# HG changeset patch
# User crs4
# Date 1504198448 14400
# Node ID e6e6f5f9b9c45d3cebacc9dfef75755a74865f65
# Parent  407b894abb08cad75534623cc08d08a8238c979e
planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832

diff -r 407b894abb08 -r e6e6f5f9b9c4 edge_pro.xml
--- a/edge_pro.xml	Thu Nov 03 10:56:44 2016 -0400
+++ b/edge_pro.xml	Thu Aug 31 12:54:08 2017 -0400
@@ -1,110 +1,99 @@
-<tool id="edge_pro" name="EDGE-pro" version="1.0.1">
-  <description>Gene expression in Prokaryotes</description>
-  <requirements>
-    <requirement type="package" version="2.1.0">bowtie2</requirement>
-    <requirement type="package" version="1.3.1">edge-pro</requirement>
-  </requirements>
-  <command>
-    edge.pl -t \${GALAXY_SLOTS:-4} -o edge_out
-    ## Mandatory input parameters
-    -g $genome
-    -p $ptt
-    -r $rnt
+<tool id="edge_pro" name="EDGE-pro" version="1.0.2">
+    <description>Gene expression in Prokaryotes</description>
+    <requirements>
+        <requirement type="package" version="2.1.0">bowtie2</requirement>
+        <requirement type="package" version="1.3.1">edge-pro</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+edge.pl -t \${GALAXY_SLOTS:-4} -o edge_out
+## Mandatory input parameters
+-g '$genome'
+-p '$ptt'
+-r '$rnt'
 
-    #if $singlePaired.sPaired == "single"
-      -u $singlePaired.input1
-    #else if $singlePaired.sPaired == "paired"
-      -u $singlePaired.input1
-      -v $singlePaired.input2
-    #else if $singlePaired.sPaired == "pairedCollection"
-      -u $singlePaired.input.forward
-      -v $singlePaired.input.reverse
-    #end if
+#if $singlePaired.sPaired == "single"
+  -u '$singlePaired.input1'
+#else if $singlePaired.sPaired == "paired"
+  -u '$singlePaired.input1'
+  -v '$singlePaired.input2'
+#else if $singlePaired.sPaired == "pairedCollection"
+  -u '$singlePaired.input.forward'
+  -v '$singlePaired.input.reverse'
+#end if
+
+#if $singlePaired.sPaired in ("paired", "pairedCollection")
+  #if str($singlePaired.minInsertSize)
+    -m $singlePaired.minInsertSize
+  #end if
+  #if str($singlePaired.maxInsertSize)
+    -M $singlePaired.maxInsertSize
+  #end if
+#end if
 
