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comparison MapAlignerTreeGuided.xml @ 0:11e2a362ecd0 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author galaxyp
date Thu, 27 Aug 2020 22:47:10 +0000
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children 183e5c22632b
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-1:000000000000 0:11e2a362ecd0
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 CTDConverter.-->
3 <!--Proposed Tool Section: [Map Alignment]-->
4 <tool id="MapAlignerTreeGuided" name="MapAlignerTreeGuided" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Tree guided correction of retention time distortions between maps.</description>
6 <macros>
7 <token name="@EXECUTABLE@">MapAlignerTreeGuided</token>
8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
11 </macros>
12 <expand macro="requirements"/>
13 <expand macro="stdio"/>
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
15 @EXT_FOO@
16 #import re
17
18 ## Preprocessing
19 mkdir in &&
20 ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
21 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
22 mkdir out &&
23 #end if
24 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
25 mkdir trafo_out &&
26 #end if
27
28 ## Main program call
29
30 set -o pipefail &&
31 @EXECUTABLE@ -write_ctd ./ &&
32 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
33 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
34 -in
35 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
36 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
37 -out
38 ${' '.join(["'out/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext("featurexml")) for _ in $in if _])}
39 #end if
40 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
41 -trafo_out
42 ${' '.join(["'trafo_out/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext("trafoxml")) for _ in $in if _])}
43 #end if
44 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
45 | tee '$stdout'
46 #end if
47
48 ## Postprocessing
49 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
50 ${' '.join(["&& mv -n 'in/%(id)s.%(gext)s' 'out/%(id)s'"%{"id": re.sub('[^\w\-_]', '_', _.element_identifier), "gext": $gxy2omsext("featurexml")} for _ in $out if _])}
51 #end if
52 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
53 ${' '.join(["&& mv -n 'in/%(id)s.%(gext)s' 'trafo_out/%(id)s'"%{"id": re.sub('[^\w\-_]', '_', _.element_identifier), "gext": $gxy2omsext("trafoxml")} for _ in $trafo_out if _])}
54 #end if
55 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
56 && mv '@EXECUTABLE@.ctd' '$ctd_out'
57 #end if]]></command>
58 <configfiles>
59 <inputs name="args_json" data_style="paths"/>
60 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
61 </configfiles>
62 <inputs>
63 <param name="in" argument="-in" type="data" format="featurexml" multiple="true" optional="false" label="Input files to align (all must have the same file type)" help=" select featurexml data sets(s)"/>
64 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
65 <param name="model_type" argument="-algorithm:model_type" display="radio" type="select" optional="false" label="Options to control the modeling of retention time transformations from data" help="">
66 <option value="linear">linear</option>
67 <option value="b_spline" selected="true">b_spline</option>
68 <option value="lowess">lowess</option>
69 <option value="interpolated">interpolated</option>
70 <expand macro="list_string_san"/>
71 </param>
72 <section name="model" title="" help="" expanded="false">
73 <param name="type" argument="-algorithm:model:type" display="radio" type="select" optional="false" label="Type of model" help="">
74 <option value="linear">linear</option>
75 <option value="b_spline" selected="true">b_spline</option>
76 <option value="lowess">lowess</option>
77 <option value="interpolated">interpolated</option>
78 <expand macro="list_string_san"/>
79 </param>
80 <section name="linear" title="Parameters for 'linear' model" help="" expanded="false">
81 <param name="symmetric_regression" argument="-algorithm:model:linear:symmetric_regression" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Perform linear regression on 'y - x' vs" help="'y + x', instead of on 'y' vs. 'x'"/>
82 <param name="x_weight" argument="-algorithm:model:linear:x_weight" display="radio" type="select" optional="true" label="Weight x values" help="">
83 <option value="">default (nothing chosen)</option>
84 <option value="1/x">1/x</option>
85 <option value="1/x2">1/x2</option>
86 <option value="ln(x)">ln(x)</option>
87 <option value=""></option>
88 <expand macro="list_string_san"/>
89 </param>
90 <param name="y_weight" argument="-algorithm:model:linear:y_weight" display="radio" type="select" optional="true" label="Weight y values" help="">
91 <option value="">default (nothing chosen)</option>
92 <option value="1/y">1/y</option>
93 <option value="1/y2">1/y2</option>
