Mercurial > repos > galaxyp > openms_featurefindersuperhirn
annotate FeatureFinderSuperHirn.xml @ 13:6b6f5338c01c draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
| author | galaxyp |
|---|---|
| date | Tue, 13 Oct 2020 20:17:46 +0000 |
| parents | f35d5aa5d58a |
| children |
| rev | line source |
|---|---|
|
0
048af24c0e2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
1 <?xml version='1.0' encoding='UTF-8'?> |
|
7
cb6efad08345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
galaxyp
parents:
3
diff
changeset
|
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> |
|
0
048af24c0e2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
3 <!--Proposed Tool Section: [Quantitation]--> |
|
11
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
4 <tool id="FeatureFinderSuperHirn" name="FeatureFinderSuperHirn" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> |
|
0
048af24c0e2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
5 <description>Finds mass spectrometric features in mass spectra.</description> |
|
048af24c0e2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
6 <macros> |
|
048af24c0e2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
7 <token name="@EXECUTABLE@">FeatureFinderSuperHirn</token> |
|
048af24c0e2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
8 <import>macros.xml</import> |
|
11
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
9 <import>macros_autotest.xml</import> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
10 <import>macros_test.xml</import> |
|
0
048af24c0e2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
11 </macros> |
|
11
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
12 <expand macro="requirements"/> |
|
0
048af24c0e2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
13 <expand macro="stdio"/> |
|
11
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
15 @EXT_FOO@ |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
16 #import re |
|
0
048af24c0e2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
17 |
|
11
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
18 ## Preprocessing |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
19 mkdir in && |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
21 mkdir out && |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
22 |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
23 ## Main program call |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
24 |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
25 set -o pipefail && |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
26 @EXECUTABLE@ -write_ctd ./ && |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
29 -in |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
30 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
31 -out |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
32 'out/output.${gxy2omsext("featurexml")}' |
|
0
048af24c0e2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
33 |
|
11
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
34 ## Postprocessing |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
35 && mv 'out/output.${gxy2omsext("featurexml")}' '$out' |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
36 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
37 && mv '@EXECUTABLE@.ctd' '$ctd_out' |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
38 #end if]]></command> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
39 <configfiles> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
40 <inputs name="args_json" data_style="paths"/> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
42 </configfiles> |
|
0
048af24c0e2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
43 <inputs> |
|
11
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
44 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input profile data file" help=" select mzml data sets(s)"/> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
45 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false"> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
46 <section name="centroiding" title="" help="" expanded="false"> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
47 <param name="active" argument="-algorithm:centroiding:active" type="boolean" truevalue="true" falsevalue="false" checked="false" label="MS1 data centroid data" help=""/> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
48 <param name="window_width" argument="-algorithm:centroiding:window_width" type="integer" optional="true" min="1" value="5" label="Centroid window width" help=""/> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
49 <param name="absolute_isotope_mass_precision" argument="-algorithm:centroiding:absolute_isotope_mass_precision" type="float" optional="true" min="0.0" value="0.01" label="Absolute isotope mass precision (Da)" help=""/> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
50 <param name="relative_isotope_mass_precision" argument="-algorithm:centroiding:relative_isotope_mass_precision" type="float" optional="true" min="0.0" value="10.0" label="Relative isotope mass precision" help=""/> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
51 <param name="minimal_peak_height" argument="-algorithm:centroiding:minimal_peak_height" type="float" optional="true" min="0.0" value="0.0" label="Minimal peak height" help=""/> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
52 <param name="min_ms_signal_intensity" argument="-algorithm:centroiding:min_ms_signal_intensity" type="float" optional="true" min="0.0" value="50.0" label="Minimal Centroid MS Signal Intensity" help=""/> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
53 </section> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
54 <section name="ms1" title="" help="" expanded="false"> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
55 <param name="precursor_detection_scan_levels" argument="-algorithm:ms1:precursor_detection_scan_levels" type="text" optional="true" value="1" label="Precursor detection scan levels" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