-    #if $singlePaired.sPaired in ["paired", "pairedCollection"]
-      #if str($singlePaired.minInsertSize)
-        -m $singlePaired.minInsertSize
-      #end if
-      #if str($singlePaired.maxInsertSize)
-        -M $singlePaired.maxInsertSize
-      #end if
-    #end if
-    
-    ## Optional input parameters
-    #if $params.settingsType == "full"
-      #if str($params.window)
-        -w $params.window
-      #end if
-      #if str($params.utrSize)
-        -i $params.utrSize
-      #end if
-      #if str($params.similarity)
-        -x $params.similarity
-      #end if
-      #if str($params.readLength)
-        -l $params.readLength
-      #end if
-      #if str($params.minCoverage)
-        -c $params.minCoverage
-      #end if
-    #end if
-    &gt; $out_log 2&gt;&amp;1 ## need to redirect stderr because edge.pl calls bowtie2 and count which write some logging info there
-    &amp;&amp; cat edge_out.rpkm_* > $out_rpkm
-  </command>
-  <stdio>
-    <exit_code range="1:" level="fatal" />
-  </stdio>
-  <inputs>
-    <conditional name="singlePaired">
-      <param name="sPaired" type="select" label="Is this library mate-paired?">
-        <option value="single">Single-end</option>
-        <option value="paired">Paired-end</option>
-        <option value="pairedCollection">Paired-end collection</option>
-      </param>
-      <when value="single">
-        <param format="fastqsanger" name="input1" type="data" label="FASTQ file" help="FASTQ format with Sanger-scaled quality values (Galaxy fastqsanger datatype)"/>
-      </when>
-      <when value="paired">
-        <param format="fastqsanger" name="input1" type="data" label="Forward FASTQ file" help="FASTQ format with Sanger-scaled quality values (Galaxy fastqsanger datatype)" />
-        <param format="fastqsanger" name="input2" type="data" label="Reverse FASTQ file" help="FASTQ format with Sanger-scaled quality values (Galaxy fastqsanger datatype)" />
-        <param name="minInsertSize" type="integer" optional="true" min="0" value="0" label="Minimun insert size in paired-end library for Bowtie2 (-m)" />
-        <param name="maxInsertSize" type="integer" optional="true" min="1" value="500" label="Maximun insert size in paired-end library for Bowtie2 (-M)" />
-      </when>
-      <when value="pairedCollection">
-          <param format="fastqsanger" name="input" type="data_collection" collection_type="paired" label="FASTQ paired collection" help="FASTQ format with Sanger-scaled quality values (Galaxy fastqsanger datatype)" />
-          <param name="minInsertSize" type="integer" optional="true" min="0" value="0" label="Minimun insert size in paired-end library for Bowtie2 (-m)" />
-          <param name="maxInsertSize" type="integer" optional="true" min="1" value="500" label="Maximun insert size in paired-end library for Bowtie2 (-M)" />
-      </when>
-    </conditional>
-    
-    <param format="fasta" name="genome" type="data" label="Select the reference genome from your history (-g)" help="FASTA format" />
-    <param format="ptt" name="ptt" type="data" label="Coordinates of coding genes (PTT file)" help="PTT file with coordinates of coding genes (-p)" />
-    <param format="rnt" name="rnt" type="data" label="Coordinates of structural RNAs (RNT file)" help="RNT file with coordinates of structural RNA (-r)" />
-    
-    <conditional name="params">
-      <param name="settingsType" type="select" label="Parameter settings" help="For most needs, use default settings. If you want full control use Full Parameter List">
-        <option value="preSet">Use defaults</option>
-        <option value="full">Full parameter list</option>
-      </param>
-      <when value="preSet" />
-      <when value="full">
-        <param name="window" type="integer" optional="true" value="100" label="Window length for coverage distribution (-w)" help="Used to distribute the coverage between two overlapping genes. See help below for details" />
-        <param name="utrSize" type="integer" optional="true" value="40" label="Size of the untranslated region (-i)" help="Enter the size of the untranslated region between the initial transcription site and the start codon" />
-        <param name="similarity" type="float" optional="true" value="0.15" label="Percentage for similar coverage (-x)" help="Enter the percentage used to determine when two coverage values are considered similar. See help below for details" />
-        <param name="readLength" type="integer" optional="true" value="" label="Read length (-l)" help="If not specified, the first 1000 reads are used to approximate the read length" />
-        <param name="minCoverage" type="integer" optional="true" value="3" label="Minimum average coverage for expressed genes (-c)" help="Coverage less than specified is assumed to be noise and gene is considered to not be expressed" />
-      </when>
-    </conditional>
-  </inputs>
+## Optional input parameters
+#if $params.settingsType == "full"
+  #if str($params.window)
+    -w $params.window
+  #end if
+  #if str($params.utrSize)
+    -i $params.utrSize
+  #end if
+  #if str($params.similarity)
+    -x $params.similarity
+  #end if
+  #if str($params.readLength)
+    -l $params.readLength
+  #end if
+  #if str($params.minCoverage)
+    -c $params.minCoverage
+  #end if
+#end if
+> '$out_log' 2>&1 ## need to redirect stderr because edge.pl calls bowtie2 and count which write some logging info there
+&& cat edge_out.rpkm_* > '$out_rpkm'
+    ]]></command>
+    <inputs>
+        <conditional name="singlePaired">
+            <param name="sPaired" type="select" label="Is this library mate-paired?">
+                <option value="single">Single-end</option>
+                <option value="paired">Paired-end</option>
+                <option value="pairedCollection">Paired-end collection</option>
+            </param>
+            <when value="single">
+                <param name="input1" type="data" format="fastqsanger" label="FASTQ file" help="FASTQ format with Sanger-scaled quality values (Galaxy fastqsanger datatype)"/>
+            </when>
+            <when value="paired">
+                <param name="input1" type="data" format="fastqsanger" label="Forward FASTQ file" help="FASTQ format with Sanger-scaled quality values (Galaxy fastqsanger datatype)" />
+                <param name="input2" type="data" format="fastqsanger" label="Reverse FASTQ file" help="FASTQ format with Sanger-scaled quality values (Galaxy fastqsanger datatype)" />
+                <param name="minInsertSize" argument="-m" type="integer" optional="true" min="0" value="0" label="Minimun insert size in paired-end library for Bowtie2" />
+                <param name="maxInsertSize" argument="-M" type="integer" optional="true" min="1" value="500" label="Maximun insert size in paired-end library for Bowtie2" />
+            </when>
+            <when value="pairedCollection">
+                <param name="input" type="data_collection" collection_type="paired" format="fastqsanger" label="FASTQ paired collection" help="FASTQ format with Sanger-scaled quality values (Galaxy fastqsanger datatype)" />
+                <param name="minInsertSize" argument="-m" type="integer" optional="true" min="0" value="0" label="Minimun insert size in paired-end library for Bowtie2" />
+                <param name="maxInsertSize" argument="-M" type="integer" optional="true" min="1" value="500" label="Maximun insert size in paired-end library for Bowtie2" />
+            </when>
+        </conditional>
 
