Binary file miRDeep2_quantifier.tar.gz has changed

--- a/quantifier.xml	Wed Feb 04 12:45:52 2015 -0500
+++ b/quantifier.xml	Wed Jul 12 14:41:05 2017 -0400
@@ -1,17 +1,16 @@
 <tool id="rbc_mirdeep2_quantifier" name="MiRDeep2 Quantifier" version="2.0.0">
-    <description>
-<![CDATA[
-fast quantitation of reads mapping to known miRBase precursors
-]]>
-    </description>
+    <description>fast quantitation of reads mapping to known miRBase precursors</description>
     <requirements>
-        <requirement type="package" version="2.0">mirdeep2_quantifier</requirement>
-        <requirement type="package" version="0.12.7">bowtie</requirement>
-        <requirement type="package" version="5.18.1">perl</requirement>
-        <requirement type="package" version="1.8.5">vienna_rna</requirement>
-        <requirement type="package" version="2.023">pdf_api2</requirement>
+        <requirement type="package" version="2.0.0.8">mirdeep2</requirement>
     </requirements>
-
+    <stdio>
+        <!-- Anything other than zero is an error -->
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+        <!-- In case the return code has not been set propery check stderr too -->
+        <regex match="Error:" />
+        <regex match="Exception:" />
+    </stdio>
     <command>
 <![CDATA[
     quantifier.pl 
@@ -53,14 +52,6 @@
     
 ]]>
     </command>
-    <stdio>
-        <!-- Anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-        <!-- In case the return code has not been set propery check stderr too -->
-        <regex match="Error:" />
-        <regex match="Exception:" />
-    </stdio>
     <inputs>
         <param name="reads" format="fasta" type="data" label="Collapsed deep sequencing reads" help="Reads in fasta format. (-r)"/>
         <param name="precursors" format="fasta" type="data" label="Precursor sequences" help="miRNA precursor sequences from miRBase. (-p)"/>
@@ -110,9 +101,9 @@
         <param name="wholePrecursAsMature" type="boolean" checked="false" truevalue="-w" falsevalue="" label="Consider the whole precursor as the 'mature sequence'" help="(-w)"/>
         <param name="discardReadMultiMap" type="boolean" checked="false" truevalue="-U" falsevalue="" label="Discard all read multimapper" help="(-U)"/>
         
-        <param name="upstreamNtides" type="integer" value="2" minvalue="0" label="Upstream nucleotides" help="Number of nucleotides upstream of the mature sequence to consider. (-e)"/>
-        <param name="downstreamNtides" type="integer" value="5" minvalue="0" label="Downstream nucleotides" help="Number of nucleotides downstream of the mature sequence to consider. (-f)"/>
-        <param name="allowedMismatches" type="integer" value="1" minvalue="0" label="Allowed mismatches" help="Number of allowed mismatches when mapping reads to precursors. (-g)"/>
+        <param name="upstreamNtides" type="integer" value="2" min="0" label="Upstream nucleotides" help="Number of nucleotides upstream of the mature sequence to consider. (-e)"/>
+        <param name="downstreamNtides" type="integer" value="5" min="0" label="Downstream nucleotides" help="Number of nucleotides downstream of the mature sequence to consider. (-f)"/>
+        <param name="allowedMismatches" type="integer" value="1" min="0" label="Allowed mismatches" help="Number of allowed mismatches when mapping reads to precursors. (-g)"/>
     </inputs>
     <outputs>
         <data name="miRNAsExpressed" format="tabular" from_work_dir="miRNAs_expressed_all_samples_galaxy.csv" label="output of ${tool.name} on ${on_string}"/>
@@ -130,13 +121,23 @@
     </tests>
     <help>
 <![CDATA[
-**What MiRDeep2 Quantifier does**
+
+**What it does**
 
 The module maps the deep sequencing reads to predefined miRNA precursors and determines by that the expression of the corresponding miRNAs. 
 First, the predefined mature miRNA sequences are mapped to the predefined precursors. Optionally, predefined star sequences can be mapped to the precursors too. 
 By that the mature and star sequence in the precursors are determined. Second, the deep sequencing reads are mapped to the precursors. 
 The number of reads falling into an interval 2nt upstream and 5nt downstream of the mature/star sequence is determined.
 ]]>
+
+**Input**
+
+A FASTA file with precursor sequences, a FASTA file with mature miRNA sequences, a FASTA file with deep sequencing reads and optionally a FASTA file with star sequences and the 3 letter code of the species of interest.
+
+**Output**
+
+A tab separated file with miRNA identifiers and its read count, a signature file, a html file that gives an overview of all miRNAs the input data and a pdfs that contains for each miRNA a pdf file showing its signature and structure.
+
     </help>
     <citations>
         <citation type="doi">10.1093/nar/gkr688</citation>

--- a/tool_dependencies.xml	Wed Feb 04 12:45:52 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,45 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="perl" version="5.18.1">
-        <repository changeset_revision="114b6af405fa" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="bowtie" version="0.12.7">
-        <repository changeset_revision="9f9f38617a98" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="vienna_rna" version="1.8.5">
-        <repository changeset_revision="6757330f89cd" name="package_vienna_rna_1_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="pdf_api2" version="2.023">
-        <repository changeset_revision="b9b7fadfdb69" name="package_perl_pdf_api2_2_023" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="mirdeep2_quantifier" version="2.0">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">https://raw.githubusercontent.com/bgruening/download_store/master/miRDeep2/miRDeep2-quantifier.tar.gz</action>
-                <action type="move_file">
-                    <source>quantifier.pl</source>
-                    <destination>$INSTALL_DIR</destination>
-                </action>
-                <action type="move_file">
-                    <source>make_html2.pl</source>
-                    <destination>$INSTALL_DIR</destination>
-                </action>
-                <action type="move_file">
-                    <source>convert_bowtie_output.pl</source>
-                    <destination>$INSTALL_DIR</destination>
-                </action>
-                <action type="set_environment">
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-
-The module maps the deep sequencing reads to predefined miRNA precursors and determines by that the expression of the corresponding miRNAs. 
-First, the predefined mature miRNA sequences are mapped to the predefined precursors. Optionally, predefined star sequences can be mapped to the precursors too. 
-By that the mature and star sequence in the precursors are determined. Second, the deep sequencing reads are mapped to the precursors. 
-The number of reads falling into an interval 2nt upstream and 5nt downstream of the mature/star sequence is determined.
-
-        </readme>
-    </package>
-</tool_dependency>