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comparison HighResPrecursorMassCorrector.xml @ 4:6ead64a594bd draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
parents 3d84209d3178
children
comparison
equal deleted inserted replaced
3:ec62782f6c68 4:6ead64a594bd
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="HighResPrecursorMassCorrector" name="HighResPrecursorMassCorrector" version="1.12.0"> 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 <description>Corrects the precursor mz determined by the instrument software.</description> 3 <!--Proposed Tool Section: [Signal processing and preprocessing]-->
4 <macros> 4 <tool id="HighResPrecursorMassCorrector" name="HighResPrecursorMassCorrector" version="2.0.0">
5 <token name="@EXECUTABLE@">HighResPrecursorMassCorrector</token> 5 <description>Corrects the precursor mass and charge determined by the instrument software.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">HighResPrecursorMassCorrector</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>HighResPrecursorMassCorrector 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>HighResPrecursorMassCorrector
11 14
12 -in ${param_in} 15 #if $param_in:
13 -out ${param_out} 16 -in $param_in
14 -out_csv ${param_out_csv} 17 #end if
15 -threads \${GALAXY_SLOTS:-24} 18 #if $param_out:
19 -out $param_out
20 #end if
21 #if $param_out_csv:
22 -out_csv $param_out_csv
23 #end if
24 -threads \${GALAXY_SLOTS:-24}
25 #if $param_feature_in:
26 -feature:in $param_feature_in
27 #end if
28 #if $param_feature_mz_tolerance:
29 -feature:mz_tolerance $param_feature_mz_tolerance
30 #end if
31 #if $param_feature_mz_tolerance_unit:
32 -feature:mz_tolerance_unit
33 #if &quot; &quot; in str($param_feature_mz_tolerance_unit):
34 &quot;$param_feature_mz_tolerance_unit&quot;
35 #else
36 $param_feature_mz_tolerance_unit
37 #end if
38 #end if
39 #if $param_feature_rt_tolerance:
40 -feature:rt_tolerance $param_feature_rt_tolerance
41 #end if
42 #if $param_feature_believe_charge:
43 -feature:believe_charge
44 #end if
45 #if $param_feature_keep_original:
46 -feature:keep_original
47 #end if
48 #if $param_feature_assign_all_matching:
49 -feature:assign_all_matching
50 #end if
51 #if $param_nearest_peak_mz_tolerance:
52 -nearest_peak:mz_tolerance $param_nearest_peak_mz_tolerance
53 #end if
54 #if $param_nearest_peak_mz_tolerance_unit:
55 -nearest_peak:mz_tolerance_unit
56 #if &quot; &quot; in str($param_nearest_peak_mz_tolerance_unit):
57 &quot;$param_nearest_peak_mz_tolerance_unit&quot;
58 #else
59 $param_nearest_peak_mz_tolerance_unit
60 #end if
61 #end if
62 #if $adv_opts.adv_opts_selector=='advanced':
63 #if $adv_opts.param_force:
64 -force
65 #end if
66 #if $adv_opts.param_feature_max_trace:
67 -feature:max_trace $adv_opts.param_feature_max_trace
68 #end if
69 #end if
16 </command> 70 </command>
17 <inputs> 71 <inputs>
18 <param name="param_in" type="data" format="mzML" optional="False" label="input file (centroided data)" help="(-in)"/> 72 <param format="mzml" help="(-in) " label="input file (centroided data)" name="param_in" optional="False" type="data"/>
19 </inputs> 73 <param format="xml" help="(-in) " label="features used to correct precursor masses" name="param_feature_in" optional="True" type="data"/>
20 <outputs> 74 <param help="(-mz_tolerance) Used to determine matching to feature mass traces" label="The precursor mass tolerance" name="param_feature_mz_tolerance" type="float" value="5.0"/>
21 <data name="param_out" label="output file" format="mzML"/> 75 <param help="(-mz_tolerance_unit) " label="Unit of precursor mass tolerance" name="param_feature_mz_tolerance_unit" optional="True" type="select" value="ppm">
22 <data name="param_out_csv" label="Optional csv output file containing columns: precursor rt, uncorrected mz, corrected mz, delta mz#br#" format="tabular"/> 76 <option value="Da">Da</option>
23 </outputs> 77 <option value="ppm">ppm</option>
24 <help>**What it does** 78 </param>
25 79 <param help="(-rt_tolerance) " label="Additional retention time tolerance added to feature boundaries" name="param_feature_rt_tolerance" type="float" value="0.0"/>
26 Corrects the precursor mz determined by the instrument software. 80 <param checked="false" falsevalue="" help="(-believe_charge) " label="Whether precursor charge is assumed correct" name="param_feature_believe_charge" optional="True" truevalue="-feature:believe_charge" type="boolean"/>
81 <param checked="false" falsevalue="" help="(-keep_original) " label="Whether a copy of the precusor and MS2 should be made (true) or if the original should be discarded (false)" name="param_feature_keep_original" optional="True" truevalue="-feature:keep_original" type="boolean"/>
82 <param checked="false" falsevalue="" help="(-assign_all_matching) Only evaluated if copies are created (feature:keep_original)" label="Whether a precursor should be corrected to all matching features (true) or only the nearest (false)" name="param_feature_assign_all_matching" optional="True" truevalue="-feature:assign_all_matching" type="boolean"/>
83 <param help="(-mz_tolerance) Used to determine matching to next MS1 peak" label="The precursor mass tolerance" name="param_nearest_peak_mz_tolerance" type="float" value="0.0"/>
84 <param help="(-mz_tolerance_unit) " label="Unit of precursor mass tolerance" name="param_nearest_peak_mz_tolerance_unit" optional="True" type="select" value="ppm">
85 <option value="Da">Da</option>
86 <option value="ppm">ppm</option>
87 </param>
88 <expand macro="advanced_options">
89 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
90 <param help="(-max_trace) " label="Maximum isotopic trace considered in matching a precursor to a feature" name="param_feature_max_trace" type="integer" value="2"/>
91 </expand>
92 </inputs>
93 <outputs>
94 <data format="mzml" name="param_out"/>
95 <data format="tabular" name="param_out_csv"/>
96 </outputs>
97 <help>Corrects the precursor mass and charge determined by the instrument software.
27 98
28 99
29 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_HighResPrecursorMassCorrector.html 100 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_HighResPrecursorMassCorrector.html</help>
30 101 </tool>
31 @REFERENCES@
32 </help>
33 </tool>