Mercurial > repos > galaxyp > openms_mapalignerposeclustering
comparison MapAlignerPoseClustering.xml @ 6:e237cb433a92 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author | galaxyp |
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date | Wed, 09 Sep 2020 12:47:05 +0000 |
parents | e86e83ac0cd3 |
children | d17db97d139f |
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5:3c5ffd6de67a | 6:e237cb433a92 |
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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="2.3.0"> | 4 <tool id="MapAlignerPoseClustering" name="MapAlignerPoseClustering" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> |
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> | |
9 </macros> | 11 </macros> |
10 <expand macro="references"/> | 12 <expand macro="requirements"/> |
11 <expand macro="stdio"/> | 13 <expand macro="stdio"/> |
12 <expand macro="requirements"/> | 14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ |
13 <command detect_errors="aggressive"><![CDATA[ | 15 @EXT_FOO@ |
16 #import re | |
14 | 17 |
15 #import re | 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 #if $reference.file: | |
28 mkdir reference.file && | |
29 ln -s '$reference.file' 'reference.file/${re.sub("[^\w\-_]", "_", $reference.file.element_identifier)}.$gxy2omsext($reference.file.ext)' && | |
30 #end if | |
16 | 31 |
17 mkdir -p ./results_trafoxml ./results_out && | 32 ## Main program call |
18 MapAlignerPoseClustering | |
19 | 33 |
34 set -o pipefail && | |
35 @EXECUTABLE@ -write_ctd ./ && | |
36 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && | |
37 @EXECUTABLE@ -ini @EXECUTABLE@.ctd | |
20 -in | 38 -in |
21 #for $infile in $param_in: | 39 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} |
22 '$infile' | 40 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') |
23 #end for | 41 -out |
42 ${' '.join(["'out/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), _.ext) for _ in $in if _])} | |
43 #end if | |
44 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') | |
45 -trafo_out | |
46 ${' '.join(["'trafo_out/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext("trafoxml")) for _ in $in if _])} | |
47 #end if | |
48 #if $reference.file: | |
49 -reference:file | |
50 'reference.file/${re.sub("[^\w\-_]", "_", $reference.file.element_identifier)}.$gxy2omsext($reference.file.ext)' | |
51 #end if | |
52 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 | |
53 | tee '$stdout' | |
54 #end if | |
24 | 55 |
25 -out | 56 ## Postprocessing |
26 #for $infile in $param_in: | 57 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') |
27 #set escaped_element_identifier = re.sub('[^\w\-\s]', '_', str($infile.element_identifier)) | 58 ${' '.join(["&& mv -n 'in/%(id)s.%(gext)s' 'trafo_out/%(id)s'"%{"id": re.sub('[^\w\-_]', '_', _.element_identifier), "gext": $gxy2omsext("trafoxml")} for _ in $trafo_out if _])} |
28 './results_out/${escaped_element_identifier}.${infile.extension}' | |
29 #end for | |
30 | |
31 -trafo_out | |
32 #for $infile in $param_in: | |
33 #set escaped_element_identifier = re.sub('[^\w\-\s]', '_', str($infile.element_identifier)) | |
34 './results_trafoxml/${escaped_element_identifier}.trafoxml' | |
35 #end for | |
36 | |
37 #if $param_reference_file: | |
38 -reference:file $param_reference_file | |
39 #end if | 59 #end if |
40 #if $param_reference_index: | 60 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS |
41 -reference:index $param_reference_index | 61 && mv '@EXECUTABLE@.ctd' '$ctd_out' |
42 #end if | 62 #end if]]></command> |
43 #if $param_algorithm_max_num_peaks_considered: | 63 <configfiles> |
44 -algorithm:max_num_peaks_considered $param_algorithm_max_num_peaks_considered | 64 <inputs name="args_json" data_style="paths"/> |
45 #end if | 65 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
46 #if $param_algorithm_superimposer_mz_pair_max_distance: | 66 </configfiles> |
47 -algorithm:superimposer:mz_pair_max_distance $param_algorithm_superimposer_mz_pair_max_distance | |
48 #end if | |
49 #if $param_algorithm_superimposer_num_used_points: | |
50 -algorithm:superimposer:num_used_points $param_algorithm_superimposer_num_used_points | |
51 #end if | |
52 #if $param_algorithm_superimposer_scaling_bucket_size: | |
53 -algorithm:superimposer:scaling_bucket_size $param_algorithm_superimposer_scaling_bucket_size | |
54 #end if | |
55 #if $param_algorithm_superimposer_shift_bucket_size: | |
