Mercurial > repos > galaxyp > openms_mapalignerposeclustering

comparison MapAlignerPoseClustering.xml @ 10:246847b3a188 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:16:48 +0000
parents d17db97d139f
children e527a8a430dd
comparison
equal deleted inserted replaced
9:d02fe0dfd2dc 10:246847b3a188
1 <?xml version='1.0' encoding='UTF-8'?> 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.--> 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]--> 3 <!--Proposed Tool Section: [Map Alignment]-->
4 <tool id="MapAlignerPoseClustering" name="MapAlignerPoseClustering" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="MapAlignerPoseClustering" name="MapAlignerPoseClustering" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Corrects retention time distortions between maps using a pose clustering approach.</description> 5 <description>Corrects retention time distortions between maps using a pose clustering approach.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">MapAlignerPoseClustering</token> 7 <token name="@EXECUTABLE@">MapAlignerPoseClustering</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
11 </macros> 9 </macros>
12 <expand macro="requirements"/> 10 <expand macro="requirements"/>
13 <expand macro="stdio"/> 11 <expand macro="stdio"/>
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ 12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
15 @EXT_FOO@ 13 @EXT_FOO@
16 #import re 14 #import re
17 15
18 ## Preprocessing 16 ## Preprocessing
19 mkdir in && 17 mkdir in_cond.in &&
20 ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) } 18 #if $in_cond.in_select == "no"
19 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} &&
20 ${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
21 #else
22 ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
23 #end if
21 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 24 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
22 mkdir out && 25 mkdir out &&
26 mkdir ${' '.join(["'out/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} &&
23 #end if 27 #end if
24 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 28 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
25 mkdir trafo_out && 29 mkdir trafo_out &&
30 mkdir ${' '.join(["'trafo_out/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} &&
26 #end if 31 #end if
27 #if $reference.file: 32 #if $reference.file:
28 mkdir reference.file && 33 mkdir reference.file &&
29 ln -s '$reference.file' 'reference.file/${re.sub("[^\w\-_]", "_", $reference.file.element_identifier)}.$gxy2omsext($reference.file.ext)' && 34 ln -s '$reference.file' 'reference.file/${re.sub("[^\w\-_]", "_", $reference.file.element_identifier)}.$gxy2omsext($reference.file.ext)' &&
30 #end if 35 #end if
34 set -o pipefail && 39 set -o pipefail &&
35 @EXECUTABLE@ -write_ctd ./ && 40 @EXECUTABLE@ -write_ctd ./ &&
36 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && 41 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
37 @EXECUTABLE@ -ini @EXECUTABLE@.ctd 42 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
38 -in 43 -in
39 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} 44 #if $in_cond.in_select == "no"
45 ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
46 #else
47 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)'
48 #end if
40 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 49 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
41 -out 50 -out
42 ${' '.join(["'out/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), _.ext) for _ in $in if _])} 51 ${' '.join(["'out/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), f.ext) for i, f in enumerate($in_cond.in) if f])}
43 #end if 52 #end if
44 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 53 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
45 -trafo_out 54 -trafo_out
46 ${' '.join(["'trafo_out/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext("trafoxml")) for _ in $in if _])} 55 ${' '.join(["'trafo_out/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext("trafoxml")) for i, f in enumerate($in_cond.in) if f])}
47 #end if 56 #end if
48 #if $reference.file: 57 #if $reference.file:
49 -reference:file 58 -reference:file
