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comparison InternalCalibration.xml @ 0:975efdac387b draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:37:28 -0500
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children eab8c1365b7d
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-1:000000000000 0:975efdac387b
1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
3 <!--Proposed Tool Section: [Signal processing and preprocessing]-->
4 <tool id="InternalCalibration" name="InternalCalibration" version="2.1.0">
5 <description>Applies an internal mass recalibration.</description>
6 <macros>
7 <token name="@EXECUTABLE@">InternalCalibration</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>InternalCalibration
14
15 #if $param_in:
16 -in $param_in
17 #end if
18 #if $param_out:
19 -out $param_out
20 #end if
21 #if $param_rscript_executable:
22 -rscript_executable $param_rscript_executable
23 #end if
24 #if $param_ppm_match_tolerance:
25 -ppm_match_tolerance $param_ppm_match_tolerance
26 #end if
27
28 #if $rep_param_ms_level:
29 -ms_level
30 #for token in $rep_param_ms_level:
31 #if " " in str(token):
32 "$token.param_ms_level"
33 #else
34 $token.param_ms_level
35 #end if
36 #end for
37 #end if
38 #if $param_RT_chunking:
39 -RT_chunking $param_RT_chunking
40 #end if
41 #if $param_cal_id_in:
42 -cal:id_in $param_cal_id_in
43 #end if
44 #if $param_cal_lock_in:
45 -cal:lock_in $param_cal_lock_in
46 #end if
47 #if $param_cal_lock_out:
48 -cal:lock_out $param_cal_lock_out
49 #end if
50 #if $param_cal_lock_fail_out:
51 -cal:lock_fail_out $param_cal_lock_fail_out
52 #end if
53 #if $param_cal_lock_require_mono:
54 -cal:lock_require_mono
55 #end if
56 #if $param_cal_lock_require_iso:
57 -cal:lock_require_iso
58 #end if
59 #if $param_cal_model_type:
60 -cal:model_type $param_cal_model_type
61 #end if
62 #if $param_RANSAC_enabled:
63 -RANSAC:enabled
64 #end if
65 #if $param_RANSAC_threshold:
66 -RANSAC:threshold $param_RANSAC_threshold
67 #end if
68 #if $param_RANSAC_pc_inliers:
69 -RANSAC:pc_inliers $param_RANSAC_pc_inliers
70 #end if
71 #if $param_RANSAC_iter:
72 -RANSAC:iter $param_RANSAC_iter
73 #end if
74 #if $param_goodness_median:
75 -goodness:median $param_goodness_median
76 #end if
77 #if $param_goodness_MAD:
78 -goodness:MAD $param_goodness_MAD
79 #end if
80 #if $param_quality_control_models:
81 -quality_control:models $param_quality_control_models
82 #end if
83 #if $param_quality_control_models_plot:
84 -quality_control:models_plot $param_quality_control_models_plot
85 #end if
86 #if $param_quality_control_residuals:
87 -quality_control:residuals $param_quality_control_residuals
88 #end if
89 #if $param_quality_control_residuals_plot:
90 -quality_control:residuals_plot $param_quality_control_residuals_plot
91 #end if
92 #if $adv_opts.adv_opts_selector=='advanced':
93 #if $adv_opts.param_force:
94 -force
95 #end if
96 #end if
97 </command>
98 <inputs>
99 <param name="param_in" type="data" format="mzml" optional="False" label="Input peak file" help="(-in) "/>
100 <param name="param_rscript_executable" type="data" format="text" value="Rscript" label="Path to the Rscript executable (default: 'Rscript')" help="(-rscript_executable) "/>
101 <param name="param_ppm_match_tolerance" type="float" value="25.0" label="Finding calibrants in raw data uses this tolerance (for lock masses and ID's)" help="(-ppm_match_tolerance) "/>
102 <repeat name="rep_param_ms_level" min="0" max="1" title="param_ms_level">
103 <param name="param_ms_level" type="text" size="30" value="1 2 3" label="Target MS levels to apply the transformation onto" help="(-ms_level) Does not affect calibrant collection">
104 <sanitizer>
105 <valid initial="string.printable">
106 <remove value="'"/>
107 <remove value="&quot;"/>
