# HG changeset patch
# User bgruening
# Date 1509553862 14400
# Node ID c580aaece0107e33fc7cd966a08d39fc64efb236

planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a

diff -r 000000000000 -r c580aaece010 coprarna.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/coprarna.xml	Wed Nov 01 12:31:02 2017 -0400
@@ -0,0 +1,80 @@
+<tool id="coprarna" name="coprarna" version="2.1.1">
+    <description>
+        Phylogenetic target prediction for prokaryotic trans-acting small RNAs 
+    </description>
+    <requirements>
+        <requirement type="package" version="2.1.1">coprarna</requirement>
+    </requirements>
+    <command detect_errors="aggressive"><![CDATA[
+  CopraRNA2.pl
+  --srnaseq '$srnaseq'
+  --region '$region'
+  --ntup $ntup 
+  --ntdown $ntdown
+  --rcsize $rcsize 
+  --cores "\${GALAXY_SLOTS:-4}"
+  --winsize $winsize 
+  --maxbpdist $maxbpdist
+  --cons $cons
+  --topcount $topcount
+  $cop1
+  $nooi
+  --enrich $enrich
+  --root $root
+    ]]>
+    </command>
+    <inputs>
+        <param name="srnaseq" type="data" format="fasta" label="FASTA file with small RNA sequences"/>
+        <param name="region" type="select" label="Region to scan in whole genome target prediction." help="'5utr' for start codon, '3utr' for stop codon, 'cds' for entire transcript">
+            <option value="5utr" selected="true">5utr</option>
+            <option value="3utr">3utr</option>
+            <option value="cds">cds</option>
+        </param>
+        <param name="ntup" type="integer" value="200" label="Nucleotides upstream" help="Number of nucleotides upstream of 'region' to parse for targeting (def:200)" optional="true"/>
+        <param name="ntdown" type="integer" value="100" label="Nucleotides downstream" help="Number of nucleotides downstream of '--region' to parse for targeting (def:100)" optional="true"/>
+        <param name="rcsize" type="float" value="0.5" min="0" max="1" label="Fraction of putative target homologs" help="Minimum amount (%) of putative target homologs that need to be available for a target cluster to be considered in the CopraRNA1 part (see --cop1) of the prediction (def:0.5)"/>
+        <param name="winsize" type="integer" value="150" label="Window size" help="IntaRNA target (--tAccW) window size parameter (def:150)" optional="true"/>
+        <param name="maxbpdist" type="integer" value="100" label="Maximum basepair distance" help="IntaRNA target (--tAccL) maximum base pair distance parameter (def:100)" optional="true"/>
+        <param name="cons" type="select" label="Controls consensus prediction" help="'0' for off, '1' for organism of interest based consensus, '2' for overall consensus based prediction">
+            <option value="0" selected="true">Off</option>
+            <option value="1">Organism of interest based consensus</option>
+            <option value="2">Overall consensus based prediction</option>
+        </param>
+        <param name="topcount" type="integer" value="200" label="Top predictions" help="Specifies the number of top predictions to return and use for the extended regions plots (def:200)" optional="true"/>
+        <param name="cop1" truevalue="--cop1" falsevalue="" checked="False" type="boolean" label="CopraRNA1 prediction" help="Switch for CopraRNA1 prediction (def:off)"/>
+        <param name="nooi" truevalue="--nooi" falsevalue="" checked="False" type="boolean" label="No focus on the organism of interest" help="If set then the CopraRNA2 prediction mode is set not to focus on the organism of interest (def:off)"/>
+        <param name="enrich" type="integer" value="0" label="DAVID-WS functional enrichment" help="If set DAVID-WS functional enrichment is calculated with given number of top predictions (def:off)" optional="true"/>
+        <param name="root" type="float" value="1" label="Root function" help="Specifies root function to apply to the weights (def:1)"/>
+    </inputs>
+    <outputs>
+        <data format="csv" name="result" from_work_dir="./CopraRNA_result.csv" label="CopraRNA result csv"/>
+        <data format="pdf" name="conservationheatmap" from_work_dir="./sRNA_conservation_heatmap.pdf" label="sRNA conservation heatmap"/>
+        <data format="pdf" name="functionheatmap" from_work_dir="./Enrichment/enriched_heatmap_big.pdf" label="Functional enrichment heatmap"/>
+    </outputs>
+    <tests>
+        <test expect_exit_code="1" expect_failure="true">
+            <param name="srnaseq" value="copra.fa"/>
+            <assert_stderr>
+                <has_text text="Error: The input file" />
+            </assert_stderr>
+        </test>
+    </tests>
+    <help>   
+<![CDATA[
+             
+**What it does**
+
+Phylogenetic target prediction for prokaryotic trans-acting small RNAs
+
+CopraRNA is a tool for sRNA target prediction. It computes whole genome target predictions by combination of distinct whole genome IntaRNA predictions. As input CopraRNA requires at least 3 homologous sRNA sequences from 3 distinct organisms in FASTA format. Furthermore, each organisms' genome has to be part of the NCBI Reference Sequence (RefSeq) database (i.e. it should have exactly this NZ_* or this NC_XXXXXX format where * stands for any character and X stands for a digit between 0 and 9). Depending on sequence length (target and sRNA), amount of input organisms and genome sizes, CopraRNA can take up to 24h or longer to compute. In most cases it is significantly faster.
+
+**Output**
+List of conserved identified interactions
+
+    ]]>
+
+    </help>
+    <citations>
+        <citation type="doi">10.1093/nar/gku359</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r c580aaece010 test-data/copra.fa