comparison macros.xml @ 2:cf0d72c7b482 draft

Update.
author galaxyp
date Fri, 10 May 2013 17:31:05 -0400
parents
children 1183846e70a1
comparison
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1:5c65f8116244 2:cf0d72c7b482
1 <macros>
2 <macro name="stdio">
3 <stdio>
4 <exit_code range="1:" level="fatal" description="Error running OpenMS tool." />
5 </stdio>
6 </macro>
7 <macro name="requires">
8 <requirements>
9 <requirement type="package">openms</requirement>
10 <yield />
11 </requirements>
12 </macro>
13 <macro name="sampling_rate_param">
14 <param name="sampling_rate_param" label="Sampling Rate" help="New sampling rate in m/z dimension." value="0.1" type="float" />
15 </macro>
16 <macro name="id_inputs">
17 <param name="input1" label="Input Peak List (mzML)" type="data" format="mzml" />
18 <param name="database" label="Database" type="data" format="fasta" />
19 </macro>
20 <macro name="id_outputs">
21 <outputs>
22 <data format="idxml" name="out" />
23 </outputs>
24 </macro>
25 <macro name="precursor_mass_tolerance_param">
26 <param name="precursor_mass_tolerance" label="Precursor Mass Tolerance" value="1.5" type="float" />
27 </macro>
28 <macro name="precursor_mass_tolerance_unit_param">
29 <param name="precursor_mass_tolerance_unit" label="Precursor Mass Tolerance Units" type="select">
30 <option value="Da" selected="true">Daltons</option>
31 <option value="ppm">ppm</option>
32 </param>
33 </macro>
34 <macro name="fragment_mass_tolerance_param">
35 <param name="fragment_mass_tolerance" label="Fragment Mass Tolerance" value="0.3" type="float" />
36 </macro>
37 <macro name="fragment_mass_tolerance_unit_param">
38 <param name="fragment_mass_tolerance_unit" label="Fragment Mass Tolerance Units" type="select">
39 <option value="Da" selected="true">Daltons</option>
40 <option value="ppm">ppm</option>
41 </param>
42 </macro>
43 <macro name="fixed_modifications_param">
44 <param name="fixed_modifications" type="select" label="Fixed Modification" multiple="true">
45 <options from_file="openms_mods.loc">
46 <column name="name" index="0" />
47 <column name="value" index="0" />
48 </options>
49 </param>
50 </macro>
51 <macro name="variable_modifications_param">
52 <param name="variable_modifications" type="select" label="Variable Modification" multiple="true">
53 <options from_file="openms_mods.loc">
54 <column name="name" index="0" />
55 <column name="value" index="0" />
56 </options>
57 </param>
58 </macro>
59 <macro name="precursor_charge_params">
60 <param name="min_precursor_charge" label="Minimum Precursor Charge" value="1" type="integer" />
61 <param name="max_precursor_charge" label="Maximum Precursor Charge" value="4" type="integer" />
62 </macro>
63 <macro name="raw_feature_finder_params">
64 <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." />
65 <param name="rt_min" type="float" value="0" label="RT Minimum" help="Lower bound for the retention time [s]." />
66 <param name="intensity_cutoff" type="float" value="10000" label="Intensity Cutoff" help="Lower bound for the intensity of isotopic peaks in a SILAC pattern." />
67 <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." />
68 <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 )." />
69 <param name="min_charge" type="integer" value="2" label="Minimum Charge" />
70 <param name="max_charge" type="integer" value="4" label="Maximum Charge" />
71 <param name="min_peaks_per_peptide" type="integer" value="3" label="Minimum Number of Peaks Per Peptide" />
72 <param name="max_peaks_per_peptide" type="integer" value="5" label="Maximum Number of Peaks Per Peptide" />
73 </macro>
74 <macro name="map_input">
75 </macro>
76 <macro name="map_output">
77 <data format="consensusxml" name="map_output">
78 <change_format>
79 <when input="input_type" value="featurexml" format="featurexml" />
80 </change_format>
81 </data>
82 </macro>
83 </macros>