Mercurial > repos > galaxyp > openms_featurelinkerunlabeled

comparison FeatureLinkerUnlabeled.xml @ 11:6b88274392ce draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author galaxyp
date Wed, 09 Sep 2020 12:49:46 +0000
parents bc21e5dd5ff0
children a6e006df7659
comparison
equal deleted inserted replaced
10:180927fe6a29 11:6b88274392ce
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="FeatureLinkerUnlabeled" name="FeatureLinkerUnlabeled" version="2.3.0"> 4 <tool id="FeatureLinkerUnlabeled" name="FeatureLinkerUnlabeled" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Groups corresponding features from multiple maps.</description> 5 <description>Groups corresponding features from multiple maps.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">FeatureLinkerUnlabeled</token> 7 <token name="@EXECUTABLE@">FeatureLinkerUnlabeled</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[FeatureLinkerUnlabeled 15 @EXT_FOO@
16 #import re
14 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 mkdir out &&
22 #if $design:
23 mkdir design &&
24 ln -s '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' &&
25 #end if
26
27 ## Main program call
28
29 set -o pipefail &&
30 @EXECUTABLE@ -write_ctd ./ &&
31 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
32 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
15 -in 33 -in
16 #for token in $param_in: 34 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
17 $token 35 -out
18 #end for 36 'out/output.${gxy2omsext("consensusxml")}'
19 #if $param_out: 37 #if $design:
20 -out $param_out 38 -design
39 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)'
21 #end if 40 #end if
22 #if $param_design: 41
23 -design $param_design 42 ## Postprocessing
24 #end if 43 && mv 'out/output.${gxy2omsext("consensusxml")}' '$out'
25 #if $param_keep_subelements: 44 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
26 -keep_subelements 45 && mv '@EXECUTABLE@.ctd' '$ctd_out'
27 #end if 46 #end if]]></command>
28 #if $param_algorithm_second_nearest_gap: 47 <configfiles>
29 -algorithm:second_nearest_gap $param_algorithm_second_nearest_gap 48 <inputs name="args_json" data_style="paths"/>
30 #end if 49 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
31 #if $param_algorithm_use_identifications: 50 </configfiles>
32 -algorithm:use_identifications
33 #end if
34 #if $param_algorithm_ignore_charge:
35 -algorithm:ignore_charge
36 #end if
37 #if $param_algorithm_distance_RT_max_difference:
38 -algorithm:distance_RT:max_difference $param_algorithm_distance_RT_max_difference
39 #end if
40 #if $param_algorithm_distance_MZ_max_difference:
41 -algorithm:distance_MZ:max_difference $param_algorithm_distance_MZ_max_difference
42 #end if
43 #if $param_algorithm_distance_MZ_unit:
44 -algorithm:distance_MZ:unit
45 #if " " in str($param_algorithm_distance_MZ_unit):
46 "$param_algorithm_distance_MZ_unit"
47 #else
48 $param_algorithm_distance_MZ_unit
49 #end if
50 #end if
51 #if $adv_opts.adv_opts_selector=='advanced':
52 #if $adv_opts.param_force:
53 -force
54 #end if
55 #if $adv_opts.param_algorithm_distance_RT_exponent:
56 -algorithm:distance_RT:exponent $adv_opts.param_algorithm_distance_RT_exponent
57 #end if
58 #if $adv_opts.param_algorithm_distance_RT_weight:
59 -algorithm:distance_RT:weight $adv_opts.param_algorithm_distance_RT_weight
60 #end if
61 #if $adv_opts.param_algorithm_distance_MZ_exponent:
62 -algorithm:distance_MZ:exponent $adv_opts.param_algorithm_distance_MZ_exponent
63 #end if
64 #if $adv_opts.param_algorithm_distance_MZ_weight:
65 -algorithm:distance_MZ:weight $adv_opts.param_algorithm_distance_MZ_weight
66 #end if
67 #if $adv_opts.param_algorithm_distance_intensity_exponent:
68 -algorithm:distance_intensity:exponent $adv_opts.param_algorithm_distance_intensity_exponent
69 #end if
70 #if $adv_opts.param_algorithm_distance_intensity_weight:
71 -algorithm:distance_intensity:weight $adv_opts.param_algorithm_distance_intensity_weight
72 #end if
73 #if $adv_opts.param_algorithm_distance_intensity_log_transform:
74 -algorithm:distance_intensity:log_transform
75 #if " " in str($adv_opts.param_algorithm_distance_intensity_log_transform):
76 "$adv_opts.param_algorithm_distance_intensity_log_transform"
77 #else
78 $adv_opts.param_algorithm_distance_intensity_log_transform
79 #end if
80 #end if
81 #end if
82 ]]></command>
83 <inputs> 51 <inputs>
84 <param name="param_in" type="data" format="featurexml,consensusxml" multiple="true" optional="False" size="30" label="input files separated by blanks" help="(-in) "> 52 <param name="in" argument="-in" type="data" format="consensusxml,featurexml" multiple="true" optional="false" label="input files separated by blanks" help=" select consensusxml,featurexml data sets(s)"/>
85 <sanitizer> 53 <param name="design" argument="-design" type="data" format="tabular" optional="true" label="input file containing the experimental design" help=" select tabular data sets(s)"/>
86 <valid initial="string.printable"> 54 <param name="keep_subelements" argument="-keep_subelements" type="boolean" truevalue="true" falsevalue="false" checked="false" label="For consensusXML input only: If set, the sub-features of the inputs are transferred to the output" help=""/>
87 <remove value="'"/> 55 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
88 <remove value="&quot;"/> 56 <param name="second_nearest_gap" argument="-algorithm: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=""/>
89 </valid> 57 <param name="use_identifications" argument="-algorithm: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=""/>
90 </sanitizer> 58 <param name="ignore_charge" argument="-algorithm: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=""/>
