diff msgf2pin.xml @ 0:3a49065a05d6 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/msgf2pin.xml	Wed Dec 07 16:43:51 2016 -0500
@@ -0,0 +1,65 @@
+<tool id="msgfplus2pin" name="MS-GF+ output to Pin converter" version="3.0">
+    <description>to create Percolator input files</description>
+    <requirements>
+        <requirement type="package" version="3.0">percolator</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:"/>
+    </stdio>
+    <command>
+             msgf2pin -o $pinout -e $enzyme
+             #if $matches
+             -m $matches
+             #end if
+             $aafreq $ptm $pngase $isotope
+             "$target" "$decoy"
+    </command>
+    <inputs>
+        <param name="target" type="data" format="mzid,meta2pin" label="Target MSGF+ results or metafile pointing to them" />
+        <param name="decoy" type="data" format="mzid,meta2pin" label="Decoy MSGF+ results or metafile pointing to them" />
+        <param name="enzyme" type="select" label="Enzyme used">
+          <option value="trypsin">trypsin</option>
+          <option value="no_enzyme">no enzyme</option>
+          <option value="elastase">elastase</option>
+          <option value="pepsin">pepsin</option>
+          <option value="proteinasek">proteinase K</option>
+          <option value="thermolysin">thermolysin</option>
+          <option value="chymotrypsin">chymotrypsin</option>
+          <option value="lys-n">lys-N</option>
+          <option value="lys-c">lys-C</option>
+          <option value="arg-c">arg-C</option>
+          <option value="asp-n">asp-N</option>
+          <option value="glu-c">glu-C</option>
+        </param>
+        <param name="matches" type="integer" optional="true" label="Max number of PSMs for a spectrum" />
+	<param name="aafreq" type="boolean" label="Calculate amino acid frequency features" truevalue="-a" falsevalue="" />
+        <param name="ptm" type="boolean" label="Calculate feature for number of PTMs" truevalue="-b" falsevalue="" />
+        <param name="pngase" type="boolean" label="Calculate feature based on N-linked glycosylation resulting from PNGaseF" truevalue="-N" falsevalue="" />
+        <param name="isotope" type="boolean" label="Calculate mass difference to closest isotope instead of avg. mass" truevalue="-M" falsevalue="" />
+    </inputs>
+    <outputs>
+        <data format="percin" name="pinout"/>
+    </outputs>
+    <tests>
+        <test>
+          <param name="target" value="target.mzid"/>
+          <param name="decoy" value="decoy.mzid"/>
+          <param name="ptm" value="true"/>
+          <param name="matches" value="1"/>
+          <output name="pinout" value="percolatorInresult.txt" compare="sim_size" delta="20" />
+        </test>
+    </tests>
+    <help>
+The percolator converter msgf2pin converts mzIdentML to input for percolator.
+Target and decoy inputs are MzIdentML-files of MS-GF+ from
+separate target and decoy searches. Internal MS-GF+ target/decoy
+analysis should be turned off, and the addFeatures options turned on.
+Multiple MzIdentML-files can be merged by replacing target and decoy
+filepaths with meta files. Meta files are text files containing the
+the paths of mzid-files, one path per line. For successful results,
+the different runs should be generated under similar conditions.
+    </help>
+    <citations>
+        <citation type="doi">10.1021/pr400937n</citation>
+    </citations>
+</tool>