Mercurial > repos > galaxyp > openms_spectrafilterparentpeakmower

comparison SpectraFilterParentPeakMower.xml @ 9:e60558a87656 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, 03 Sep 2020 16:16:33 +0000
parents d484676f03cd
children 75492ef0bff5
comparison
equal deleted inserted replaced
8:6a15c0b39d25 9:e60558a87656
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: [Identification]--> 3 <!--Proposed Tool Section: [Identification]-->
4 <tool id="SpectraFilterParentPeakMower" name="SpectraFilterParentPeakMower" version="2.3.0"> 4 <tool id="SpectraFilterParentPeakMower" name="SpectraFilterParentPeakMower" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Applies thresholdfilter to peak spectra.</description> 5 <description>Applies thresholdfilter to peak spectra.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">SpectraFilterParentPeakMower</token> 7 <token name="@EXECUTABLE@">SpectraFilterParentPeakMower</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[SpectraFilterParentPeakMower 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 22
20 #end if 23 ## Main program call
21 #if $param_algorithm_window_size: 24
22 -algorithm:window_size $param_algorithm_window_size 25 set -o pipefail &&
23 #end if 26 @EXECUTABLE@ -write_ctd ./ &&
24 #if $param_algorithm_default_charge: 27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
25 -algorithm:default_charge $param_algorithm_default_charge 28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
26 #end if 29 -in
27 #if $param_algorithm_consider_NH3_loss: 30 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
28 -algorithm:consider_NH3_loss $param_algorithm_consider_NH3_loss 31 -out
29 #end if 32 'out/output.${gxy2omsext("mzml")}'
30 #if $param_algorithm_consider_H2O_loss: 33
31 -algorithm:consider_H2O_loss $param_algorithm_consider_H2O_loss 34 ## Postprocessing
32 #end if 35 && mv 'out/output.${gxy2omsext("mzml")}' '$out'
33 #if $adv_opts.adv_opts_selector=='advanced': 36 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
34 #if $adv_opts.param_force: 37 && mv '@EXECUTABLE@.ctd' '$ctd_out'
35 -force 38 #end if]]></command>
36 #end if 39 <configfiles>
37 #if $adv_opts.param_algorithm_clean_all_charge_states: 40 <inputs name="args_json" data_style="paths"/>
38 -algorithm:clean_all_charge_states $adv_opts.param_algorithm_clean_all_charge_states 41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
39 #end if 42 </configfiles>
40 #if $adv_opts.param_algorithm_reduce_by_factor:
41 -algorithm:reduce_by_factor $adv_opts.param_algorithm_reduce_by_factor
42 #end if
43 #if $adv_opts.param_algorithm_factor:
44 -algorithm:factor $adv_opts.param_algorithm_factor
45 #end if
46 #if $adv_opts.param_algorithm_set_to_zero:
47 -algorithm:set_to_zero $adv_opts.param_algorithm_set_to_zero
48 #end if
49 #end if
50 ]]></command>
51 <inputs> 43 <inputs>
52 <param name="param_in" type="data" format="mzml" optional="False" label="input file" help="(-in) "/> 44 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/>
53 <param name="param_algorithm_window_size" type="float" value="2.0" label="The size of the m/z window where the peaks are removed, +/- window_size" help="(-window_size) "/> 45 <section name="algorithm" title="Algorithm parameter subsection" help="" expanded="false">
54 <param name="param_algorithm_default_charge" type="integer" value="2" label="If the precursor has no charge set, the default charge is assumed" help="(-default_charge) "/> 46 <param name="window_size" argument="-algorithm:window_size" type="float" optional="true" value="2.0" label="The size of the m/z window where the peaks are removed, +/- window_size" help=""/>
55 <param name="param_algorithm_consider_NH3_loss" type="integer" value="1" label="Whether NH3 loss peaks from the precursor should be removed" help="(-consider_NH3_loss) "/> 47 <param name="default_charge" argument="-algorithm:default_charge" type="integer" optional="true" value="2" label="If the precursor has no charge set, the default charge is assumed" help=""/>
56 <param name="param_algorithm_consider_H2O_loss" type="integer" value="1" label="Whether H2O loss peaks from the precursor should be removed" help="(-consider_H2O_loss) "/> 48 <param name="clean_all_charge_states" argument="-algorithm:clean_all_charge_states" type="integer" optional="true" value="1" label="Set to 1 if precursor ions of all possible charge states should be removed" help=""/>
57 <expand macro="advanced_options"> 49 <param name="consider_NH3_loss" argument="-algorithm:consider_NH3_loss" type="integer" optional="true" value="1" label="Whether NH3 loss peaks from the precursor should be removed" help=""/>
58 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 50 <param name="consider_H2O_loss" argument="-algorithm:consider_H2O_loss" type="integer" optional="true" value="1" label="Whether H2O loss peaks from the precursor should be removed" help=""/>
59 <param name="param_algorithm_clean_all_charge_states" type="integer" value="1" label="Set to 1 if precursor ions of all possible charge states should be removed" help="(-clean_all_charge_states) "/> 51 <param name="reduce_by_factor" argument="-algorithm:reduce_by_factor" type="integer" optional="true" value="0" label="Reduce the intensities of the precursor and related ions by a given factor (set 'set_to_zero' to 0)" help=""/>
60 <param name="param_algorithm_reduce_by_factor" type="integer" value="0" label="Reduce the intensities of the precursor and related ions by a given factor (set 'set_to_zero' to 0)" help="(-reduce_by_factor) "/> 52 <param name="factor" argument="-algorithm:factor" type="float" optional="true" value="1000.0" label="Factor which is used to reduce the intensities if 'reduce_by_factor' is selected" help=""/>
61 <param name="param_algorithm_factor" type="float" value="1000.0" label="Factor which is used to reduce the intensities if 'reduce_by_factor' is selected" help="(-factor) "/> 53 <param name="set_to_zero" argument="-algorithm:set_to_zero" type="integer" optional="true" value="1" label="Reduce the intensities of the precursor and related ions to zero" help=""/>
62 <param name="param_algorithm_set_to_zero" type="integer" value="1" label="Reduce the intensities of the precursor and related ions to zero" help="(-set_to_zero) "/> 54 </section>
55 <expand macro="adv_opts_macro">
56 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
57 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
58 <expand macro="list_string_san"/>
59 </param>
63 </expand> 60 </expand>
61 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
62 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
63 </param>
64 </inputs> 64 </inputs>
65 <outputs> 65 <outputs>
66 <data name="param_out" format="mzml"/> 66 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
67 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
68 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
69 </data>
67 </outputs> 70 </outputs>
68 <help>Applies thresholdfilter to peak spectra. 71 <tests>
72 <expand macro="autotest_SpectraFilterParentPeakMower"/>
73 <expand macro="manutest_SpectraFilterParentPeakMower"/>
74 </tests>
75 <help><![CDATA[Applies thresholdfilter to peak spectra.
69 76
70 77
71 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_SpectraFilterParentPeakMower.html</help> 78 For more information, visit http://www.openms.de/documentation/TOPP_SpectraFilterParentPeakMower.html]]></help>
79 <expand macro="references"/>
72 </tool> 80 </tool>