diff macros.xml @ 2:cf0d72c7b482 draft

Update.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Fri May 10 17:31:05 2013 -0400
@@ -0,0 +1,83 @@
+<macros>
+  <macro name="stdio">
+    <stdio>
+      <exit_code range="1:"  level="fatal"   description="Error running OpenMS tool." />
+    </stdio>
+  </macro>
+  <macro name="requires">
+    <requirements>
+      <requirement type="package">openms</requirement>
+      <yield />
+    </requirements>
+  </macro>
+  <macro name="sampling_rate_param">
+    <param name="sampling_rate_param" label="Sampling Rate" help="New sampling rate in m/z dimension." value="0.1" type="float" />
+  </macro>
+  <macro name="id_inputs">
+    <param name="input1" label="Input Peak List (mzML)" type="data" format="mzml" />
+    <param name="database" label="Database" type="data" format="fasta" />
+  </macro>
+  <macro name="id_outputs">
+    <outputs>
+      <data format="idxml" name="out" />
+    </outputs>
+  </macro>
+  <macro name="precursor_mass_tolerance_param">
+    <param name="precursor_mass_tolerance" label="Precursor Mass Tolerance" value="1.5" type="float" />
+  </macro>
+  <macro name="precursor_mass_tolerance_unit_param">
+    <param name="precursor_mass_tolerance_unit" label="Precursor Mass Tolerance Units" type="select">
+      <option value="Da" selected="true">Daltons</option>
+      <option value="ppm">ppm</option>
+    </param>
+  </macro>
+  <macro name="fragment_mass_tolerance_param">
+    <param name="fragment_mass_tolerance" label="Fragment Mass Tolerance" value="0.3" type="float" />
+  </macro>
+  <macro name="fragment_mass_tolerance_unit_param">
+    <param name="fragment_mass_tolerance_unit" label="Fragment Mass Tolerance Units" type="select">
+      <option value="Da" selected="true">Daltons</option>
+      <option value="ppm">ppm</option>
+    </param>
+  </macro>
+  <macro name="fixed_modifications_param">
+    <param name="fixed_modifications" type="select" label="Fixed Modification" multiple="true">
+      <options from_file="openms_mods.loc">
+        <column name="name" index="0" />
+        <column name="value" index="0" />
+      </options>
+    </param>
+  </macro>
+  <macro name="variable_modifications_param">
+    <param name="variable_modifications" type="select" label="Variable Modification" multiple="true">
+      <options from_file="openms_mods.loc">
+        <column name="name" index="0" />
+        <column name="value" index="0" />
+      </options>
+    </param>
+  </macro>
+  <macro name="precursor_charge_params">
+    <param name="min_precursor_charge" label="Minimum Precursor Charge" value="1" type="integer" />
+    <param name="max_precursor_charge" label="Maximum Precursor Charge" value="4" type="integer" />
+  </macro>
+  <macro name="raw_feature_finder_params">
+    <param name="rt_threshold" type="float" value="30" label="RT Threshold" help="Upper bound for the retention time [s] over which a characteristic peptide elutes." />
+    <param name="rt_min" type="float" value="0" label="RT Minimum" help="Lower bound for the retention time [s]." />
+    <param name="intensity_cutoff" type="float" value="10000" label="Intensity Cutoff" help="Lower bound for the intensity of isotopic peaks in a SILAC pattern." />
+    <param name="intensity_correlation" type="float" value="0.7" label="Intensity Correlation" help="Lower bound for the Pearson correlation coefficient, which measures how well intensity profiles of different isotopic peaks correlate." />
+    <param name="model_deviation" type="float" value="3" label="Model Deviation" help="Upper bound on the factor by which the ratios of observed isotopic peaks are allowed to differ from the ratios of the theoretic averagine model, i.e. ( theoretic_ratio / model_deviation ) &lt; observed_ratio &lt; ( theoretic_ratio * model_deviation )." />
+    <param name="min_charge" type="integer" value="2" label="Minimum Charge" />
+    <param name="max_charge" type="integer" value="4" label="Maximum Charge" />
+    <param name="min_peaks_per_peptide" type="integer" value="3" label="Minimum Number of Peaks Per Peptide" />
+    <param name="max_peaks_per_peptide" type="integer" value="5" label="Maximum Number of Peaks Per Peptide" />
+  </macro>
+  <macro name="map_input">
+  </macro>
+  <macro name="map_output">
+    <data format="consensusxml" name="map_output">
+      <change_format>
+        <when input="input_type" value="featurexml" format="featurexml" />
+      </change_format>
+    </data>
+  </macro>
+</macros>
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