="5" 
+                    <param name="ehmmre" type="float" value="" size="5"
                         label="Set the target HMM mean match state relative entropy (--ehmmre)" help=""/>
 
-                    <param name="eset" type="integer" value="" size="5" 
+                    <param name="eset" type="integer" value="" size="5"
                         label="Set the effective sequence number for entropy weighting (--eset)" help=""/>
                 </when>
             </conditional>
@@ -138,10 +140,10 @@
                         </when>
                     </conditional>
 
-                    <param name="l" truevalue="-l" falsevalue="" checked="False" type="boolean" 
+                    <param name="l" truevalue="-l" falsevalue="" checked="False" type="boolean"
                         label="Turn on the local alignment algorithm" help="... which allows the alignment to span two or more subsequences if necessary"/>
 
-                    <param name="notrunc" truevalue="--notrunc" falsevalue="" checked="False" type="boolean" 
+                    <param name="notrunc" truevalue="--notrunc" falsevalue="" checked="False" type="boolean"
                         label="Turn off the truncated alignment algorithm" help=""/>
 
                     <param name="cyk" type="select" label="Options for refining the input alignment" help="">
@@ -149,14 +151,14 @@
                         <option value="--cyk">align with the CYK algorithm</option>
                     </param>
 
-                    <param name="refine_output" truevalue="" falsevalue="" checked="False" type="boolean" 
+                    <param name="refine_output" truevalue="" falsevalue="" checked="False" type="boolean"
                         label="Output the refined alignment file as it is used to build the covariance model" help=""/>
 
                 </when>
             </conditional>
 
 
-            <param name="is_summery_output" truevalue="" falsevalue="" checked="False" type="boolean" 
+            <param name="is_summery_output" truevalue="" falsevalue="" checked="False" type="boolean"
                 label="Output a summery file?" help=""/>
 
         </inputs>
@@ -179,6 +181,7 @@
 
     </outputs>
     <help>
+<![CDATA[
 
 
 **What it does**
@@ -261,14 +264,12 @@
 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>