--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/flashlfq.xml	Wed Dec 06 08:54:47 2017 -0500
@@ -0,0 +1,91 @@
+<tool id="flashlfq" name="FlashLFQ" version="0.1.0">
+    <description>ultrafast label-free quantification for mass-spectrometry proteomics</description>
+    <requirements>
+        <requirement type="package" version="0.199.0">flashlfq</requirement>
+    </requirements>
+    <command><![CDATA[
+        FlashLFQ --idt $idt --rep Test2 --ppm $psm --iso $iso
+        #if $intensity == 'integrate':
+        --int true
+        #end if
+        #if $charge == 'precursor':
+        --chg true
+        #end if
+        --pau false
+    ]]></command>
+    <inputs>
+        <param name="idt" type="data" format="tabular" label="identification file"/>
+        <param name="scans" type="data" format="mzml" multiple="true" label="spectrum files"/>
+        <param name="ppm" type="float" value="10" min="1" max="20" label="monoisotopic ppm tolerance"/>
+        <param name="iso" type="float" value="5" min="1" max="10" label="isotopic distribution tolerance in ppm"/>
+        <param name="nis" type="integer" value="2" min="1" max="30" label="number of isotopes required to be observed"/>
+        <param name="intensity" type="select" label="intensity">
+            <option value="apex" selected="true">use the apex intensity</option>
+            <option value="integrate">integrate chromatographic peak intensity</option>
+        </param>
+        <param name="charge" type="select" label="charge">
+            <option value="all" selected="true">use all identification detected charge states</option>
+            <option value="precursor">use precursor charge</option>
+        </param>
+        <!--
+        -->
+    </inputs>
+    <outputs>
+        <data name="log" format="text" label="${tool.name} on ${on_string}: Log" />
+        <data name="quantifiedBaseSequences" format="tabular" label="${tool.name} on ${on_string}: QuantifiedBaseSequences.tsv" />
+        <data name="quantifiedModifiedSequences" format="tabular" label="${tool.name} on ${on_string}: QuantifiedModifiedSequences.tsv" />
+        <data name="quantifiedPeaks" format="tabular" label="${tool.name} on ${on_string}: QuantifiedPeaks.tsv" />
+        <data name="quantifiedProteins" format="tabular" label="${tool.name} on ${on_string}: QuantifiedProteins.tsv" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="idt" value="aggregatePSMs_5ppmAroundZero.psmtsv" ftype="tabular"/>
+            <param name="scans" value="sliced-mzml.mzML" ftype="mzml"/>
+            <param name="ppm" value="12"/>
+            <param name="iso" value="6"/>
+            <output name="log">
+                <assert_contents>
+                    <has_text text="ppmTolerance = 10" />
+                    <has_text text="isotopePpmTolerance = 6" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+
+
+**Accepted command-line arguments:**
+
+    --idt [string | identification file path (TSV format)]
+    
+    --raw [string | MS data file (.raw or .mzML)]
+    
+    --rep [string | repository containing MS data files]
+    
+    --ppm [double | monoisotopic ppm tolerance] (default = 10)
+    
+    --iso [double | isotopic distribution tolerance in ppm] (default = 5)
+    
+    --sil [boolean | silent mode; no console output] (default = false)
+    
+    --pau [boolean | pause at end of run] (default = true)
+    
+    --int [boolean | integrate chromatographic peak intensity instead of using 
+          the apex intensity] (default = false)
+    
+    --chg [boolean | use only precursor charge state; when set to false, FlashLFQ looks 
+          for all charge states detected in the MS/MS identification file for each peptide] (default = false)
+   
+    --mbr [bool|match between runs]
+
+    --rmm [bool|require observed monoisotopic mass peak]
+   
+    --nis [int|number of isotopes required to be observed]
+
+
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1021/acs.jproteome.7b00608</citation>
+    </citations>
+</tool>