50 'reference.file/${re.sub("[^\w\-_]", "_", $reference.file.element_identifier)}.$gxy2omsext($reference.file.ext)' 59 'reference.file/${re.sub("[^\w\-_]", "_", $reference.file.element_identifier)}.$gxy2omsext($reference.file.ext)'
51 #end if 60 #end if
53 | tee '$stdout' 62 | tee '$stdout'
54 #end if 63 #end if
55 64
56 ## Postprocessing 65 ## Postprocessing
57 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 66 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
58 ${' '.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 _])} 67 ${' '.join(["&& mv -n 'trafo_out/%(bn)s/%(id)s.%(gext)s' 'trafo_out/%(bn)s/%(id)s'"%{"bn": i, "id": re.sub('[^\w\-_]', '_', f.element_identifier), "gext": $gxy2omsext("trafoxml")} for i, f in enumerate($in_cond.in) if f])}
59 #end if 68 #end if
60 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS 69 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
61 && mv '@EXECUTABLE@.ctd' '$ctd_out' 70 && mv '@EXECUTABLE@.ctd' '$ctd_out'
62 #end if]]></command> 71 #end if]]></command>
63 <configfiles> 72 <configfiles>
64 <inputs name="args_json" data_style="paths"/> 73 <inputs name="args_json" data_style="paths"/>
65 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 74 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
66 </configfiles> 75 </configfiles>
67 <inputs> 76 <inputs>
68 <param name="in" argument="-in" type="data" format="featurexml,mzml" multiple="true" optional="false" label="Input files to align (all must have the same file type)" help=" select featurexml,mzml data sets(s)"/> 77 <conditional name="in_cond">
78 <param name="in_select" type="select" label="Run tool in batch mode for -in">
79 <option value="no">No: process all datasets jointly</option>
80 <option value="yes">Yes: process each dataset in an independent job</option>
81 </param>
82 <when value="no">
83 <param argument="-in" type="data" format="featurexml,mzml" multiple="true" optional="false" label="Input files to align (all must have the same file type)" help=" select featurexml,mzml data sets(s)"/>
84 </when>
85 <when value="yes">
86 <param argument="-in" type="data" format="featurexml,mzml" multiple="false" optional="false" label="Input files to align (all must have the same file type)" help=" select featurexml,mzml data sets(s)"/>
87 </when>
88 </conditional>
69 <section name="reference" title="Options to define a reference file (use either 'file' or 'index', not both)" help="" expanded="false"> 89 <section name="reference" title="Options to define a reference file (use either 'file' or 'index', not both)" help="" expanded="false">
70 <param name="file" argument="-reference:file" type="data" format="featurexml,mzml" optional="true" label="File to use as reference (same file format as input files required)" help=" select featurexml,mzml data sets(s)"/> 90 <param name="file" argument="-reference:file" type="data" format="featurexml,mzml" optional="true" label="File to use as reference (same file format as input files required)" help=" select featurexml,mzml data sets(s)"/>
71 <param name="index" argument="-reference:index" type="integer" optional="true" min="0" value="0" label="Use one of the input files as reference ('1' for the first file, etc.)" help="If '0', no explicit reference is set - the algorithm will select a reference"/> 91 <param name="index" argument="-reference:index" type="integer" optional="true" min="0" value="0" label="Use one of the input files as reference ('1' for the first file, etc.)" help="If '0', no explicit reference is set - the algorithm will select a reference"/>
72 </section> 92 </section>
73 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false"> 93 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
79 <param name="scaling_bucket_size" argument="-algorithm:superimposer:scaling_bucket_size" type="float" optional="true" min="0.0" value="0.005" label="The scaling of the retention time interval is being hashed into buckets of this size during pose clustering" help="A good choice for this would be a bit smaller than the error you would expect from repeated runs"/> 99 <param name="scaling_bucket_size" argument="-algorithm:superimposer:scaling_bucket_size" type="float" optional="true" min="0.0" value="0.005" label="The scaling of the retention time interval is being hashed into buckets of this size during pose clustering" help="A good choice for this would be a bit smaller than the error you would expect from repeated runs"/>
