# HG changeset patch
# User bgruening
# Date 1423815124 18000
# Node ID ffa96097e5b24a8b05121e23c160f2091f6e005f
# Parent  c17ed5a530d2e0b930ec4e1ccce32c3372f8aa9e
Uploaded

diff -r c17ed5a530d2 -r ffa96097e5b2 cmalign.xml
--- a/cmalign.xml	Fri Nov 08 10:48:11 2013 -0500
+++ b/cmalign.xml	Fri Feb 13 03:12:04 2015 -0500
@@ -4,18 +4,19 @@
     <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);
 
-        cmsearch 
+        cmsearch
             ## Infernal Options
             --cpu "\${GALAXY_SLOTS:-12}"
             -o /dev/null
-            --tformat $seqdb.ext ##target format: fasta, embl, genbank, ddbj, stockholm, pfam, a2m, afa, clustal, and phylip 
+            --tformat $seqdb.ext ##target format: fasta, embl, genbank, ddbj, stockholm, pfam, a2m, afa, clustal, and phylip
             $bottomonly
             $toponly
             $cyk
@@ -52,13 +53,14 @@
 
             ## sequence file
             $seqdb
-            2>&#38;1
+            2>&1
             ;
 
             ## 1. replace all lines starting # (comment lines)
             ## 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>
 
@@ -82,32 +84,32 @@
                 </when>
             </conditional>
 
-            <param name="g" truevalue="-g" falsevalue="" checked="False" type="boolean" 
+            <param name="g" truevalue="-g" falsevalue="" checked="False" type="boolean"
                 label="Turn on the glocal alignment algorithm" help="... global with respect to the query model and local with respect to the target database."/>
 
-            <param name="bottomonly" truevalue="--bottomonly" falsevalue="" checked="False" type="boolean" 
+            <param name="bottomonly" truevalue="--bottomonly" falsevalue="" checked="False" type="boolean"
                 label="Only search the bottom (Crick) strand of target sequences" help="in the sequence database"/>
-            <param name="toponly" truevalue="--toponly" falsevalue="" checked="False" type="boolean" 
+            <param name="toponly" truevalue="--toponly" falsevalue="" checked="False" type="boolean"
                 label="Only search the top (Watson) strand of target sequences" help="in the sequence database"/>
 
-            <param name="cyk" truevalue="--cyk" falsevalue="" checked="False" type="boolean" 
+            <param name="cyk" truevalue="--cyk" falsevalue="" checked="False" type="boolean"
                 label="Use the CYK algorithm, not Inside, to determine the final score of all hits" help=""/>
-            <param name="--acyk" truevalue="--cyk" falsevalue="" checked="False" type="boolean" 
+            <param name="--acyk" truevalue="--cyk" falsevalue="" checked="False" type="boolean"
                 label="Use the CYK algorithm to align hits" help="By default, the Durbin/Holmes optimal accuracy algorithm is used, which finds the alignment that maximizes the expected accuracy of all aligned residues."/>
 
-            <param name="notrunc" truevalue="--notrunc" falsevalue="" checked="False" type="boolean" 
+            <param name="notrunc" truevalue="--notrunc" falsevalue="" checked="False" type="boolean"
                 label="Turn off truncated hit detection" help=""/>
 
             <!-- accelleration pipeline -->
 
-            <param name="max" truevalue="--max" falsevalue="" checked="False" type="boolean" 
+            <param name="max" truevalue="--max" falsevalue="" checked="False" type="boolean"
                 label="Turn off all filters, and run non-banded Inside on every full-length target sequence" help="This
                 increases sensitivity somewhat, at an extremely large cost in speed."/>
 
-            <param name="nohmm" truevalue="--nohmm" falsevalue="" checked="False" type="boolean" 
+            <param name="nohmm" truevalue="--nohmm" falsevalue="" checked="False" type="boolean"
                 label="Turn off all HMM filter stages " help=""/>
 
-            <param name="mid" truevalue="--mid" falsevalue="" checked="False" type="boolean" 
+            <param name="mid" truevalue="--mid" falsevalue="" checked="False" type="boolean"
                 label="Turn off the HMM SSV and Viterbi filter stages" help=""/>
 
