--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lfq_protein_quant.xml	Tue Oct 02 16:30:33 2018 -0400
@@ -0,0 +1,98 @@
+<tool id="lfq_protein_quant" name="Label free protein" version="1.0">
+    <description>
+        summarisation and quantitation
+    </description>
+    <requirements>
+        <requirement type="package" version="2.2.0">bioconductor-msnbase</requirement>
+        <requirement type="package" version="2.12.0">bioconductor-mzr</requirement>
+        <requirement type="package" version="1.2.1">r-tidyverse</requirement>
+        <requirement type="package" version="1.1_18_1">r-lme4</requirement>
+        <requirement type="package" version="0.1.0">r-furrr</requirement>
+        <requirement type="package" version="0.7.5">r-msqrob</requirement>
+    </requirements>
+    <command detect_errors="exit_code">
+    <![CDATA[
+        ln -s '${moff_file}' moff.tsv &&
+        ln -s '${meta_file}' meta.tsv &&
+        Rscript '$__tool_directory__/quantitation.r'
+            moff.tsv
+            meta.tsv
+            $only_summarisation
+            \${GALAXY_SLOTS:-4}
+    ]]>
+    </command>
+    <inputs>
+        <param name="moff_file" type="data" format="tabular"
+               label="Peptide summary output from moFF or other peptide quantitation tools" />
+        <param name="meta_file" type="data" format="tabular" label="Metadata with sample names and condition" />
+        <param name="only_summarisation" type="boolean" truevalue="1" falsevalue="0"
+            label="Only summarisiation" help="This option will deactivate the quantifiation of data." />
+
+    </inputs>
+    <outputs>
+        <data format="tabular" name="quant" from_work_dir="quantitation.tsv" label="${tool.name} on ${on_string}: quantification">
+            <filter>not only_summarisation</filter>
+        </data>
+        <data format="tabular" name="summary" from_work_dir="summarised_proteins.tsv" label="${tool.name} on ${on_string}: summary"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="moff_file" value="moff.tab"/>
+            <param name="meta_file" value="meta.tab"/>
+            <param name="only_summerisation" value="true"/>
+            <output name="quant" file="quantitation.tsv" />
+            <output name="summary" file="summarised_proteins.tsv" />
+        </test>
+    </tests>
+    <help>
+        <![CDATA[
+**What it does**
+
+Protein summarisation and label free quantitation.
+
+----
+
+    **Inputs** 
+
+    - Quantification input: Tabular file with the summary output from moFF or in case other tools were used for peptide quantitation with the following columns: 'peptides' containing the amino acid sequence; 'prot' with the Uniprot Accession and then one column per sample with the quantitation values.
+
+            ::
+
+                  peptides     prot       sample1    sample2
+                  AAABDEK      B9DM54     1809446    563862
+                  TELATASDR    Q9CFE8     294282     457023
+                  AMGLATK      P85660     194023     428277
+                    ...
+                    ...
+
+
+    - Metadata input: Separate columns with sample names, condition and optionally also lab and machine. Sample names must match exactly the sample names from the peptide quantitation columns in the previous tabular file.
+
+
+            ::
+
+                  sample     condition 
+                  sample1    healthy
+                  sample2    disease
+                    ...
+                    ...
+
+
+    **Options** 
+
+    - Summarisation only: Summarisation is done through robust regression to take also the peptide effect into account. In case only sample column is provided median protein intensity is calculated.
+    - Summarisation and quantification: Relative quantification is performed according to the information provided in the metadata file. 
+
+
+    **Outputs** 
+
+    - Summarised protein output: Uniprot accession and quantitation values per sample and protein
+    - Quantification output: Uniprot accession, comparison between conditions, fold change, p-value, q-value
+
+        ]]>
+    </help>
+    <citations>
+        <citation type="doi">10.1074/mcp.M115.055897</citation>
+        <citation type="doi">10.1093/bioinformatics/btr645</citation>
+    </citations>
+</tool>