80 <param name="shift_bucket_size" argument="-algorithm:superimposer:shift_bucket_size" type="float" optional="true" min="0.0" value="3.0" label="The shift at the lower (respectively, higher) end of the retention time interval is being hashed into buckets of this size during pose clustering" help="A good choice for this would be about the time between consecutive MS scans"/> 100 <param name="shift_bucket_size" argument="-algorithm:superimposer:shift_bucket_size" type="float" optional="true" min="0.0" value="3.0" label="The shift at the lower (respectively, higher) end of the retention time interval is being hashed into buckets of this size during pose clustering" help="A good choice for this would be about the time between consecutive MS scans"/>
81 <param name="max_shift" argument="-algorithm:superimposer:max_shift" type="float" optional="true" min="0.0" value="1000.0" label="Maximal shift which is considered during histogramming (in seconds)" help="This applies for both directions"/> 101 <param name="max_shift" argument="-algorithm:superimposer:max_shift" type="float" optional="true" min="0.0" value="1000.0" label="Maximal shift which is considered during histogramming (in seconds)" help="This applies for both directions"/>
82 <param name="max_scaling" argument="-algorithm:superimposer:max_scaling" type="float" optional="true" min="1.0" value="2.0" label="Maximal scaling which is considered during histogramming" help="The minimal scaling is the reciprocal of this"/> 102 <param name="max_scaling" argument="-algorithm:superimposer:max_scaling" type="float" optional="true" min="1.0" value="2.0" label="Maximal scaling which is considered during histogramming" help="The minimal scaling is the reciprocal of this"/>
83 <param name="dump_buckets" argument="-algorithm:superimposer:dump_buckets" type="text" optional="true" value="" label="[DEBUG] If non-empty, base filename where hash table buckets will be dumped to" help="A serial number for each invocation will be appended automatically"> 103 <param name="dump_buckets" argument="-algorithm:superimposer:dump_buckets" type="text" optional="true" value="" label="[DEBUG] If non-empty, base filename where hash table buckets will be dumped to" help="A serial number for each invocation will be appended automatically">
84 <expand macro="list_string_san"/> 104 <expand macro="list_string_san" name="dump_buckets"/>
85 </param> 105 </param>
86 <param name="dump_pairs" argument="-algorithm:superimposer:dump_pairs" type="text" optional="true" value="" label="[DEBUG] If non-empty, base filename where the individual hashed pairs will be dumped to (large!)" help="A serial number for each invocation will be appended automatically"> 106 <param name="dump_pairs" argument="-algorithm:superimposer:dump_pairs" type="text" optional="true" value="" label="[DEBUG] If non-empty, base filename where the individual hashed pairs will be dumped to (large!)" help="A serial number for each invocation will be appended automatically">
87 <expand macro="list_string_san"/> 107 <expand macro="list_string_san" name="dump_pairs"/>
88 </param> 108 </param>
89 </section> 109 </section>
90 <section name="pairfinder" title="" help="" expanded="false"> 110 <section name="pairfinder" title="" help="" expanded="false">
91 <param name="second_nearest_gap" argument="-algorithm:pairfinder:second_nearest_gap" type="float" optional="true" min="1.0" value="2.0" label="Only link features whose distance to the second nearest neighbors (for both sides) is larger by 'second_nearest_gap' than the distance between the matched pair itself" help=""/> 111 <param name="second_nearest_gap" argument="-algorithm:pairfinder:second_nearest_gap" type="float" optional="true" min="1.0" value="2.0" label="Only link features whose distance to the second nearest neighbors (for both sides) is larger by 'second_nearest_gap' than the distance between the matched pair itself" help=""/>
92 <param name="use_identifications" argument="-algorithm:pairfinder:use_identifications" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Never link features that are annotated with different peptides (features without ID's always match; only the best hit per peptide identification is considered)" help=""/> 112 <param name="use_identifications" argument="-algorithm:pairfinder:use_identifications" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Never link features that are annotated with different peptides (features without ID's always match; only the best hit per peptide identification is considered)" help=""/>