 
@@ -181,7 +183,7 @@
                 </when>
             </conditional>
 
-            <param name="A" truevalue="-A" falsevalue="" checked="False" type="boolean" 
+            <param name="A" truevalue="-A" falsevalue="" checked="False" type="boolean"
                 label="Save a multiple alignment of all significant hits" help="... those satisfying inclusion thresholds"/>
 
         </inputs>
@@ -194,6 +196,7 @@
 
     </outputs>
     <help>
+<![CDATA[
 
 
 **What it does**
@@ -345,8 +348,8 @@
 (7) mdl to (model coord): The end of the alignment of this hit with respect to the profile (CM or HMM), numbered 1..N for a profile of N consensus positions.
 (8) seq from (ali coord): The start of the alignment of this hit with respect to the sequence, numbered 1..L for a sequence of L residues.
 (9) seq to (ali coord): The end of the alignment of this hit with respect to the sequence, numbered 1..L for a sequence of L residues.
-(10) strand: The strand on which the hit occurs on the sequence. ’+’ if the hit is on the top (Watson) strand, ’-’ if the hit is on the bottom (Crick) strand. If on the top strand, the “seq from” value will be less than or equal to the “seq to” value, else it will be greater than or equal to it. 
-(11) trunc: Indicates if this is predicted to be a truncated CM hit or not. This will be “no” if it is a CM hit that is not predicted to be truncated by the end of the sequence, “5’ ” or “3’ ” if the hit is predicted to have one or more 5’ or 3’ residues missing due to a artificial truncation of the sequence, or “5’&amp;3”’ if the hit is predicted to have one or more 5’ residues missing and one or more 3’ residues missing. If the hit is an HMM hit, this will always be ’-’.
+(10) strand: The strand on which the hit occurs on the sequence. ’+’ if the hit is on the top (Watson) strand, ’-’ if the hit is on the bottom (Crick) strand. If on the top strand, the “seq from” value will be less than or equal to the “seq to” value, else it will be greater than or equal to it.
+(11) trunc: Indicates if this is predicted to be a truncated CM hit or not. This will be “no” if it is a CM hit that is not predicted to be truncated by the end of the sequence, “5’ ” or “3’ ” if the hit is predicted to have one or more 5’ or 3’ residues missing due to a artificial truncation of the sequence, or “5’&3”’ if the hit is predicted to have one or more 5’ residues missing and one or more 3’ residues missing. If the hit is an HMM hit, this will always be ’-’.
 (12) pass: Indicates what “pass” of the pipeline the hit was detected on. This is probably only useful for testing and debugging. Non-truncated hits are found on the first pass, truncated hits are found on successive passes.
 (13) gc: Fraction of G and C nucleotides in the hit.
 (14) bias: The biased-composition correction: the bit score difference contributed by the null3 model for CM hits, or the null2 model for HMM hits. High bias scores may be a red flag for a false positive. It is difficult to correct for all possible ways in which a nonrandom but nonhomologous biological sequences can appear to be similar, such as short-period tandem repeats, so there are cases where the bias correction is not strong enough (creating false positives).
@@ -364,14 +367,12 @@
 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>
diff -r c17ed5a530d2 -r ffa96097e5b2 cmbuild.xml
--- 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>
diff -r c17ed5a530d2 -r ffa96097e5b2 cmsearch.xml
--- a/cmsearch.xml	Fri Nov 08 10:48:11 2013 -0500
+++ b/cmsearch.xml	Fri Feb 13 03:12:04 2015 -0500
@@ -1,21 +1,22 @@
 <tool id="infernal_cmsearch" name="Search covariance model(s)" version="1.1.0.2">
     <description>against a sequence database (cmsearch)</description>
-    <parallelism method="multi" split_inputs="seqdb" split_mode="to_size" split_size="100" shared_inputs="" merge_outputs="outfile,multiple_alignment_output"></parallelism>
+    <parallelism method="multi" split_inputs="seqdb" split_mode="to_size" split_size="500" shared_inputs="" merge_outputs="outfile,multiple_alignment_output"></parallelism>
     <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);
 