56 -algorithm:superimposer:shift_bucket_size $param_algorithm_superimposer_shift_bucket_size | |
57 #end if | |
58 #if $param_algorithm_pairfinder_second_nearest_gap: | |
59 -algorithm:pairfinder:second_nearest_gap $param_algorithm_pairfinder_second_nearest_gap | |
60 #end if | |
61 #if $param_algorithm_pairfinder_use_identifications: | |
62 -algorithm:pairfinder:use_identifications | |
63 #end if | |
64 #if $param_algorithm_pairfinder_ignore_charge: | |
65 -algorithm:pairfinder:ignore_charge | |
66 #end if | |
67 #if $param_algorithm_pairfinder_distance_RT_max_difference: | |
68 -algorithm:pairfinder:distance_RT:max_difference $param_algorithm_pairfinder_distance_RT_max_difference | |
69 #end if | |
70 #if $param_algorithm_pairfinder_distance_MZ_max_difference: | |
71 -algorithm:pairfinder:distance_MZ:max_difference $param_algorithm_pairfinder_distance_MZ_max_difference | |
72 #end if | |
73 #if $param_algorithm_pairfinder_distance_MZ_unit: | |
74 -algorithm:pairfinder:distance_MZ:unit | |
75 #if " " in str($param_algorithm_pairfinder_distance_MZ_unit): | |
76 "$param_algorithm_pairfinder_distance_MZ_unit" | |
77 #else | |
78 $param_algorithm_pairfinder_distance_MZ_unit | |
79 #end if | |
80 #end if | |
81 #if $adv_opts.adv_opts_selector=='advanced': | |
82 #if $adv_opts.param_force: | |
83 -force | |
84 #end if | |
85 #if $adv_opts.param_algorithm_superimposer_rt_pair_distance_fraction: | |
86 -algorithm:superimposer:rt_pair_distance_fraction $adv_opts.param_algorithm_superimposer_rt_pair_distance_fraction | |
87 #end if | |
88 #if $adv_opts.param_algorithm_superimposer_max_shift: | |
89 -algorithm:superimposer:max_shift $adv_opts.param_algorithm_superimposer_max_shift | |
90 #end if | |
91 #if $adv_opts.param_algorithm_superimposer_max_scaling: | |
92 -algorithm:superimposer:max_scaling $adv_opts.param_algorithm_superimposer_max_scaling | |
93 #end if | |
94 #if $adv_opts.param_algorithm_superimposer_dump_buckets: | |
95 -algorithm:superimposer:dump_buckets "$adv_opts.param_algorithm_superimposer_dump_buckets" | |
96 #end if | |
97 #if $adv_opts.param_algorithm_superimposer_dump_pairs: | |
98 -algorithm:superimposer:dump_pairs "$adv_opts.param_algorithm_superimposer_dump_pairs" | |
99 #end if | |
100 #if $adv_opts.param_algorithm_pairfinder_distance_RT_exponent: | |
101 -algorithm:pairfinder:distance_RT:exponent $adv_opts.param_algorithm_pairfinder_distance_RT_exponent | |
102 #end if | |
103 #if $adv_opts.param_algorithm_pairfinder_distance_RT_weight: | |
104 -algorithm:pairfinder:distance_RT:weight $adv_opts.param_algorithm_pairfinder_distance_RT_weight | |
105 #end if | |
106 #if $adv_opts.param_algorithm_pairfinder_distance_MZ_exponent: | |
107 -algorithm:pairfinder:distance_MZ:exponent $adv_opts.param_algorithm_pairfinder_distance_MZ_exponent | |
108 #end if | |
109 #if $adv_opts.param_algorithm_pairfinder_distance_MZ_weight: | |
110 -algorithm:pairfinder:distance_MZ:weight $adv_opts.param_algorithm_pairfinder_distance_MZ_weight | |
111 #end if | |
112 #if $adv_opts.param_algorithm_pairfinder_distance_intensity_exponent: | |
113 -algorithm:pairfinder:distance_intensity:exponent $adv_opts.param_algorithm_pairfinder_distance_intensity_exponent | |
114 #end if | |
115 #if $adv_opts.param_algorithm_pairfinder_distance_intensity_weight: | |
116 -algorithm:pairfinder:distance_intensity:weight $adv_opts.param_algorithm_pairfinder_distance_intensity_weight | |
117 #end if | |
118 #if $adv_opts.param_algorithm_pairfinder_distance_intensity_log_transform: | |
119 -algorithm:pairfinder:distance_intensity:log_transform | |
120 #if " " in str($adv_opts.param_algorithm_pairfinder_distance_intensity_log_transform): | |
121 "$adv_opts.param_algorithm_pairfinder_distance_intensity_log_transform" | |
122 #else | |
123 $adv_opts.param_algorithm_pairfinder_distance_intensity_log_transform | |
124 #end if | |
125 #end if | |
126 #end if | |
127 ]]> | |
128 </command> | |
129 <inputs> | 67 <inputs> |
130 <param name="param_in" type="data" format="mzML,featureXML" multiple="true" label="Input files to align (all must have the same file type)" help="(-in) "/> | 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)"/> |
131 <param name="param_reference_file" type="data" format="mzML,featureXML" optional="True" label="File to use as reference (same file format as input files required)" help="(-file) "/> | 69 <section name="reference" title="Options to define a reference file (use either 'file' or 'index', not both)" help="" expanded="false"> |