97 <param name="exponent" argument="-algorithm:pairfinder:distance_RT:exponent" type="float" optional="true" min="0.0" value="1.0" label="Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/> 117 <param name="exponent" argument="-algorithm:pairfinder:distance_RT:exponent" type="float" optional="true" min="0.0" value="1.0" label="Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
98 <param name="weight" argument="-algorithm:pairfinder:distance_RT:weight" type="float" optional="true" min="0.0" value="1.0" label="Final RT distances are weighted by this facto" help=""/> 118 <param name="weight" argument="-algorithm:pairfinder:distance_RT:weight" type="float" optional="true" min="0.0" value="1.0" label="Final RT distances are weighted by this facto" help=""/>
99 </section> 119 </section>
100 <section name="distance_MZ" title="Distance component based on m/z differences" help="" expanded="false"> 120 <section name="distance_MZ" title="Distance component based on m/z differences" help="" expanded="false">
101 <param name="max_difference" argument="-algorithm:pairfinder:distance_MZ:max_difference" type="float" optional="true" min="0.0" value="0.3" label="Never pair features with larger m/z distance (unit defined by 'unit')" help=""/> 121 <param name="max_difference" argument="-algorithm:pairfinder:distance_MZ:max_difference" type="float" optional="true" min="0.0" value="0.3" label="Never pair features with larger m/z distance (unit defined by 'unit')" help=""/>
102 <param name="unit" argument="-algorithm:pairfinder:distance_MZ:unit" display="radio" type="select" optional="false" label="Unit of the 'max_difference' paramete" help=""> 122 <param name="unit" argument="-algorithm:pairfinder:distance_MZ:unit" type="select" optional="true" label="Unit of the 'max_difference' paramete" help="">
103 <option value="Da" selected="true">Da</option> 123 <option value="Da" selected="true">Da</option>
104 <option value="ppm">ppm</option> 124 <option value="ppm">ppm</option>
105 <expand macro="list_string_san"/> 125 <expand macro="list_string_san" name="unit"/>
106 </param> 126 </param>
107 <param name="exponent" argument="-algorithm:pairfinder:distance_MZ:exponent" type="float" optional="true" min="0.0" value="2.0" label="Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/> 127 <param name="exponent" argument="-algorithm:pairfinder:distance_MZ:exponent" type="float" optional="true" min="0.0" value="2.0" label="Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
108 <param name="weight" argument="-algorithm:pairfinder:distance_MZ:weight" type="float" optional="true" min="0.0" value="1.0" label="Final m/z distances are weighted by this facto" help=""/> 128 <param name="weight" argument="-algorithm:pairfinder:distance_MZ:weight" type="float" optional="true" min="0.0" value="1.0" label="Final m/z distances are weighted by this facto" help=""/>
109 </section> 129 </section>
110 <section name="distance_intensity" title="Distance component based on differences in relative intensity (usually relative to highest peak in the whole data set)" help="" expanded="false"> 130 <section name="distance_intensity" title="Distance component based on differences in relative intensity (usually relative to highest peak in the whole data set)" help="" expanded="false">
111 <param name="exponent" argument="-algorithm:pairfinder:distance_intensity:exponent" type="float" optional="true" min="0.0" value="1.0" label="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/> 131 <param name="exponent" argument="-algorithm:pairfinder:distance_intensity:exponent" type="float" optional="true" min="0.0" value="1.0" label="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
112 <param name="weight" argument="-algorithm:pairfinder:distance_intensity:weight" type="float" optional="true" min="0.0" value="0.0" label="Final intensity distances are weighted by this facto" help=""/> 132 <param name="weight" argument="-algorithm:pairfinder:distance_intensity:weight" type="float" optional="true" min="0.0" value="0.0" label="Final intensity distances are weighted by this facto" help=""/>