-        cmsearch 
+        cmsearch
             ## Infernal Options
             --cpu "\${GALAXY_SLOTS:-12}"
             -o /dev/null
-            --tformat $seqdb.ext ##target format: fasta, embl, genbank, ddbj, stockholm, pfam, a2m, afa, clustal, and phylip 
+            --tformat $seqdb.ext ##target format: fasta, embl, genbank, ddbj, stockholm, pfam, a2m, afa, clustal, and phylip
             $bottomonly
             $toponly
             $cyk
@@ -52,13 +53,14 @@
 
             ## sequence file
             $seqdb
-            2>&#38;1
+            2>&1
             ;
 
             ## 1. replace all lines starting # (comment lines)
             ## 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 > $outfile
+            sed -e 's/#.*$//' -e '/^$/d' -e 's/\s\+/\t/g' -e 's/\t/ /18g' \$temp_tabular_output > $outfile
 
+]]>
     </command>
         <inputs>
 
@@ -83,32 +85,32 @@
                 </when>
             </conditional>
 
-            <param name="g" truevalue="-g" falsevalue="" checked="False" type="boolean" 
+            <param name="g" truevalue="-g" falsevalue="" checked="False" type="boolean"
                 label="Turn on the glocal alignment algorithm" help="... global with respect to the query model and local with respect to the target database."/>
 
-            <param name="bottomonly" truevalue="--bottomonly" falsevalue="" checked="False" type="boolean" 
+            <param name="bottomonly" truevalue="--bottomonly" falsevalue="" checked="False" type="boolean"
                 label="Only search the bottom (Crick) strand of target sequences" help="in the sequence database"/>
-            <param name="toponly" truevalue="--toponly" falsevalue="" checked="False" type="boolean" 
+            <param name="toponly" truevalue="--toponly" falsevalue="" checked="False" type="boolean"
                 label="Only search the top (Watson) strand of target sequences" help="in the sequence database"/>
 
-            <param name="cyk" truevalue="--cyk" falsevalue="" checked="False" type="boolean" 
+            <param name="cyk" truevalue="--cyk" falsevalue="" checked="False" type="boolean"
                 label="Use the CYK algorithm, not Inside, to determine the final score of all hits" help=""/>
-            <param name="--acyk" truevalue="--cyk" falsevalue="" checked="False" type="boolean" 
+            <param name="--acyk" truevalue="--cyk" falsevalue="" checked="False" type="boolean"
                 label="Use the CYK algorithm to align hits" help="By default, the Durbin/Holmes optimal accuracy algorithm is used, which finds the alignment that maximizes the expected accuracy of all aligned residues."/>
 
-            <param name="notrunc" truevalue="--notrunc" falsevalue="" checked="False" type="boolean" 
+            <param name="notrunc" truevalue="--notrunc" falsevalue="" checked="False" type="boolean"
                 label="Turn off truncated hit detection" help=""/>
 
             <!-- accelleration pipeline -->
 
-            <param name="max" truevalue="--max" falsevalue="" checked="False" type="boolean" 
+            <param name="max" truevalue="--max" falsevalue="" checked="False" type="boolean"
                 label="Turn off all filters, and run non-banded Inside on every full-length target sequence" help="This
                 increases sensitivity somewhat, at an extremely large cost in speed."/>
 
-            <param name="nohmm" truevalue="--nohmm" falsevalue="" checked="False" type="boolean" 
+            <param name="nohmm" truevalue="--nohmm" falsevalue="" checked="False" type="boolean"
                 label="Turn off all HMM filter stages " help=""/>
 
-            <param name="mid" truevalue="--mid" falsevalue="" checked="False" type="boolean" 
+            <param name="mid" truevalue="--mid" falsevalue="" checked="False" type="boolean"
                 label="Turn off the HMM SSV and Viterbi filter stages" help=""/>
 
