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comparison MapAlignerIdentification.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="MapAlignerIdentification" name="MapAlignerIdentification" 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 retention time distortions between maps based on common peptide identifications.</description> 3 <!--Proposed Tool Section: [Map Alignment]-->
4 <macros> 4 <tool id="MapAlignerIdentification" name="MapAlignerIdentification" version="2.0.0">
5 <token name="@EXECUTABLE@">MapAlignerIdentification</token> 5 <description>Corrects retention time distortions between maps based on common peptide identifications.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">MapAlignerIdentification</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>MapAlignerIdentification 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>MapAlignerIdentification
11 14
12 -in ${param_in} 15 -in
13 -out ${param_out} 16 #for token in $param_in:
14 -trafo_out ${param_trafo_out} 17 $token
15 -threads \${GALAXY_SLOTS:-24} 18 #end for
16 -reference:file ${param_file} 19
17 -reference:index ${param_index} 20 #if $rep_param_out:
18 -algorithm:peptide_score_threshold ${param_peptide_score_threshold} 21 -out
19 -algorithm:min_run_occur ${param_min_run_occur} 22 #for token in $rep_param_out:
20 -algorithm:max_rt_shift ${param_max_rt_shift} 23 #if &quot; &quot; in str(token):
21 ${param_use_unassigned_peptides} 24 &quot;$token.param_out&quot;
22 ${param_use_feature_rt} 25 #else
23 -model:type ${param_type} 26 $token.param_out
24 ${param_symmetric_regression} 27 #end if
25 -model:interpolated:interpolation_type ${param_interpolation_type} 28 #end for
29 #end if
30
31 #if $rep_param_trafo_out:
32 -trafo_out
33 #for token in $rep_param_trafo_out:
34 #if &quot; &quot; in str(token):
35 &quot;$token.param_trafo_out&quot;
36 #else
37 $token.param_trafo_out
38 #end if
39 #end for
40 #end if
41 -threads \${GALAXY_SLOTS:-24}
42 #if $param_reference_file:
43 -reference:file $param_reference_file
44 #end if
45 #if $param_reference_index:
46 -reference:index $param_reference_index
47 #end if
48 #if $param_algorithm_peptide_score_threshold:
49 -algorithm:peptide_score_threshold $param_algorithm_peptide_score_threshold
50 #end if
51 #if $param_algorithm_min_run_occur:
52 -algorithm:min_run_occur $param_algorithm_min_run_occur
53 #end if
54 #if $param_algorithm_max_rt_shift:
55 -algorithm:max_rt_shift $param_algorithm_max_rt_shift
56 #end if
57 #if $param_algorithm_use_unassigned_peptides:
58 -algorithm:use_unassigned_peptides
59 #end if
60 #if $param_algorithm_use_feature_rt:
61 -algorithm:use_feature_rt
62 #end if
63 #if $param_model_type:
64 -model:type
65 #if &quot; &quot; in str($param_model_type):
66 &quot;$param_model_type&quot;
67 #else
68 $param_model_type
69 #end if
70 #end if
71 #if $param_model_linear_symmetric_regression:
72 -model:linear:symmetric_regression
73 #end if
74 #if $param_model_b_spline_wavelength:
75 -model:b_spline:wavelength $param_model_b_spline_wavelength
76 #end if
77 #if $param_model_b_spline_num_nodes:
78 -model:b_spline:num_nodes $param_model_b_spline_num_nodes
79 #end if
80 #if $param_model_b_spline_extrapolate:
81 -model:b_spline:extrapolate
82 #if &quot; &quot; in str($param_model_b_spline_extrapolate):
83 &quot;$param_model_b_spline_extrapolate&quot;
84 #else
85 $param_model_b_spline_extrapolate
86 #end if
87 #end if
88 #if $param_model_b_spline_boundary_condition:
89 -model:b_spline:boundary_condition $param_model_b_spline_boundary_condition
90 #end if
91 #if $param_model_interpolated_interpolation_type:
92 -model:interpolated:interpolation_type
93 #if &quot; &quot; in str($param_model_interpolated_interpolation_type):
94 &quot;$param_model_interpolated_interpolation_type&quot;
95 #else
96 $param_model_interpolated_interpolation_type
97 #end if
98 #end if
99 #if $adv_opts.adv_opts_selector=='advanced':
100 #if $adv_opts.param_force:
101 -force
102 #end if
103 #end if
26 </command> 104 </command>
27 <inputs> 105 <inputs>
28 <param name="param_in" type="data" format="featureXML,consensusXML,idXML" optional="False" size="20" label="Input files separated by blanks (all must have the same file type)" help="(-in)"/> 106 <param format="xml,consensusxml" help="(-in) " label="Input files to align (all must have the same file type)" multiple="true" name="param_in" optional="False" size="30" type="data">
29 <param name="param_file" type="data" format="featureXML,consensusXML,idXML" optional="True" label="File to use as reference (same file format as input files required)" help="(-file)"/> 107 <sanitizer>