132 <param name="param_reference_index" type="integer" min="0" optional="True" value="0" label="Use one of the input files as reference ('1' for the first file, etc.)" help="(-index) <br>If '0', no explicit reference is set - the algorithm will select a reference"/> | 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)"/> |
133 <param name="param_algorithm_max_num_peaks_considered" type="integer" min="-1" optional="True" value="1000" label="The maximal number of peaks/features to be considered per map" help="(-max_num_peaks_considered) To use all, set to '-1'"/> | 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"/> |
134 <param name="param_algorithm_superimposer_mz_pair_max_distance" type="float" min="0.0" optional="True" value="0.5" label="Maximum of m/z deviation of corresponding elements in different maps" help="(-mz_pair_max_distance) This condition applies to the pairs considered in hashing"/> | 72 </section> |
135 <param name="param_algorithm_superimposer_num_used_points" type="integer" min="-1" optional="True" value="2000" label="Maximum number of elements considered in each map (selected by intensity)" help="(-num_used_points) Use this to reduce the running time and to disregard weak signals during alignment. For using all points, set this to -1"/> | 73 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false"> |
136 <param name="param_algorithm_superimposer_scaling_bucket_size" type="float" min="0.0" optional="True" value="0.005" label="The scaling of the retention time interval is being hashed into buckets of this size during pose clustering" help="(-scaling_bucket_size) A good choice for this would be a bit smaller than the error you would expect from repeated runs"/> | 74 <param name="max_num_peaks_considered" argument="-algorithm:max_num_peaks_considered" type="integer" optional="true" min="-1" value="1000" label="The maximal number of peaks/features to be considered per map" help="To use all, set to '-1'"/> |
137 <param name="param_algorithm_superimposer_shift_bucket_size" type="float" min="0.0" optional="True" 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="(-shift_bucket_size) A good choice for this would be about the time between consecutive MS scans"/> | 75 <section name="superimposer" title="" help="" expanded="false"> |
138 <param name="param_algorithm_pairfinder_second_nearest_gap" type="float" min="1.0" optional="True" 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="(-second_nearest_gap) "/> | 76 <param name="mz_pair_max_distance" argument="-algorithm:superimposer:mz_pair_max_distance" type="float" optional="true" min="0.0" value="0.5" label="Maximum of m/z deviation of corresponding elements in different maps" help="This condition applies to the pairs considered in hashing"/> |
139 <param name="param_algorithm_pairfinder_use_identifications" display="radio" type="boolean" truevalue="-algorithm:pairfinder:use_identifications" falsevalue="" checked="false" optional="True" 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="(-use_identifications) "/> | 77 <param name="rt_pair_distance_fraction" argument="-algorithm:superimposer:rt_pair_distance_fraction" type="float" optional="true" min="0.0" max="1.0" value="0.1" label="Within each of the two maps, the pairs considered for pose clustering must be separated by at least this fraction of the total elution time interval" help="(i.e., max - min). "/> |
140 <param name="param_algorithm_pairfinder_ignore_charge" display="radio" type="boolean" truevalue="-algorithm:pairfinder:ignore_charge" falsevalue="" checked="false" optional="True" label="false [default]: pairing requires equal charge state (or at least one unknown charge '0'); true: Pairing irrespective of charge state" help="(-ignore_charge) "/> | 78 <param name="num_used_points" argument="-algorithm:superimposer:num_used_points" type="integer" optional="true" min="-1" value="2000" label="Maximum number of elements considered in each map (selected by intensity)" help="Use this to reduce the running time and to disregard weak signals during alignment. For using all points, set this to -1"/> |
141 <param name="param_algorithm_pairfinder_distance_RT_max_difference" type="float" min="0.0" optional="True" value="100.0" label="Never pair features with a larger RT distance (in seconds)" help="(-max_difference) "/> | 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"/> |
