--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cpm_tpm_rpk.xml	Wed Jul 25 13:05:17 2018 -0400
@@ -0,0 +1,161 @@
+<tool id="cpm_tpm_rpk" name="Generate CPM, TPM, RPK" version="0.1.0">
+    <description>from raw counts expression values</description>
+    <requirements>
+        <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" level="fatal" description="Tool exception" />
+    </stdio>
+    <command detect_errors="exit_code"><![CDATA[ 
+Rscript $__tool_directory__/cpm_tpm_rpk.R 
+-d $input 
+-t $option.type_transfo 
+-s $input_sep 
+-c $input_header 
+#if $option.type_transfo == "tpm":
+-f $option.gene_file 
+--gene_sep $option.gene_sep 
+--gene_header $option.gene_header
+#end if 
+#if $option.type_transfo == "rpk":
+-f $option.gene_file 
+--gene_sep $option.gene_sep 
+--gene_header $option.gene_header
+#end if
+-l $log
+#if $log == "FALSE":
+-o ${output}
+#end if
+#if $log == "TRUE":
+-o ${output_log}
+#end if
+]]></command>
+    <inputs>
+        <param name="input" type="data" format="txt" label="Raw counts of expression data"/>
+        <param name="input_sep" type="select" label="Input column separator">
+            <option value="tab" selected="true">Tabs</option>
+            <option value=",">Comma</option>
+            <option value="\ ">Whitespace</option>
+            <option value=".">Dots</option>
+                        <option value="_">Underscores</option>
+                        <option value="-">Dashes</option>
+        </param>
+        <param name="input_header" type="select" label="Consider first line of input file as header?">
+            <option value="TRUE" selected="true">Yes</option>
+            <option value="FALSE">No</option>
+        </param>
+                <conditional name="option">
+                    <param name="type_transfo" type="select" label="Type of transformation">
+                              <option value="cpm" selected="true">CPM</option>
+                               <option value="tpm">TPM</option>
+                               <option value="rpk">RPK</option>
+                       </param>
+            <when value="tpm">
+                <param name="gene_file" type="data" format="txt" label="Gene length file"/> 
+                <param name="gene_sep" type="select" label="Gene length column separator">
+                    <option value="tab" selected="true">Tabs</option>
+                           <option value=",">Commas</option>
+                    <option value="\ ">Whitespaces</option>
+                    <option value=".">Dots</option>
+                    <option value="_">Underscores</option>
+                    <option value="-">Dashes</option>
+                </param>
+                <param name="gene_header" type="select" label="Consider first line of gene length file as header ?">
+                    <option value="TRUE" selected="true">Yes</option>
+                    <option value="FALSE">No</option>
+                </param>
+            </when>
+                        <when value="rpk">
+                                <param name="gene_file" type="data" format="txt" label="Gene length file"/>
+                                <param name="gene_sep" type="select" label="Gene length column separator">
+                                        <option value="tab" selected="true">Tabs</option>
+                                        <option value=",">Commas</option>
+                                        <option value="\ ">Whitespaces</option>
+                                        <option value=".">Dots</option>
+                                        <option value="_">Underscores</option>
+                                        <option value="-">Dashes</option>
+                                </param>
+                                <param name="gene_header" type="select" label="Consider first line of gene length file as header ?">
+                                        <option value="TRUE" selected="true">Yes</option>
+                                        <option value="FALSE">No</option>
+                                </param>
+                        </when>
+            <when value="cpm">
+            </when>
+        </conditional>
+        <param name="log" type="select" label="Data should be log transformed ?">
+            <option value="FALSE" selected="true">No</option>
+            <option value="TRUE">Yes</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular" label="${option.type_transfo} from ${on_string}">
+            <filter>log == "FALSE"</filter>
+        </data>
+        <data name="output_log" format="tabular" label="log2(${option.type_transfo} +1) from ${on_string}">
+            <filter>log == "TRUE"</filter>
+                </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="counts.tab" ftype="tabular"/>
+            <param name="type_transfo" value="cpm"/>
+            <output name="output" file="cpm.tab" ftype="tabular"/>
+        </test>
+        <test>
+            <param name="input" value="counts.tab" ftype="tabular"/>
+            <param name="type_transfo" value="cpm"/>
+            <param name="log" value="TRUE"/>
+            <output name="output" file="logcpm.tab" ftype="tabular"/>
+        </test>
+        <test>
+            <param name="input" value="counts.tab" ftype="tabular"/>
+            <param name="type_transfo" value="tpm"/>
+            <param name="gene_file" value="gene_length.tab" ftype="tabular"/>
+            <param name="gene_header" value="TRUE"/>
+            <output name="output" file="tpm.tab" ftype="tabular"/>
+        </test>
+        <test>
+            <param name="input" value="counts.tab" ftype="tabular"/>
+            <param name="type_transfo" value="tpm"/>
+            <param name="gene_file" value="gene_length.tab" ftype="tabular"/>
+            <param name="gene_header" value="TRUE"/>
+            <param name="log" value="TRUE"/>
+            <output name="output" file="logtpm.tab" ftype="tabular"/>
+        </test>
+        <test>
+            <param name="input" value="counts.tab" ftype="tabular"/>
+            <param name="type_transfo" value="rpk"/>
+            <param name="gene_file" value="gene_length.tab" ftype="tabular"/>
+            <param name="gene_header" value="TRUE"/>
+            <output name="output" file="rpk.tab" ftype="tabular"/>
+        </test>
+        <test>
+            <param name="input" value="counts.tab" ftype="tabular"/>
+            <param name="type_transfo" value="rpk"/>
+            <param name="gene_file" value="gene_length.tab" ftype="tabular"/>
+            <param name="gene_header" value="TRUE"/>
+            <param name="log" value="TRUE"/>
+            <output name="output" file="logrpk.tab" ftype="tabular"/>
+        </test>
+    </tests>
+    <help>
+
+**What it does**
+
+And returns a table of normalized expression values.
+
+Normalization can be:
+
+- CPM (Counts Per Million) are obtained by dividing counts by the library counts sum and multiplying the results by a million.
+- RPK (Reads Per Kilobases) are obtained by dividing read counts by gene lengths (expressed in kilo-nucleotides).
+- TPM (Transcripts Per Million) are obtained by dividing RPK values by the sum of all RPK values in a sample and multiplying the results by 1 million.
+
+RPK and TPM require a two-column correspondance table gene_name - gene length where the length is specified in nucleotide. Both these metrics are relevant only for sequencing of full length RNAs.
+
+Note: do not comment you header line if you have header line in you tabular input (ie do not start the header line with a '#' character)
+
+Computed values may be log-transformed (log2([CPM or RPK or TPM]+1))
+
+    </help>
+</tool>