-  <outputs>
-    <data format="sam" name="out_aln" label="${tool.name} on ${on_string}: alignment" from_work_dir="edge_out.alignments" />
-    <data format="tabular" name="out_rpkm" label="${tool.name} on ${on_string}: rpkm"/>
-    <data format="txt" name="out_log" label="${tool.name} on ${on_string}: log"/>
-  </outputs>
+        <param name="genome" argument="-g" type="data" format="fasta" label="Select the reference genome from your history" help="In FASTA format" />
+        <param name="ptt" argument="-p" type="data" format="ptt" label="Coordinates of coding genes (PTT file)" help="PTT file with coordinates of coding genes" />
+        <param name="rnt" argument="-r" type="data" format="rnt" label="Coordinates of structural RNAs (RNT file)" help="RNT file with coordinates of structural RNA" />
 
-  <help>
+        <section name="params" title="Advanced parameters" expanded="false">
+            <param name="window" argument="-w" type="integer" optional="true" value="100" label="Window length for coverage distribution" help="Used to distribute the coverage between two overlapping genes. See help below for details" />
+            <param name="utrSize" argument="-i" type="integer" optional="true" value="40" label="Size of the untranslated region" help="Enter the size of the untranslated region between the initial transcription site and the start codon" />
+            <param name="similarity" argument="-x" type="float" optional="true" value="0.15" label="Percentage for similar coverage" help="Enter the percentage used to determine when two coverage values are considered similar. See help below for details" />
+            <param name="readLength" argument="-l" type="integer" optional="true" value="" label="Read length" help="If not specified, the first 1000 reads are used to approximate the read length" />
+            <param name="minCoverage" argument="-c" type="integer" optional="true" value="3" label="Minimum average coverage for expressed genes" help="Coverage less than specified is assumed to be noise and gene is considered to not be expressed" />
+        </section>
+    </inputs>
 
+    <outputs>
+        <data name="out_aln" format="sam" label="${tool.name} on ${on_string}: alignment" from_work_dir="edge_out.alignments" />
+        <data name="out_rpkm" format="tabular" label="${tool.name} on ${on_string}: rpkm"/>
+        <data name="out_log" format="txt" label="${tool.name} on ${on_string}: log"/>
+    </outputs>
+
+    <help><![CDATA[
 **What it does**
 
 `EDGE-pro`_, Estimated Degree of Gene Expression in PROkaryots is an efficient software system to estimate gene expression levels in prokaryotic genomes from RNA-seq data. EDGE-pro uses Bowtie2 for alignment and then estimates expression directly from the alignment results.
@@ -117,7 +106,7 @@
 Input files with gene coordinates in PTT and RNT format can be retrieved with the Get EDGE-pro Files tool available in Galaxy, or downloaded from the `NCBI ftp repository`_.
 This tool accepts files in Sanger FASTQ format (Galaxy *fastqsanger* datatype). Use the FASTQ Groomer tool to prepare your files.
 
-.. _NCBI ftp repository: ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/
+.. _NCBI ftp repository: ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/bacteria/
 
 .. class:: warningmark
 
@@ -128,20 +117,14 @@
 This Galaxy tool is Copyright © 2012-2014 `CRS4 Srl.`_ and is released under the `MIT license`_.
 
 .. _CRS4 Srl.: http://www.crs4.it/
-.. _MIT license: http://opensource.org/licenses/MIT
+.. _MIT license: https://opensource.org/licenses/MIT
 
 You can use this tool only if you agree to the license terms of: `EDGE-pro`_.
 
 .. _EDGE-pro: http://ccb.jhu.edu/software/EDGE-pro/
-
-If you use this tool, please cite:
-
-- |Cuccuru2014|_
-- |Magoc2013|_.
-
-.. |Cuccuru2014| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2014) Orione, a web-based framework for NGS analysis in microbiology. *Bioinformatics* 30(13), 1928-1929
-.. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/30/13/1928
-.. |Magoc2013| replace:: Magoc, T., Wood, D., Salzberg, S. L. (2013) EDGE-pro: Estimated Degree of Gene Expression in Prokaryotic Genomes. *Evol. Bioinform.* 2013:9, 127-136
-.. _Magoc2013: http://www.la-press.com/edge-pro-estimated-degree-of-gene-expression-in-prokaryotic-genomes-article-a3586
-  </help>
+    ]]></help>
+    <citations>
+        <citation type="doi">10.4137/EBO.S11250</citation>
+        <citation type="doi">10.1093/bioinformatics/btu135</citation>
+    </citations>
 </tool>