30 <param name="param_index" type="integer" min="0" optional="True" value="0" label="Use one of the input files as reference ('1' for the first file, etc.).#br#If '0', no explicit reference is set - the algorithm will select a reference." help="(-index)"/> 108 <valid initial="string.printable">
31 <param name="param_peptide_score_threshold" type="float" value="0.0" label="Score threshold for peptide hits to be used in the alignment.#br#Select a value that allows only 'high confidence' matches." help="(-peptide_score_threshold)"/> 109 <remove value="'"/>
32 <param name="param_min_run_occur" type="integer" min="2" optional="True" value="2" label="Minimum number of runs (incl. reference, if any) a peptide must occur in to be used for the alignment.#br#Unless you have very few runs or identifications, increase this value to focus on more informative peptides." help="(-min_run_occur)"/> 110 <remove value="&quot;"/>
33 <param name="param_max_rt_shift" type="float" min="0.0" optional="True" value="0.5" label="Maximum realistic RT difference for a peptide (median per run vs. reference). Peptides with higher shifts (outliers) are not used to compute the alignment.#br#If 0, no limit (disable filter); if &gt; 1, the final value in seconds; if &lt;= 1, taken as a fraction of the range of the reference RT scale." help="(-max_rt_shift)"/> 111 </valid>
34 <param name="param_use_unassigned_peptides" type="boolean" truevalue="-algorithm:use_unassigned_peptides true" falsevalue="-algorithm:use_unassigned_peptides false" checked="true" optional="True" label="Should unassigned peptide identifications be used when computing an alignment of feature maps? If 'false', only peptide IDs assigned to features will be used." help="(-use_unassigned_peptides)"/> 112 </sanitizer>
35 <param name="param_use_feature_rt" type="boolean" truevalue="-algorithm:use_feature_rt true" falsevalue="-algorithm:use_feature_rt false" checked="false" optional="True" label="When aligning feature maps, don't use the retention time of a peptide identification directly; instead, use the retention time of the centroid of the feature (apex of the elution profile) that the peptide was matched to. If different identifications are matched to one feature, only the peptide closest to the centroid in RT is used.#br#Precludes 'use_unassigned_peptides'." help="(-use_feature_rt)"/> 113 </param>
36 <param name="param_type" type="select" optional="True" value="interpolated" label="Type of model" help="(-type)"> 114 <param format="xml,consensusxml" help="(-file) " label="File to use as reference" name="param_reference_file" optional="True" type="data"/>
37 <option value="linear">linear</option> 115 <param help="(-index) &lt;br&gt;If '0', no explicit reference is set - the algorithm will select a reference" label="Use one of the input files as reference ('1' for the first file, etc.)" min="0" name="param_reference_index" optional="True" type="integer" value="0"/>
38 <option value="b_spline">b_spline</option> 116 <param help="(-peptide_score_threshold) &lt;br&gt;Select a value that allows only 'high confidence' matches" label="Score threshold for peptide hits to be used in the alignment" name="param_algorithm_peptide_score_threshold" type="float" value="0.0"/>
39 <option value="interpolated">interpolated</option> 117 <param help="(-min_run_occur) reference, if any) a peptide must occur in to be used for the alignment. &lt;br&gt;Unless you have very few runs or identifications, increase this value to focus on more informative peptides" label="Minimum number of runs (incl" min="2" name="param_algorithm_min_run_occur" optional="True" type="integer" value="2"/>
40 </param> 118 <param help="(-max_rt_shift) reference). Peptides with higher shifts (outliers) are not used to compute the alignment. &lt;br&gt;If 0, no limit (disable filter); if &gt; 1, the final value in seconds; if &lt;= 1, taken as a fraction of the range of the reference RT scale" label="Maximum realistic RT difference for a peptide (median per run vs" min="0.0" name="param_algorithm_max_rt_shift" optional="True" type="float" value="0.5"/>
41 <param name="param_symmetric_regression" type="boolean" truevalue="-model:linear:symmetric_regression true" falsevalue="-model:linear:symmetric_regression false" checked="false" optional="True" label="Perform linear regression on 'y - x' vs. 'y + x', instead of on 'y' vs. 'x'." help="(-symmetric_regression)"/> 119 <param checked="true" falsevalue="" help="(-use_unassigned_peptides) If 'false', only peptide IDs assigned to features will be used" label="Should unassigned peptide identifications be used when computing an alignment of feature maps?" name="param_algorithm_use_unassigned_peptides" optional="True" truevalue="-algorithm:use_unassigned_peptides" type="boolean"/>