94 <option value="ln(y)">ln(y)</option>
95 <option value=""></option>
96 <expand macro="list_string_san"/>
97 </param>
98 <param name="x_datum_min" argument="-algorithm:model:linear:x_datum_min" type="float" optional="true" value="1e-15" label="Minimum x value" help=""/>
99 <param name="x_datum_max" argument="-algorithm:model:linear:x_datum_max" type="float" optional="true" value="1000000000000000.0" label="Maximum x value" help=""/>
100 <param name="y_datum_min" argument="-algorithm:model:linear:y_datum_min" type="float" optional="true" value="1e-15" label="Minimum y value" help=""/>
101 <param name="y_datum_max" argument="-algorithm:model:linear:y_datum_max" type="float" optional="true" value="1000000000000000.0" label="Maximum y value" help=""/>
102 </section>
103 <section name="b_spline" title="Parameters for 'b_spline' model" help="" expanded="false">
104 <param name="wavelength" argument="-algorithm:model:b_spline:wavelength" type="float" optional="true" min="0.0" value="0.0" label="Determines the amount of smoothing by setting the number of nodes for the B-spline" help="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"/>
105 <param name="num_nodes" argument="-algorithm:model:b_spline:num_nodes" type="integer" optional="true" min="0" value="5" label="Number of nodes for B-spline fitting" help="Overrides 'wavelength' if set (to two or greater). A lower value means more smoothing"/>
106 <param name="extrapolate" argument="-algorithm:model:b_spline:extrapolate" display="radio" type="select" optional="false" label="Method to use for extrapolation beyond the original data range" help="'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)">
107 <option value="linear" selected="true">linear</option>
108 <option value="b_spline">b_spline</option>
109 <option value="constant">constant</option>
110 <option value="global_linear">global_linear</option>
111 <expand macro="list_string_san"/>
112 </param>
113 <param name="boundary_condition" argument="-algorithm:model:b_spline:boundary_condition" type="integer" optional="true" min="0" max="2" value="2" label="Boundary condition at B-spline endpoints: 0 (value zero), 1 (first derivative zero) or 2 (second derivative zero)" help=""/>
114 </section>
115 <section name="lowess" title="Parameters for 'lowess' model" help="" expanded="false">
116 <param name="span" argument="-algorithm:model:lowess:span" type="float" optional="true" min="0.0" max="1.0" value="0.666666666666667" label="Fraction of datapoints (f) to use for each local regression (determines the amount of smoothing)" help="Choosing this parameter in the range .2 to .8 usually results in a good fit"/>
117 <param name="num_iterations" argument="-algorithm:model:lowess:num_iterations" type="integer" optional="true" min="0" value="3" label="Number of robustifying iterations for lowess fitting" help=""/>
118 <param name="delta" argument="-algorithm:model:lowess:delta" type="float" optional="true" value="-1.0" label="Nonnegative parameter which may be used to save computations (recommended value is 0.01 of the range of the input" help="e.g. for data ranging from 1000 seconds to 2000 seconds, it could be set to 10). Setting a negative value will automatically do this"/>
119 <param name="interpolation_type" argument="-algorithm:model:lowess:interpolation_type" display="radio" type="select" optional="false" label="Method to use for interpolation between datapoints computed by lowess" help="'linear': Linear interpolation. 'cspline': Use the cubic spline for interpolation. 'akima': Use an akima spline for interpolation">
120 <option value="linear">linear</option>
121 <option value="cspline" selected="true">cspline</option>
122 <option value="akima">akima</option>
123 <expand macro="list_string_san"/>
124 </param>
125 <param name="extrapolation_type" argument="-algorithm:model:lowess:extrapolation_type" display="radio" type="select" optional="false" label="Method to use for extrapolation outside the data range" help="'two-point-linear': Uses a line through the first and last point to extrapolate. 'four-point-linear': Uses a line through the first and second point to extrapolate in front and and a line through the last and second-to-last point in the end. 'global-linear': Uses a linear regression to fit a line through all data points and use it for interpolation">
126 <option value="two-point-linear">two-point-linear</option>
127 <option value="four-point-linear" selected="true">four-point-linear</option>
128 <option value="global-linear">global-linear</option>
129 <expand macro="list_string_san"/>
130 </param>
131 </section>
132 <section name="interpolated" title="Parameters for 'interpolated' model" help="" expanded="false">
133 <param name="interpolation_type" argument="-algorithm:model:interpolated:interpolation_type" display="radio" type="select" optional="false" label="Type of interpolation to apply" help="">
