Mercurial > repos > galaxyp > openms_featurelinkerlabeled

comparison FeatureLinkerLabeled.xml @ 11:fc56e75d8b14 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 12:43:02 +0000
parents 6cd2f41fa20b
children a33857ab19d0
comparison
equal deleted inserted replaced
10:898f5e7df62e 11:fc56e75d8b14
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="FeatureLinkerLabeled" name="FeatureLinkerLabeled" version="2.3.0"> 4 <tool id="FeatureLinkerLabeled" name="FeatureLinkerLabeled" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Groups corresponding isotope-labeled features in a feature map.</description> 5 <description>Groups corresponding isotope-labeled features in a feature map.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">FeatureLinkerLabeled</token> 7 <token name="@EXECUTABLE@">FeatureLinkerLabeled</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[FeatureLinkerLabeled 15 @EXT_FOO@
16 #import re
14 17
15 #if $param_in: 18 ## Preprocessing
16 -in $param_in 19 mkdir in &&
17 #end if 20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
18 #if $param_out: 21 mkdir out &&
19 -out $param_out
20 #end if
21 #if $param_algorithm_rt_estimate:
22 -algorithm:rt_estimate
23 #if " " in str($param_algorithm_rt_estimate):
24 "$param_algorithm_rt_estimate"
25 #else
26 $param_algorithm_rt_estimate
27 #end if
28 #end if
29 #if $param_algorithm_rt_pair_dist:
30 -algorithm:rt_pair_dist $param_algorithm_rt_pair_dist
31 #end if
32 #if $param_algorithm_rt_dev_low:
33 -algorithm:rt_dev_low $param_algorithm_rt_dev_low
34 #end if
35 #if $param_algorithm_rt_dev_high:
36 -algorithm:rt_dev_high $param_algorithm_rt_dev_high
37 #end if
38 22
39 #if $rep_param_algorithm_mz_pair_dists: 23 ## Main program call
40 -algorithm:mz_pair_dists 24
41 #for token in $rep_param_algorithm_mz_pair_dists: 25 set -o pipefail &&
42 #if " " in str(token): 26 @EXECUTABLE@ -write_ctd ./ &&
43 "$token.param_algorithm_mz_pair_dists" 27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
44 #else 28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
45 $token.param_algorithm_mz_pair_dists 29 -in
46 #end if 30 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
47 #end for 31 -out
48 #end if 32 'out/output.${gxy2omsext("consensusxml")}'
49 #if $param_algorithm_mz_dev: 33
50 -algorithm:mz_dev $param_algorithm_mz_dev 34 ## Postprocessing
51 #end if 35 && mv 'out/output.${gxy2omsext("consensusxml")}' '$out'
52 #if $adv_opts.adv_opts_selector=='advanced': 36 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
53 #if $adv_opts.param_force: 37 && mv '@EXECUTABLE@.ctd' '$ctd_out'
54 -force 38 #end if]]></command>
55 #end if 39 <configfiles>
56 #if $adv_opts.param_algorithm_mrm: 40 <inputs name="args_json" data_style="paths"/>
57 -algorithm:mrm 41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
58 #end if 42 </configfiles>
59 #end if
60 ]]></command>
61 <inputs> 43 <inputs>
62 <param name="param_in" type="data" format="featurexml" optional="False" label="Input file" help="(-in) "/> 44 <param name="in" argument="-in" type="data" format="featurexml" optional="false" label="Input file" help=" select featurexml data sets(s)"/>
63 <param name="param_algorithm_rt_estimate" display="radio" type="select" optional="False" value="true" label="If 'true' the optimal RT pair distance and deviation are estimated by fitting a gaussian distribution to the histogram of pair distance" help="(-rt_estimate) Note that this works only datasets with a significant amount of pairs! If 'false' the parameters 'rt_pair_dist', 'rt_dev_low' and 'rt_dev_high' define the optimal distance"> 45 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
64 <option value="true" selected="true">true</option> 46 <param name="rt_estimate" argument="-algorithm:rt_estimate" type="boolean" truevalue="true" falsevalue="false" checked="true" label="If 'true' the optimal RT pair distance and deviation are estimated by fitting a gaussian distribution to the histogram of pair distance" help="Note that this works only datasets with a significant amount of pairs! If 'false' the parameters 'rt_pair_dist', 'rt_dev_low' and 'rt_dev_high' define the optimal distance"/>
