--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rcorrector.xml	Thu Sep 13 07:00:00 2018 -0400
@@ -0,0 +1,136 @@
+<tool id="rcorrector" name="RNA-seq Rcorrector" version="1.0.3">
+	<description>a kmer-based error correction method for RNA-seq data</description>
+    <requirements>
+        <requirement type="package" version="1.0.3">rcorrector</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        #if $library.lib == "single":
+            ln -s '$library.input1' input_1.fq &&
+        #end if
+        #if $library.lib == "paired":
+            ln -s '$library.input1' input_1.fq && ln -s '$library.input2' input_2.fq &&
+        #end if
+        run_rcorrector.pl
+        #if $library.lib == "single":
+            -s input_1.fq
+        #end if
+        #if $library.lib == "paired":
+            -1 input_1.fq -2 input_2.fq
+        #end if
+        -k '$advanced.kmers' -t \${GALAXY_SLOTS:-4} -maxcorK '$advanced.maxcorK' -wk '$advanced.wk' -ek '$advanced.ek' -od output_file_directory 
+        
+        #if $library.lib == "paired":
+            #if $library.filter:
+                && python '$__tool_directory__/FilterUncorrectabledPEfastq.py'
+                -1 output_file_directory/input_1.cor.fq -2 output_file_directory/input_2.cor.fq -o fixed 2>&1 > rmunfixable.log && cat rmunfixable.log
+            #end if
+        #end if
+    ]]></command>
+    <inputs>
+        <conditional name="library">
+            <param name="lib" type="select" label="Is this library paired- or single-end?">
+                <option value="single">single</option>
+                <option value="paired" selected="True">paired</option>
+            </param>
+            <when value="single">
+                <param type="data" name="input1" label="FastQ file" format="fastq,fastqsanger" />
+            </when>
+            <when value="paired">
+                <param type="data" name="input1" label="FastQ file R1 (left)" format="fastq,fastqsanger" />
+                <param type="data" name="input2" label="FastQ file R2 (right)" format="fastq,fastqsanger" />
+                <param name="filter" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Filter uncorrectable reads" help="This will run FilterUncorrectabledPEfastq and remove uncorrectable reads."/>
+            </when>
+        </conditional> 
+        <conditional name="advanced">
+            <param name="adv" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Additional options"/>
+            <when value="TRUE">
+                <param name="kmers" label="kmer length" value="23" max="32" type="integer" help="(smaller 33, default: 23)"/>
+                <param name="maxcorK" label="max correction within k-bp window" value="4" type="integer" help="the maximum number of correction within k-bp window (default: 4)"/>
+                <param name="wk" label="estimate weak kmer count" value="0.95" type="float" help="the proportion of kmers that are used to estimate weak kmer count threshold, lower for more divergent genome (default: 0.95)"/>
+                <param name="ek" label="expected number of kmers" value="100000000" type="integer" help="expected_number_of_kmers: does not affect the correctness of program but affect the memory usage (default: 100000000)"/>
+            </when>
+            <when value="FALSE">
+                <param name="kmers" value="23" type="hidden"/>
+                <param name="maxcorK" value="4" type="hidden"/>
+                <param name="wk" value="0.95" type="hidden"/>
+                <param name="ek" value="100000000" type="hidden"/>
+            </when>
+        </conditional> 
+    </inputs>
+    <outputs>
+        <data name="output1" format="fastq" label="${tool.name} on ${on_string}" from_work_dir="output_file_directory/input_1.cor.fq">
+            <filter>library['lib'] == 'single'</filter>
+        </data> 
+        <data name="output2" format="fastq" label="${tool.name} on ${on_string}: cor R1" from_work_dir="output_file_directory/input_1.cor.fq">
+            <filter>library['lib'] == 'paired' and library['filter'] is False</filter>
+        </data> 
+        <data name="output3" format="fastq" label="${tool.name} on ${on_string}: cor R2" from_work_dir="output_file_directory/input_2.cor.fq"> 
+            <filter>library['lib'] == 'paired' and library['filter'] is False</filter>
+        </data> 
+        <data name="output4" format="fastq" label="${tool.name} on ${on_string}: fixed R1" from_work_dir="fixed_input_1.cor.fq">
+            <filter>library['lib'] == 'paired' and library['filter']</filter>
+        </data> 
+        <data name="output5" format="fastq" label="${tool.name} on ${on_string}: fixed R2" from_work_dir="fixed_input_2.cor.fq"> 
+            <filter>library['lib'] == 'paired' and library['filter']</filter>
+        </data> 
+    </outputs>
+	<tests>
+        <test>
+            <conditional name="library">
+                <param name="lib" value="paired"/>
+                <param name="input1" value="sample_read1.fq" ftype="fastq"/>
+                <param name="input2" value="sample_read2.fq" ftype="fastq"/>
+            </conditional>
+            <conditional name="advanced">
+                <param name="kmers" value="23"/>
+                <param name="maxcorK" value="4"/>
+                <param name="wk" value="0.95"/>
+                <param name="ek" value="100000000"/>
+            </conditional>
+            <output name="output2" file="sample_read1.cor.fq" ftype="fastq"/>
+            <output name="output3" file="sample_read2.cor.fq" ftype="fastq"/>
+        </test>
+        <test>
+            <conditional name="library">
+                <param name="lib" value="paired"/>
+                <param name="input1" value="sample_read1.fq" ftype="fastq"/>
+                <param name="input2" value="sample_read2.fq" ftype="fastq"/>
+                <param name="filter" value="TRUE"/>
+            </conditional>
+            <conditional name="advanced">
+                <param name="kmers" value="23"/>
+                <param name="maxcorK" value="4"/>
+                <param name="wk" value="0.95"/>
+                <param name="ek" value="100000000"/>
+            </conditional>
+            <output name="output2" file="fixed_sample_read1.cor.fq" compare="sim_size"/>
+            <output name="output3" file="fixed_sample_read2.cor.fq" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+What is Rcorrector?
+
+Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data.
+Rcorrector can also be applied to other type of sequencing data where the read coverage is non-uniform, such as single-cell sequencing.
+
+Uncorrectable paired-end reads can be removed using FilterUncorrectabledPEfastq.
+
+More informations, see citations.
+
+    ]]>
+    </help>
+    <citations>
+        <citation type="doi">10.1186/s13742-015-0089-y</citation>
+        <citation type="bibtex">
+            @misc{githubFilterUncorrectabledPEfastq,
+            author = {Adam H. Freedman},
+            year = {2016},
+            title = {FilterUncorrectabledPEfastq},
+            publisher = {GitHub},
+            journal = {GitHub repository},
+            url = {https://github.com/harvardinformatics/TranscriptomeAssemblyTools/blob/master/FilterUncorrectabledPEfastq.py}
+            }
+        </citation>
+    </citations>
+</tool>