diff MassCalculator.xml @ 0:3d84209d3178 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/MassCalculator.xml	Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,59 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="MassCalculator" name="MassCalculator" version="1.12.0">
+  <description>Calculates masses and mass-to-charge ratios of peptide sequences</description>
+  <macros>
+    <token name="@EXECUTABLE@">MassCalculator</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>MassCalculator
+
+-in ${param_in}
+-in_seq ${param_in_seq}
+-out ${param_out}
+-charge ${param_charge}
+-format ${param_format}
+${param_average_mass}
+-fragment_type ${param_fragment_type}
+-separator ${param_separator}
+-threads \${GALAXY_SLOTS:-24} 
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="txt" optional="True" label="Input file with peptide sequences and optionally charge numbers (mutually exclusive to 'in_seq')" help="(-in)"/>
+    <param name="param_in_seq" type="text" size="20" label="List of peptide sequences (mutually exclusive to 'in')" help="(-in_seq)"/>
+    <param name="param_charge" type="text" size="20" value="0" label="List of charge states; required if 'in_seq' is given" help="(-charge)"/>
+    <param name="param_format" type="select" optional="True" value="list" label="Output format ('list': human-readable list, 'table': CSV-like table, 'mass_only': mass values only, 'mz_only': m/z values only)#br#" help="(-format)">
+      <option value="list">list</option>
+      <option value="table">table</option>
+      <option value="mass_only">mass_only</option>
+      <option value="mz_only">mz_only</option>
+    </param>
+    <param name="param_average_mass" type="boolean" truevalue="-average_mass true" falsevalue="-average_mass false" checked="false" optional="True" label="Compute average (instead of monoisotopic) peptide masses" help="(-average_mass)"/>
+    <param name="param_fragment_type" type="select" optional="True" value="full" label="For what type of sequence/fragment the mass should be computed#br#" help="(-fragment_type)">
+      <option value="full">full</option>
+      <option value="internal">internal</option>
+      <option value="N-terminal">N-terminal</option>
+      <option value="C-terminal">C-terminal</option>
+      <option value="a-ion">a-ion</option>
+      <option value="b-ion">b-ion</option>
+      <option value="c-ion">c-ion</option>
+      <option value="x-ion">x-ion</option>
+      <option value="y-ion">y-ion</option>
+      <option value="z-ion">z-ion</option>
+    </param>
+    <param name="param_separator" type="text" size="20" label="Field separator for 'table' output format; by default, the 'tab' character is used" help="(-separator)"/>
+  </inputs>
+  <outputs>
+    <data name="param_out" label="Output file; if empty, output is written to the screen" format="txt"/>
+  </outputs>
+  <help>**What it does**
+
+Calculates masses and mass-to-charge ratios of peptide sequences
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MassCalculator.html
+
+@REFERENCES@
+</help>
+</tool>