134 <option value="linear">linear</option>
135 <option value="cspline" selected="true">cspline</option>
136 <option value="akima">akima</option>
137 <expand macro="list_string_san"/>
138 </param>
139 <param name="extrapolation_type" argument="-algorithm:model:interpolated:extrapolation_type" display="radio" type="select" optional="false" label="Type of extrapolation to apply: two-point-linear: use the first and last data point to build a single linear model, four-point-linear: build two linear models on both ends using the first two / last two points, global-linear: use all points to build a single linear model" help="Note that global-linear may not be continuous at the border">
140 <option value="two-point-linear" selected="true">two-point-linear</option>
141 <option value="four-point-linear">four-point-linear</option>
142 <option value="global-linear">global-linear</option>
143 <expand macro="list_string_san"/>
144 </param>
145 </section>
146 </section>
147 <section name="align_algorithm" title="" help="" expanded="false">
148 <param name="score_cutoff" argument="-algorithm:align_algorithm:score_cutoff" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If only IDs above a score cutoff should be used" help="Used together with min_score"/>
149 <param name="min_score" argument="-algorithm:align_algorithm:min_score" type="float" optional="true" value="0.05" label="Minimum score for an ID to be considered" help="Applies to the last score calculated.. Unless you have very few runs or identifications, increase this value to focus on more informative peptides"/>
150 <param name="min_run_occur" argument="-algorithm:align_algorithm:min_run_occur" type="integer" optional="true" min="2" value="2" label="Minimum number of runs (incl" help="reference, if any) in which a peptide must occur to be used for the alignment.. Unless you have very few runs or identifications, increase this value to focus on more informative peptides"/>
151 <param name="max_rt_shift" argument="-algorithm:align_algorithm:max_rt_shift" type="float" optional="true" min="0.0" value="0.5" label="Maximum realistic RT difference for a peptide (median per run vs" help="reference). Peptides with higher shifts (outliers) are not used to compute the alignment.. 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"/>
152 <param name="use_unassigned_peptides" argument="-algorithm:align_algorithm:use_unassigned_peptides" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Should unassigned peptide identifications be used when computing an alignment of feature or consensus maps" help="If 'false', only peptide IDs assigned to features will be used"/>
153 <param name="use_feature_rt" argument="-algorithm:align_algorithm:use_feature_rt" type="boolean" truevalue="true" falsevalue="false" checked="true" label="When aligning feature or consensus 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" help="If different identifications are matched to one feature, only the peptide closest to the centroid in RT is used.. Precludes 'use_unassigned_peptides'"/>
154 </section>
155 </section>
156 <expand macro="adv_opts_macro">
157 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
158 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
159 <expand macro="list_string_san"/>
160 </param>
161 </expand>
162 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="false">
163 <option value="out_FLAG">out (When aligning feature or consensus 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)</option>
164 <option value="trafo_out_FLAG">trafo_out (When aligning feature or consensus 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)</option>
165 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
166 </param>
167 </inputs>
168 <outputs>
169 <collection type="list" name="out" label="${tool.name} on ${on_string}: out">
170 <discover_datasets directory="out" format="featurexml" pattern="__name__"/>
171 <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
172 </collection>
173 <collection type="list" name="trafo_out" label="${tool.name} on ${on_string}: trafo_out">
174 <discover_datasets directory="trafo_out" format="trafoxml" pattern="__name__"/>
175 <filter>OPTIONAL_OUTPUTS is not None and "trafo_out_FLAG" in OPTIONAL_OUTPUTS</filter>
176 </collection>
177 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
178 <filter>OPTIONAL_OUTPUTS is None</filter>
179 </data>
180 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
181 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
182 </data>
183 </outputs>
184 <tests>
185 <expand macro="autotest_MapAlignerTreeGuided"/>
186 <expand macro="manutest_MapAlignerTreeGuided"/>
187 </tests>
188 <help><![CDATA[Tree guided correction of retention time distortions between maps.
189
190
191 For more information, visit http://www.openms.de/documentation/TOPP_MapAlignerTreeGuided.html]]></help>
192 <expand macro="references"/>
193 </tool>