 
@@ -131,7 +133,7 @@
                     <option value="--incE">Use E-value</option>
                     <option value="--incT">Use bit score</option>
                 </param>
-                <when />
+                <when value=""/>
                 <when value="--incE">
                     <param name="incE" type="float" value="0.01" size="5" label="Use E-value" help="of &lt;= X as the hit inclusion threshold.">
                         <sanitizer>
@@ -161,7 +163,7 @@
                     <option value="-E">Use E-value</option>
                     <option value="-T">Use bit score</option>
                 </param>
-                <when />
+                <when value=""/>
                 <when value="-E">
                     <param name="E" type="float" value="10.0" size="5" label="Use E-value" help="of &lt;= X as the hit reporting threshold. The default is 10.0, meaning that on average, about 10 false positives will be reported per query, so you can see the top of the noise and decide for yourself if it’s really noise.">
                         <sanitizer>
@@ -182,7 +184,7 @@
                 </when>
             </conditional>
 
-            <param name="A" truevalue="-A" falsevalue="" checked="False" type="boolean" 
+            <param name="A" truevalue="-A" falsevalue="" checked="False" type="boolean"
                 label="Save a multiple alignment of all significant hits" help="... those satisfying inclusion thresholds"/>
 
         </inputs>
@@ -195,13 +197,14 @@
 
     </outputs>
     <help>
+<![CDATA[
 
 
 **What it does**
 
 Infernal is used to search sequence databases for homologs of structural RNA sequences, and to make
 sequence- and structure-based RNA sequence alignments. Infernal needs a profile from a structurally
-annotated multiple sequence alignment of an RNA family with a position-specific scoring system for substitutions, 
+annotated multiple sequence alignment of an RNA family with a position-specific scoring system for substitutions,
 insertions, and deletions. Positions in the profile that are basepaired in the consensus secondary
 structure of the alignment are modeled as dependent on one another, allowing Infernal’s scoring system to
 consider the secondary structure, in addition to the primary sequence, of the family being modeled. Infernal
@@ -209,7 +212,7 @@
 grammar (SCFG) (Lari and Young, 1990).
 
 Compared to other alignment and database search tools based only on sequence comparison, Infernal
-aims to be significantly more accurate and more able to detect remote homologs because it models sequence 
+aims to be significantly more accurate and more able to detect remote homologs because it models sequence
 and structure.
 
 
@@ -225,8 +228,8 @@
 (7) mdl to (model coord): The end of the alignment of this hit with respect to the profile (CM or HMM), numbered 1..N for a profile of N consensus positions.
 (8) seq from (ali coord): The start of the alignment of this hit with respect to the sequence, numbered 1..L for a sequence of L residues.
 (9) seq to (ali coord): The end of the alignment of this hit with respect to the sequence, numbered 1..L for a sequence of L residues.
-(10) strand: The strand on which the hit occurs on the sequence. ’+’ if the hit is on the top (Watson) strand, ’-’ if the hit is on the bottom (Crick) strand. If on the top strand, the “seq from” value will be less than or equal to the “seq to” value, else it will be greater than or equal to it. 
-(11) trunc: Indicates if this is predicted to be a truncated CM hit or not. This will be “no” if it is a CM hit that is not predicted to be truncated by the end of the sequence, “5’ ” or “3’ ” if the hit is predicted to have one or more 5’ or 3’ residues missing due to a artificial truncation of the sequence, or “5’&amp;3”’ if the hit is predicted to have one or more 5’ residues missing and one or more 3’ residues missing. If the hit is an HMM hit, this will always be ’-’.
+(10) strand: The strand on which the hit occurs on the sequence. ’+’ if the hit is on the top (Watson) strand, ’-’ if the hit is on the bottom (Crick) strand. If on the top strand, the “seq from” value will be less than or equal to the “seq to” value, else it will be greater than or equal to it.
+(11) trunc: Indicates if this is predicted to be a truncated CM hit or not. This will be “no” if it is a CM hit that is not predicted to be truncated by the end of the sequence, “5’ ” or “3’ ” if the hit is predicted to have one or more 5’ or 3’ residues missing due to a artificial truncation of the sequence, or “5’&3”’ if the hit is predicted to have one or more 5’ residues missing and one or more 3’ residues missing. If the hit is an HMM hit, this will always be ’-’.
 (12) pass: Indicates what “pass” of the pipeline the hit was detected on. This is probably only useful for testing and debugging. Non-truncated hits are found on the first pass, truncated hits are found on successive passes.
 (13) gc: Fraction of G and C nucleotides in the hit.
 (14) bias: The biased-composition correction: the bit score difference contributed by the null3 model for CM hits, or the null2 model for HMM hits. High bias scores may be a red flag for a false positive. It is difficult to correct for all possible ways in which a nonrandom but nonhomologous biological sequences can appear to be similar, such as short-period tandem repeats, so there are cases where the bias correction is not strong enough (creating false positives).
@@ -244,14 +247,12 @@
 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>
diff -r c17ed5a530d2 -r ffa96097e5b2 cmstat.xml
--- 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>
diff -r c17ed5a530d2 -r ffa96097e5b2 readme.rst
--- a/readme.rst	Fri Nov 08 10:48:11 2013 -0500
+++ b/readme.rst	Fri Feb 13 03:12:04 2015 -0500
@@ -19,21 +19,16 @@
 .. _Infernal: http://infernal.janelia.org/
 