142 <param name="param_algorithm_pairfinder_distance_MZ_max_difference" type="float" min="0.0" optional="True" value="0.3" label="Never pair features with larger m/z distance (unit defined by 'unit')" help="(-max_difference) "/> | 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"/> |
143 <param name="param_algorithm_pairfinder_distance_MZ_unit" display="radio" type="select" optional="False" value="Da" label="Unit of the 'max_difference' paramete" help="(-unit) "> | 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"/> |
144 <option value="Da" selected="true">Da</option> | 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"/> |
145 <option value="ppm">ppm</option> | 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"> |
146 </param> | 84 <expand macro="list_string_san"/> |
147 <expand macro="advanced_options"> | 85 </param> |
148 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> | 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"> |
149 <param name="param_algorithm_superimposer_rt_pair_distance_fraction" type="float" min="0.0" max="1.0" optional="True" value="0.1" label="Within each of the two maps, the pairs considered for pose clustering must be separated by at least this fraction of the total elution time interval (i.e., max - min)" help="(-rt_pair_distance_fraction) "/> | 87 <expand macro="list_string_san"/> |
150 <param name="param_algorithm_superimposer_max_shift" type="float" min="0.0" optional="True" value="1000.0" label="Maximal shift which is considered during histogramming (in seconds)" help="(-max_shift) This applies for both directions"/> | 88 </param> |
151 <param name="param_algorithm_superimposer_max_scaling" type="float" min="1.0" optional="True" value="2.0" label="Maximal scaling which is considered during histogramming" help="(-max_scaling) The minimal scaling is the reciprocal of this"/> | 89 </section> |
152 <param name="param_algorithm_superimposer_dump_buckets" type="text" size="30" label="[DEBUG] If non-empty, base filename where hash table buckets will be dumped to" help="(-dump_buckets) A serial number for each invocation will be appended automatically"> | 90 <section name="pairfinder" title="" help="" expanded="false"> |
153 <sanitizer> | 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=""/> |
154 <valid initial="string.printable"> | 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=""/> |
155 <remove value="'"/> | 93 <param name="ignore_charge" argument="-algorithm:pairfinder:ignore_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="false [default]: pairing requires equal charge state (or at least one unknown charge '0'); true: Pairing irrespective of charge state" help=""/> |
156 <remove value="""/> | 94 <param name="ignore_adduct" argument="-algorithm:pairfinder:ignore_adduct" type="boolean" truevalue="true" falsevalue="false" checked="true" label="true [default]: pairing requires equal adducts (or at least one without adduct annotation); true: Pairing irrespective of adducts" help=""/> |
157 </valid> | 95 <section name="distance_RT" title="Distance component based on RT differences" help="" expanded="false"> |
158 </sanitizer> | 96 <param name="max_difference" argument="-algorithm:pairfinder:distance_RT:max_difference" type="float" optional="true" min="0.0" value="100.0" label="Never pair features with a larger RT distance (in seconds)" help=""/> |
159 </param> | 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=""/> |
160 <param name="param_algorithm_superimposer_dump_pairs" type="text" size="30" label="[DEBUG] If non-empty, base filename where the individual hashed pairs will be dumped to (large!)" help="(-dump_pairs) A serial number for each invocation will be appended automatically"> | 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=""/> |
161 <sanitizer> | 99 </section> |
162 <valid initial="string.printable"> | 100 <section name="distance_MZ" title="Distance component based on m/z differences" help="" expanded="false"> |
163 <remove value="'"/> | 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=""/> |
164 <remove value="""/> | 102 <param name="unit" argument="-algorithm:pairfinder:distance_MZ:unit" display="radio" type="select" optional="false" label="Unit of the 'max_difference' paramete" help=""> |
165 </valid> | 103 <option value="Da" selected="true">Da</option> |
166 </sanitizer> | 104 <option value="ppm">ppm</option> |
167 </param> | 105 <expand macro="list_string_san"/> |
168 <param name="param_algorithm_pairfinder_distance_RT_exponent" type="float" min="0.0" optional="True" 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="(-exponent) "/> | 106 </param> |