65 <option value="false">false</option> 47 <param name="rt_pair_dist" argument="-algorithm:rt_pair_dist" type="float" optional="true" value="-20.0" label="optimal pair distance in RT [sec] from light to heavy feature" help=""/>
48 <param name="rt_dev_low" argument="-algorithm:rt_dev_low" type="float" optional="true" min="0.0" value="15.0" label="maximum allowed deviation below optimal retention time distance" help=""/>
49 <param name="rt_dev_high" argument="-algorithm:rt_dev_high" type="float" optional="true" min="0.0" value="15.0" label="maximum allowed deviation above optimal retention time distance" help=""/>
50 <param name="mz_pair_dists" argument="-algorithm:mz_pair_dists" type="text" optional="true" value="4.0" label="optimal pair distances in m/z [Th] for features with charge +1 (adapted to +2, +3" help="by division through charge) (space separated list, in order to allow for spaces in list items surround them by single quotes)">
51 <expand macro="list_float_valsan"/>
52 </param>
53 <param name="mz_dev" argument="-algorithm:mz_dev" type="float" optional="true" min="0.0" value="0.05" label="maximum allowed deviation from optimal m/z distance" help=""/>
54 <param name="mrm" argument="-algorithm:mrm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="this option should be used if the features correspond mrm chromatograms (additionally the precursor is taken into account)" help=""/>
55 </section>
56 <expand macro="adv_opts_macro">
57 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
58 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
59 <expand macro="list_string_san"/>
60 </param>
61 </expand>
62 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
63 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
66 </param> 64 </param>
67 <param name="param_algorithm_rt_pair_dist" type="float" value="-20.0" label="optimal pair distance in RT [sec] from light to heavy feature" help="(-rt_pair_dist) "/>
68 <param name="param_algorithm_rt_dev_low" type="float" min="0.0" optional="True" value="15.0" label="maximum allowed deviation below optimal retention time distance" help="(-rt_dev_low) "/>
69 <param name="param_algorithm_rt_dev_high" type="float" min="0.0" optional="True" value="15.0" label="maximum allowed deviation above optimal retention time distance" help="(-rt_dev_high) "/>
70 <repeat name="rep_param_algorithm_mz_pair_dists" min="0" max="1" title="param_algorithm_mz_pair_dists">
71 <param name="param_algorithm_mz_pair_dists" type="text" size="30" value="4.0" label="optimal pair distances in m/z [Th] for features with charge +1 (adapted to +2, +3, ." help="(-mz_pair_dists) by division through charge)">
72 <sanitizer>
73 <valid initial="string.printable">
74 <remove value="'"/>
75 <remove value="&quot;"/>
76 </valid>
77 </sanitizer>
78 </param>
79 </repeat>
80 <param name="param_algorithm_mz_dev" type="float" min="0.0" optional="True" value="0.05" label="maximum allowed deviation from optimal m/z distance" help="(-mz_dev) "/>
81 <expand macro="advanced_options">
82 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
83 <param name="param_algorithm_mrm" display="radio" type="boolean" truevalue="-algorithm:mrm" falsevalue="" checked="false" optional="True" label="this option should be used if the features correspond mrm chromatograms (additionally the precursor is taken into account)" help="(-mrm) "/>
84 </expand>
85 </inputs> 65 </inputs>
86 <outputs> 66 <outputs>
87 <data name="param_out" format="consensusxml"/> 67 <data name="out" label="${tool.name} on ${on_string}: out" format="consensusxml"/>
68 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
69 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
70 </data>
88 </outputs> 71 </outputs>
89 <help>Groups corresponding isotope-labeled features in a feature map. 72 <tests>
73 <expand macro="autotest_FeatureLinkerLabeled"/>
74 <expand macro="manutest_FeatureLinkerLabeled"/>
75 </tests>
76 <help><![CDATA[Groups corresponding isotope-labeled features in a feature map.
90 77
91 78
92 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_FeatureLinkerLabeled.html</help> 79 For more information, visit http://www.openms.de/documentation/TOPP_FeatureLinkerLabeled.html]]></help>
80 <expand macro="references"/>
93 </tool> 81 </tool>