 
-E. P. Nawrocki, D. L. Kolbe, and S. R. Eddy, Infernal 1.0: Inference of RNA alignments , Bioinformatics 25:1335-1337 (2009), . 
+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).
 
 
 ============
 Installation
 ============
 
-Please download install Infernal and the tool wrappers with the Galaxy Tool Shed:
+Please install Infernal and the tool wrappers with the Galaxy Tool Shed from
 
-=============
-Miscellaneous
-=============
-
-Included in that repository is a CM datatype for INFERNAL 1.1 and TOCKHOLM .
-If you need that datatype in an additionl package, I can source it out as separate package. Please contact me in that case.
+http://toolshed.g2.bx.psu.edu/view/bgruening/infernal 
 
 
 =======
@@ -43,27 +38,30 @@
  - v1.1.0: Initial public release
 
 
+Bug Reports
+===========
+
+You can file an issue here https://github.com/bgruening/galaxytools/issues or ask
+us on the Galaxy development list http://lists.bx.psu.edu/listinfo/galaxy-dev
 
 
-===============================
-Wrapper Licence (MIT/BSD style)
-===============================
+Licence (MIT)
+=============
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
 
-Permission to use, copy, modify, and distribute this software and its
-documentation with or without modifications and for any purpose and
-without fee is hereby granted, provided that any copyright notices
-appear in all copies and that both those copyright notices and this
-permission notice appear in supporting documentation, and that the
-names of the contributors or copyright holders not be used in
-advertising or publicity pertaining to distribution of the software
-without specific prior permission.
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
 
-THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
-WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
-WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
-CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
-OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
-OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
-OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
-OR PERFORMANCE OF THIS SOFTWARE.
-
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
diff -r c17ed5a530d2 -r ffa96097e5b2 repository_dependencies.xml
--- a/repository_dependencies.xml	Fri Nov 08 10:48:11 2013 -0500
+++ b/repository_dependencies.xml	Fri Feb 13 03:12:04 2015 -0500
@@ -1,4 +1,4 @@
 <?xml version="1.0"?>
 <repositories description="This requires the datatype definitions for Multiple Sequence Alignment (MSA) formats (e.g. STOCKHOLM, SELEX, ClustalW).">
-    <repository changeset_revision="ba3eba35a79d" name="msa_datatypes" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="ba3eba35a79d" name="msa_datatypes" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
 </repositories>
diff -r c17ed5a530d2 -r ffa96097e5b2 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Nov 08 10:48:11 2013 -0500
+++ b/tool_dependencies.xml	Fri Feb 13 03:12:04 2015 -0500
@@ -1,9 +1,9 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="infernal" version="1.1">
-        <repository changeset_revision="429f1a518beb" name="package_infernal_1_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="429f1a518beb" name="package_infernal_1_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="gnu_coreutils" version="8.21">
-        <repository changeset_revision="83be2b421d3b" name="package_gnu_coreutils_8_21" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <package name="gnu_coreutils" version="8.22">
+        <repository changeset_revision="b638666e399d" name="package_gnu_coreutils_8_22" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>