91 </param> 59 <param name="ignore_adduct" argument="-algorithm: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=""/>
92 <param name="param_design" type="data" format="tabular" optional="True" label="input file containing the experimental design" help="(-design) "/> 60 <section name="distance_RT" title="Distance component based on RT differences" help="" expanded="false">
93 <param name="param_keep_subelements" display="radio" type="boolean" truevalue="-keep_subelements" falsevalue="" checked="false" optional="True" label="For consensusXML input only: If set, the sub-features of the inputs are transferred to the output" help="(-keep_subelements) "/> 61 <param name="max_difference" argument="-algorithm: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=""/>
94 <param name="param_algorithm_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) "/> 62 <param name="exponent" argument="-algorithm: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=""/>
95 <param name="param_algorithm_use_identifications" display="radio" type="boolean" truevalue="-algorithm: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) "/> 63 <param name="weight" argument="-algorithm:distance_RT:weight" type="float" optional="true" min="0.0" value="1.0" label="Final RT distances are weighted by this facto" help=""/>
96 <param name="param_algorithm_ignore_charge" display="radio" type="boolean" truevalue="-algorithm: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) "/> 64 </section>
97 <param name="param_algorithm_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) "/> 65 <section name="distance_MZ" title="Distance component based on m/z differences" help="" expanded="false">
98 <param name="param_algorithm_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) "/> 66 <param name="max_difference" argument="-algorithm: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=""/>
99 <param name="param_algorithm_distance_MZ_unit" display="radio" type="select" optional="False" value="Da" label="Unit of the 'max_difference' paramete" help="(-unit) "> 67 <param name="unit" argument="-algorithm:distance_MZ:unit" display="radio" type="select" optional="false" label="Unit of the 'max_difference' paramete" help="">
100 <option value="Da" selected="true">Da</option> 68 <option value="Da" selected="true">Da</option>
101 <option value="ppm">ppm</option> 69 <option value="ppm">ppm</option>
102 </param> 70 <expand macro="list_string_san"/>
103 <expand macro="advanced_options"> 71 </param>
104 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 72 <param name="exponent" argument="-algorithm: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=""/>
105 <param name="param_algorithm_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) "/> 73 <param name="weight" argument="-algorithm:distance_MZ:weight" type="float" optional="true" min="0.0" value="1.0" label="Final m/z distances are weighted by this facto" help=""/>
106 <param name="param_algorithm_distance_RT_weight" type="float" min="0.0" optional="True" value="1.0" label="Final RT distances are weighted by this facto" help="(-weight) "/> 74 </section>
107 <param name="param_algorithm_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) "/> 75 <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">
108 <param name="param_algorithm_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) "/> 76 <param name="exponent" argument="-algorithm: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=""/>
109 <param name="param_algorithm_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) "/> 77 <param name="weight" argument="-algorithm:distance_intensity:weight" type="float" optional="true" min="0.0" value="0.0" label="Final intensity distances are weighted by this facto" help=""/>
110 <param name="param_algorithm_distance_intensity_weight" type="float" min="0.0" optional="True" value="0.0" label="Final intensity distances are weighted by this facto" help="(-weight) "/> 78 <param name="log_transform" argument="-algorithm: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))">
111 <param name="param_algorithm_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))"> 79 <option value="enabled">enabled</option>
112 <option value="enabled">enabled</option> 80 <option value="disabled" selected="true">disabled</option>
113 <option value="disabled" selected="true">disabled</option> 81 <expand macro="list_string_san"/>
82 </param>
83 </section>
84 </section>
85 <expand macro="adv_opts_macro">
86 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
87 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
88 <expand macro="list_string_san"/>
114 </param> 89 </param>
115 </expand> 90 </expand>
91 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
92 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
93 </param>
116 </inputs> 94 </inputs>
117 <outputs> 95 <outputs>
118 <data name="param_out" format="consensusxml"/> 96 <data name="out" label="${tool.name} on ${on_string}: out" format="consensusxml"/>
97 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
98 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
99 </data>
119 </outputs> 100 </outputs>
120 <help>Groups corresponding features from multiple maps. 101 <tests>
102 <expand macro="autotest_FeatureLinkerUnlabeled"/>
103 <expand macro="manutest_FeatureLinkerUnlabeled"/>
104 </tests>
105 <help><![CDATA[Groups corresponding features from multiple maps.
121 106
122 107
123 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_FeatureLinkerUnlabeled.html</help> 108 For more information, visit http://www.openms.de/documentation/TOPP_FeatureLinkerUnlabeled.html]]></help>
109 <expand macro="references"/>
124 </tool> 110 </tool>