113 <param name="log_transform" argument="-algorithm:pairfinder:distance_intensity:log_transform" display="radio" type="select" optional="false" label="Log-transform intensities" help="If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))"> 133 <param name="log_transform" argument="-algorithm:pairfinder:distance_intensity:log_transform" type="select" optional="true" label="Log-transform intensities" help="If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))">
114 <option value="enabled">enabled</option> 134 <option value="enabled">enabled</option>
115 <option value="disabled" selected="true">disabled</option> 135 <option value="disabled" selected="true">disabled</option>
116 <expand macro="list_string_san"/> 136 <expand macro="list_string_san" name="log_transform"/>
117 </param> 137 </param>
118 </section> 138 </section>
119 </section> 139 </section>
120 </section> 140 </section>
121 <expand macro="adv_opts_macro"> 141 <expand macro="adv_opts_macro">
122 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 142 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
123 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 143 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
124 <expand macro="list_string_san"/> 144 <expand macro="list_string_san" name="test"/>
125 </param> 145 </param>
126 </expand> 146 </expand>
127 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 147 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
128 <option value="out_FLAG">out (Output files (same file type as 'in'))</option> 148 <option value="out_FLAG">out (Output files (same file type as 'in'))</option>
129 <option value="trafo_out_FLAG">trafo_out (Transformation output files)</option> 149 <option value="trafo_out_FLAG">trafo_out (Transformation output files)</option>
130 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 150 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
131 </param> 151 </param>
132 </inputs> 152 </inputs>
133 <outputs> 153 <outputs>
134 <collection type="list" name="out" label="${tool.name} on ${on_string}: out"> 154 <collection type="list" name="out" label="${tool.name} on ${on_string}: out">
135 <discover_datasets directory="out" pattern="__name_and_ext__"/> 155 <discover_datasets directory="out" recurse="true" pattern="__name_and_ext__"/>
136 <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter> 156 <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
137 </collection> 157 </collection>
138 <collection type="list" name="trafo_out" label="${tool.name} on ${on_string}: trafo_out"> 158 <collection type="list" name="trafo_out" label="${tool.name} on ${on_string}: trafo_out">
139 <discover_datasets directory="trafo_out" format="trafoxml" pattern="__name__"/> 159 <discover_datasets directory="trafo_out" recurse="true" format="trafoxml" pattern="__name__"/>
140 <filter>OPTIONAL_OUTPUTS is not None and "trafo_out_FLAG" in OPTIONAL_OUTPUTS</filter> 160 <filter>OPTIONAL_OUTPUTS is not None and "trafo_out_FLAG" in OPTIONAL_OUTPUTS</filter>
141 </collection> 161 </collection>
142 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout"> 162 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
143 <filter>OPTIONAL_OUTPUTS is None</filter> 163 <filter>OPTIONAL_OUTPUTS is None</filter>
144 </data> 164 </data>
145 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 165 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
146 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 166 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
147 </data> 167 </data>
148 </outputs> 168 </outputs>
149 <tests> 169 <tests><!-- TOPP_MapAlignerPoseClustering_1 -->
150 <expand macro="autotest_MapAlignerPoseClustering"/> 170 <test expect_num_outputs="3">
151 <expand macro="manutest_MapAlignerPoseClustering"/> 171 <section name="adv_opts">
172 <param name="force" value="false"/>
173 <param name="test" value="true"/>
174 </section>
175 <conditional name="in_cond">
176 <param name="in" value="MapAlignerPoseClustering_1_input1.featureXML,MapAlignerPoseClustering_1_input2.featureXML,MapAlignerPoseClustering_1_input3.featureXML"/>
177 </conditional>
178 <output_collection name="out" count="3"/>
179 <output_collection name="trafo_out" count="3"/>