169 <param name="param_algorithm_pairfinder_distance_RT_weight" type="float" min="0.0" optional="True" value="1.0" label="Final RT distances are weighted by this facto" help="(-weight) "/> | 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=""/> |
170 <param name="param_algorithm_pairfinder_distance_MZ_exponent" type="float" min="0.0" optional="True" 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="(-exponent) "/> | 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=""/> |
171 <param name="param_algorithm_pairfinder_distance_MZ_weight" type="float" min="0.0" optional="True" value="1.0" label="Final m/z distances are weighted by this facto" help="(-weight) "/> | 109 </section> |
172 <param name="param_algorithm_pairfinder_distance_intensity_exponent" type="float" min="0.0" optional="True" 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="(-exponent) "/> | 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"> |
173 <param name="param_algorithm_pairfinder_distance_intensity_weight" type="float" min="0.0" optional="True" value="0.0" label="Final intensity distances are weighted by this facto" help="(-weight) "/> | 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=""/> |
174 <param name="param_algorithm_pairfinder_distance_intensity_log_transform" display="radio" type="select" optional="False" value="disabled" label="Log-transform intensities?" help="(-log_transform) If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))"> | 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=""/> |
175 <option value="enabled">enabled</option> | 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))"> |
176 <option value="disabled" selected="true">disabled</option> | 114 <option value="enabled">enabled</option> |
115 <option value="disabled" selected="true">disabled</option> | |
116 <expand macro="list_string_san"/> | |
117 </param> | |
118 </section> | |
119 </section> | |
120 </section> | |
121 <expand macro="adv_opts_macro"> | |
122 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite 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=""> | |
124 <expand macro="list_string_san"/> | |
177 </param> | 125 </param> |
178 </expand> | 126 </expand> |
179 </inputs> | 127 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="false"> |
180 <outputs> | 128 <option value="out_FLAG">out (Log-transform intensities)</option> |
181 <collection name="out" type="list"> | 129 <option value="trafo_out_FLAG">trafo_out (Log-transform intensities)</option> |
182 <discover_datasets pattern="__designation_and_ext__" directory="results_out"/> | 130 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> |
183 </collection> | 131 </param> |
132 </inputs> | |
133 <outputs> | |
134 <collection type="list" name="out" label="${tool.name} on ${on_string}: out"> | |
135 <discover_datasets directory="out" pattern="__name_and_ext__"/> | |
136 <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter> | |
137 </collection> | |
138 <collection type="list" name="trafo_out" label="${tool.name} on ${on_string}: trafo_out"> | |
139 <discover_datasets directory="trafo_out" format="trafoxml" pattern="__name__"/> | |
140 <filter>OPTIONAL_OUTPUTS is not None and "trafo_out_FLAG" in OPTIONAL_OUTPUTS</filter> | |
141 </collection> | |
142 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout"> | |
143 <filter>OPTIONAL_OUTPUTS is None</filter> | |
144 </data> | |
145 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | |
146 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | |
147 </data> | |
148 </outputs> | |
149 <tests> | |
150 <expand macro="autotest_MapAlignerPoseClustering"/> | |
151 <expand macro="manutest_MapAlignerPoseClustering"/> | |
152 </tests> | |
153 <help><![CDATA[Corrects retention time distortions between maps using a pose clustering approach. | |
184 | 154 |
185 <collection name="trafo_out" type="list"> | |
186 <discover_datasets pattern="__designation_and_ext__" directory="results_trafoxml"/> | |
187 </collection> | |
188 </outputs> | |
189 <help>Corrects retention time distortions between maps using a pose clustering approach. | |
190 | 155 |
191 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_MapAlignerPoseClustering.html</help> | 156 For more information, visit http://www.openms.de/documentation/TOPP_MapAlignerPoseClustering.html]]></help> |
157 <expand macro="references"/> | |
192 </tool> | 158 </tool> |