108 </valid>
109 </sanitizer>
110 </param>
111 </repeat>
112 <param name="param_RT_chunking" type="float" value="300.0" label="RT window (one-sided, i.e" help="(-RT_chunking) left-&gt;center, or center-&gt;right) around an MS scan in which calibrants are collected to build a model. Set to -1 to use ALL calibrants for all scans, i.e. a global model"/>
113 <param name="param_cal_id_in" type="data" format="featurexml,idxml" optional="True" label="Identifications or features whose peptide ID's serve as calibration masses" help="(-id_in) "/>
114 <param name="param_cal_lock_in" type="data" format="tabular" optional="True" label="Input file containing reference m/z values (text file with each line as: m/z ms-level charge) which occur in all scans" help="(-lock_in) "/>
115 <param name="param_cal_lock_require_mono" display="radio" type="boolean" truevalue="-cal:lock_require_mono" falsevalue="" checked="false" optional="True" label="Require all lock masses to be monoisotopic, i.e" help="(-lock_require_mono) not the iso1, iso2 etc ('charge' column is used to determine the spacing). Peaks which are not mono-isotopic are not used"/>
116 <param name="param_cal_lock_require_iso" display="radio" type="boolean" truevalue="-cal:lock_require_iso" falsevalue="" checked="false" optional="True" label="Require all lock masses to have at least the +1 isotope" help="(-lock_require_iso) Peaks without isotope pattern are not used"/>
117 <param name="param_cal_model_type" display="radio" type="select" optional="False" value="linear_weighted" label="Type of function to be fitted to the calibration points" help="(-model_type) ">
118 <option value="linear">linear</option>
119 <option value="linear_weighted" selected="true">linear_weighted</option>
120 <option value="quadratic">quadratic</option>
121 <option value="quadratic_weighted">quadratic_weighted</option>
122 </param>
123 <param name="param_RANSAC_enabled" display="radio" type="boolean" truevalue="-RANSAC:enabled" falsevalue="" checked="false" optional="True" label="Apply RANSAC to calibration points to remove outliers before fitting a model" help="(-enabled) "/>
124 <param name="param_RANSAC_threshold" type="float" value="10.0" label="Threshold for accepting inliers (instrument precision (not accuracy!) as ppm^2 distance)" help="(-threshold) "/>
125 <param name="param_RANSAC_pc_inliers" type="integer" min="1" max="99" optional="True" value="30" label="Minimum percentage (of available data) of inliers (&lt;threshold away from model) to accept the model" help="(-pc_inliers) "/>
126 <param name="param_RANSAC_iter" type="integer" value="70" label="Maximal # iterations" help="(-iter) "/>
127 <param name="param_goodness_median" type="float" value="4.0" label="The median ppm error of calibrated masses must be smaller than this threshold" help="(-median) "/>
128 <param name="param_goodness_MAD" type="float" value="1.0" label="The median absolute deviation of the ppm error of calibrated masses must be smaller than this threshold" help="(-MAD) "/>
129 <expand macro="advanced_options">
130 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
131 </expand>
132 </inputs>
133 <outputs>
134 <data name="param_out" format="mzml"/>
135 <data name="param_cal_lock_out" format="mzml"/>
136 <data name="param_cal_lock_fail_out" format="mzml"/>
137 <data name="param_quality_control_models" format="tabular"/>
138 <data name="param_quality_control_models_plot" format="png"/>
139 <data name="param_quality_control_residuals" format="tabular"/>
140 <data name="param_quality_control_residuals_plot" format="png"/>
141 </outputs>
142 <help>Applies an internal mass recalibration.
143
144
145 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_InternalCalibration.html</help>
146 </tool>