180 <section name="reference">
181 <param name="index" value="0"/>
182 </section>
183 <section name="algorithm">
184 <param name="max_num_peaks_considered" value="400"/>
185 <section name="superimposer">
186 <param name="mz_pair_max_distance" value="0.5"/>
187 <param name="rt_pair_distance_fraction" value="0.1"/>
188 <param name="num_used_points" value="2000"/>
189 <param name="scaling_bucket_size" value="0.005"/>
190 <param name="shift_bucket_size" value="3.0"/>
191 <param name="max_shift" value="1000.0"/>
192 <param name="max_scaling" value="2.0"/>
193 <param name="dump_buckets" value=""/>
194 <param name="dump_pairs" value=""/>
195 </section>
196 <section name="pairfinder">
197 <param name="second_nearest_gap" value="2.0"/>
198 <param name="use_identifications" value="false"/>
199 <param name="ignore_charge" value="true"/>
200 <param name="ignore_adduct" value="true"/>
201 <section name="distance_RT">
202 <param name="max_difference" value="30.0"/>
203 <param name="exponent" value="1.0"/>
204 <param name="weight" value="1.0"/>
205 </section>
206 <section name="distance_MZ">
207 <param name="max_difference" value="0.3"/>
208 <param name="unit" value="Da"/>
209 <param name="exponent" value="2.0"/>
210 <param name="weight" value="1.0"/>
211 </section>
212 <section name="distance_intensity">
213 <param name="exponent" value="1.0"/>
214 <param name="weight" value="0.0"/>
215 <param name="log_transform" value="disabled"/>
216 </section>
217 </section>
218 </section>
219 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,trafo_out_FLAG"/>
220 <output name="ctd_out" ftype="xml">
221 <assert_contents>
222 <is_valid_xml/>
223 </assert_contents>
224 </output>
225 </test>
226 <!-- TOPP_MapAlignerPoseClustering_2 -->
227 <test expect_num_outputs="2">
228 <section name="adv_opts">
229 <param name="force" value="false"/>
230 <param name="test" value="true"/>
231 </section>
232 <conditional name="in_cond">
233 <param name="in" value="MapAlignerPoseClustering_2_input1.mzML,MapAlignerPoseClustering_2_input2.mzML,MapAlignerPoseClustering_2_input3.mzML"/>
234 </conditional>
235 <output_collection name="out" count="3"/>
236 <section name="reference">
237 <param name="index" value="0"/>
238 </section>
239 <section name="algorithm">
240 <param name="max_num_peaks_considered" value="400"/>
241 <section name="superimposer">
242 <param name="mz_pair_max_distance" value="0.5"/>
243 <param name="rt_pair_distance_fraction" value="0.1"/>
244 <param name="num_used_points" value="2000"/>
245 <param name="scaling_bucket_size" value="0.005"/>
246 <param name="shift_bucket_size" value="3.0"/>
247 <param name="max_shift" value="1000.0"/>
248 <param name="max_scaling" value="2.0"/>
249 <param name="dump_buckets" value=""/>
250 <param name="dump_pairs" value=""/>
251 </section>
252 <section name="pairfinder">
253 <param name="second_nearest_gap" value="2.0"/>
254 <param name="use_identifications" value="false"/>
255 <param name="ignore_charge" value="false"/>
256 <param name="ignore_adduct" value="true"/>
257 <section name="distance_RT">
258 <param name="max_difference" value="100.0"/>
259 <param name="exponent" value="1.0"/>
260 <param name="weight" value="1.0"/>
261 </section>
262 <section name="distance_MZ">
263 <param name="max_difference" value="0.3"/>
264 <param name="unit" value="Da"/>
265 <param name="exponent" value="2.0"/>
266 <param name="weight" value="1.0"/>
267 </section>
268 <section name="distance_intensity">
269 <param name="exponent" value="1.0"/>
270 <param name="weight" value="0.0"/>
271 <param name="log_transform" value="disabled"/>
272 </section>
273 </section>
274 </section>
275 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
276 <output name="ctd_out" ftype="xml">
277 <assert_contents>
278 <is_valid_xml/>
279 </assert_contents>
280 </output>
281 </test>
282 <!-- TOPP_MapAlignerPoseClustering_3 -->
283 <test expect_num_outputs="2">
284 <section name="adv_opts">
285 <param name="force" value="false"/>
286 <param name="test" value="true"/>
287 </section>
288 <conditional name="in_cond">
289 <param name="in" value="MapAlignerPoseClustering_1_input2.featureXML,MapAlignerPoseClustering_1_input3.featureXML"/>
290 </conditional>
291 <output_collection name="out" count="2"/>
292 <section name="reference">
293 <param name="file" value="MapAlignerPoseClustering_1_input1.featureXML"/>