42 <param name="param_interpolation_type" type="select" optional="True" value="cspline" label="Type of interpolation to apply." help="(-interpolation_type)"> 120 <param checked="false" falsevalue="" help="(-use_feature_rt) If different identifications are matched to one feature, only the peptide closest to the centroid in RT is used. &lt;br&gt;Precludes 'use_unassigned_peptides'" label="When aligning feature maps, don't use the retention time of a peptide identification directly; instead, use the retention time of the centroid of the feature (apex of the elution profile) that the peptide was matched to" name="param_algorithm_use_feature_rt" optional="True" truevalue="-algorithm:use_feature_rt" type="boolean"/>
43 <option value="linear">linear</option> 121 <param help="(-type) " label="Type of model" name="param_model_type" optional="True" type="select" value="b_spline">
44 <option value="cspline">cspline</option> 122 <option value="linear">linear</option>
45 <option value="akima">akima</option> 123 <option value="b_spline">b_spline</option>
46 </param> 124 <option value="interpolated">interpolated</option>
47 </inputs> 125 </param>
48 <outputs> 126 <param checked="false" falsevalue="" help="(-symmetric_regression) 'y + x', instead of on 'y' vs. 'x'" label="Perform linear regression on 'y - x' vs" name="param_model_linear_symmetric_regression" optional="True" truevalue="-model:linear:symmetric_regression" type="boolean"/>
49 <data name="param_out" label="Output files separated by blanks. Either 'out' or 'trafo_out' has to be provided. They can be used together." format="idXML"> 127 <param help="(-wavelength) The number is chosen so that the spline approximates a low-pass filter with this cutoff wavelength. The wavelength is given in the same units as the data; a higher value means more smoothing. '0' sets the number of nodes to twice the number of input points" label="Determines the amount of smoothing by setting the number of nodes for the B-spline" min="0.0" name="param_model_b_spline_wavelength" optional="True" type="float" value="0.0"/>
50 <change_format> 128 <param help="(-num_nodes) Overrides 'wavelength' if set (to two or greater). A lower value means more smoothing" label="Number of nodes for B-spline fitting" min="0" name="param_model_b_spline_num_nodes" optional="True" type="integer" value="5"/>
51 <when input="param_out_type" value="featureXML" format="featureXML"/> 129 <param help="(-extrapolate) 'linear': Linear extrapolation using the slope of the B-spline at the corresponding endpoint. 'b_spline': Use the B-spline (as for interpolation). 'constant': Use the constant value of the B-spline at the corresponding endpoint. 'global_linear': Use a linear fit through the data (which will most probably introduce discontinuities at the ends of the data range)" label="Method to use for extrapolation beyond the original data range" name="param_model_b_spline_extrapolate" optional="True" type="select" value="linear">
52 <when input="param_out_type" value="consensusXML" format="consensusXML"/> 130 <option value="linear">linear</option>
53 </change_format> 131 <option value="b_spline">b_spline</option>
54 </data> 132 <option value="constant">constant</option>
55 <data name="param_trafo_out" label="Transformation output files separated by blanks. Either 'out' or 'trafo_out' has to be provided. They can be used together." format="data"/> 133 <option value="global_linear">global_linear</option>
56 </outputs> 134 </param>
57 <help>**What it does** 135 <param help="(-boundary_condition) " label="Boundary condition at B-spline endpoints: 0 (value zero), 1 (first derivative zero) or 2 (second derivative zero)" max="2" min="0" name="param_model_b_spline_boundary_condition" optional="True" type="integer" value="2"/>
58 136 <param help="(-interpolation_type) " label="Type of interpolation to apply" name="param_model_interpolated_interpolation_type" optional="True" type="select" value="cspline">
59 Corrects retention time distortions between maps based on common peptide identifications. 137 <option value="linear">linear</option>
138 <option value="cspline">cspline</option>
139 <option value="akima">akima</option>
140 </param>
141 <expand macro="advanced_options">
142 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
143 </expand>
144 </inputs>
145 <outputs>
146 <data format="input" metadata_source="param_in" name="param_out"/>
147 <data format="trafoxml" name="param_trafo_out"/>
148 </outputs>
149 <help>Corrects retention time distortions between maps based on common peptide identifications.
60 150
61 151
62 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapAlignerIdentification.html 152 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapAlignerIdentification.html</help>
63 153 </tool>
64 @REFERENCES@
65 </help>
66 </tool>