294 <param name="index" value="0"/>
295 </section>
296 <section name="algorithm">
297 <param name="max_num_peaks_considered" value="400"/>
298 <section name="superimposer">
299 <param name="mz_pair_max_distance" value="0.5"/>
300 <param name="rt_pair_distance_fraction" value="0.1"/>
301 <param name="num_used_points" value="2000"/>
302 <param name="scaling_bucket_size" value="0.005"/>
303 <param name="shift_bucket_size" value="3.0"/>
304 <param name="max_shift" value="1000.0"/>
305 <param name="max_scaling" value="2.0"/>
306 <param name="dump_buckets" value=""/>
307 <param name="dump_pairs" value=""/>
308 </section>
309 <section name="pairfinder">
310 <param name="second_nearest_gap" value="2.0"/>
311 <param name="use_identifications" value="false"/>
312 <param name="ignore_charge" value="true"/>
313 <param name="ignore_adduct" value="true"/>
314 <section name="distance_RT">
315 <param name="max_difference" value="30.0"/>
316 <param name="exponent" value="1.0"/>
317 <param name="weight" value="1.0"/>
318 </section>
319 <section name="distance_MZ">
320 <param name="max_difference" value="0.3"/>
321 <param name="unit" value="Da"/>
322 <param name="exponent" value="2.0"/>
323 <param name="weight" value="1.0"/>
324 </section>
325 <section name="distance_intensity">
326 <param name="exponent" value="1.0"/>
327 <param name="weight" value="0.0"/>
328 <param name="log_transform" value="disabled"/>
329 </section>
330 </section>
331 </section>
332 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
333 <output name="ctd_out" ftype="xml">
334 <assert_contents>
335 <is_valid_xml/>
336 </assert_contents>
337 </output>
338 </test>
339 <!-- TOPP_MapAlignerPoseClustering_4 -->
340 <test expect_num_outputs="2">
341 <section name="adv_opts">
342 <param name="force" value="false"/>
343 <param name="test" value="true"/>
344 </section>
345 <conditional name="in_cond">
346 <param name="in" value="MapAlignerPoseClustering_1_input1.featureXML,MapAlignerPoseClustering_1_input2.featureXML"/>
347 </conditional>
348 <output_collection name="trafo_out" count="2"/>
349 <section name="reference">
350 <param name="index" value="2"/>
351 </section>
352 <section name="algorithm">
353 <param name="max_num_peaks_considered" value="400"/>
354 <section name="superimposer">
355 <param name="mz_pair_max_distance" value="0.5"/>
356 <param name="rt_pair_distance_fraction" value="0.1"/>
357 <param name="num_used_points" value="2000"/>
358 <param name="scaling_bucket_size" value="0.005"/>
359 <param name="shift_bucket_size" value="3.0"/>
360 <param name="max_shift" value="1000.0"/>
361 <param name="max_scaling" value="2.0"/>
362 <param name="dump_buckets" value=""/>
363 <param name="dump_pairs" value=""/>
364 </section>
365 <section name="pairfinder">
366 <param name="second_nearest_gap" value="2.0"/>
367 <param name="use_identifications" value="false"/>
368 <param name="ignore_charge" value="true"/>
369 <param name="ignore_adduct" value="true"/>
370 <section name="distance_RT">
371 <param name="max_difference" value="30.0"/>
372 <param name="exponent" value="1.0"/>
373 <param name="weight" value="1.0"/>
374 </section>
375 <section name="distance_MZ">
376 <param name="max_difference" value="0.3"/>
377 <param name="unit" value="Da"/>
378 <param name="exponent" value="2.0"/>
379 <param name="weight" value="1.0"/>
380 </section>
381 <section name="distance_intensity">
382 <param name="exponent" value="1.0"/>
383 <param name="weight" value="0.0"/>
384 <param name="log_transform" value="disabled"/>
385 </section>
386 </section>
387 </section>
388 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/>
389 <output name="ctd_out" ftype="xml">
390 <assert_contents>
391 <is_valid_xml/>
392 </assert_contents>
393 </output>
394 </test>
152 </tests> 395 </tests>
153 <help><![CDATA[Corrects retention time distortions between maps using a pose clustering approach. 396 <help><![CDATA[Corrects retention time distortions between maps using a pose clustering approach.
154 397
155 398
156 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_MapAlignerPoseClustering.html]]></help> 399 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MapAlignerPoseClustering.html]]></help>
157 <expand macro="references"/> 400 <expand macro="references"/>
158 </tool> 401 </tool>