56 <expand macro="list_integer_valsan"/> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
57 </param> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
58 <param name="max_inter_scan_distance" argument="-algorithm:ms1:max_inter_scan_distance" type="integer" optional="true" min="0" value="0" label="MS1 max inter scan distance" help=""/> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
59 <param name="tr_resolution" argument="-algorithm:ms1:tr_resolution" type="float" optional="true" min="0.0" value="0.01" label="MS1 LC retention time resolution" help=""/> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
60 <param name="intensity_threshold" argument="-algorithm:ms1:intensity_threshold" type="float" optional="true" min="0.0" value="1000.0" label="FT peak detect MS1 intensity min threshold" help=""/> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
61 <param name="max_inter_scan_rt_distance" argument="-algorithm:ms1:max_inter_scan_rt_distance" type="float" optional="true" min="0.0" value="0.1" label="MS1 max inter scan distance" help=""/> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
62 <param name="min_nb_cluster_members" argument="-algorithm:ms1:min_nb_cluster_members" type="integer" optional="true" min="0" value="4" label="FT peak detect MS1 min nb peak members" help=""/> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
63 <param name="detectable_isotope_factor" argument="-algorithm:ms1:detectable_isotope_factor" type="float" optional="true" min="0.0" value="0.05" label="Detectable isotope facto" help=""/> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
64 <param name="intensity_cv" argument="-algorithm:ms1:intensity_cv" type="float" optional="true" min="0.0" value="0.9" label="IntensityCV" help=""/> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
65 <param name="retention_time_tolerance" argument="-algorithm:ms1:retention_time_tolerance" type="float" optional="true" min="0.0" value="0.5" label="MS1 retention time tolerance (minutes)" help=""/> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
66 <param name="mz_tolerance" argument="-algorithm:ms1:mz_tolerance" type="float" optional="true" min="0.0" value="0.0" label="MS1 m/z tolerance (ppm)" help=""/> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
67 </section> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
68 <section name="ms1_feature_merger" title="" help="" expanded="false"> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
69 <param name="active" argument="-algorithm:ms1_feature_merger:active" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Activation of MS1 feature merging post processing" help=""/> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
70 <param name="tr_resolution" argument="-algorithm:ms1_feature_merger:tr_resolution" type="float" optional="true" min="0.0" value="0.01" label="MS1 LC retention time resolution" help=""/> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
71 <param name="initial_apex_tr_tolerance" argument="-algorithm:ms1_feature_merger:initial_apex_tr_tolerance" type="float" optional="true" min="0.0" value="5.0" label="Initial Apex Tr tolerance" help=""/> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
72 <param name="feature_merging_tr_tolerance" argument="-algorithm:ms1_feature_merger:feature_merging_tr_tolerance" type="float" optional="true" min="0.0" value="1.0" label="MS1 feature Tr merging tolerance" help=""/> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
73 <param name="intensity_variation_percentage" argument="-algorithm:ms1_feature_merger:intensity_variation_percentage" type="float" optional="true" min="0.0" max="100.0" value="25.0" label="Percentage of intensity variation between LC border peaks" help=""/> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
74 <param name="ppm_tolerance_for_mz_clustering" argument="-algorithm:ms1_feature_merger:ppm_tolerance_for_mz_clustering" type="float" optional="true" min="0.0" value="10.0" label="PPM value for the m/z clustering of merging candidates" help=""/> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
75 </section> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
76 <section name="ms1_feature_selection_options" title="" help="" expanded="false"> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
77 <param name="start_elution_window" argument="-algorithm:ms1_feature_selection_options:start_elution_window" type="float" optional="true" min="0.0" value="0.0" label="start elution window (minutes)" help=""/> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
78 <param name="end_elution_window" argument="-algorithm:ms1_feature_selection_options:end_elution_window" type="float" optional="true" min="0.0" value="180.0" label="end elution window (minutes)" help=""/> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
79 <param name="mz_range_min" argument="-algorithm:ms1_feature_selection_options:mz_range_min" type="float" optional="true" min="0.0" value="0.0" label="MS1 feature mz range min" help=""/> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
80 <param name="mz_range_max" argument="-algorithm:ms1_feature_selection_options:mz_range_max" type="float" optional="true" min="0.0" value="2000.0" label="MS1 feature mz range max" help=""/> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
81 <param name="chrg_range_min" argument="-algorithm:ms1_feature_selection_options:chrg_range_min" type="integer" optional="true" min="0" value="1" label="MS1 feature CHRG range min" help=""/> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
82 <param name="chrg_range_max" argument="-algorithm:ms1_feature_selection_options:chrg_range_max" type="integer" optional="true" min="0" value="5" label="MS1 feature CHRG range max" help=""/> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
83 </section> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
84 </section> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
85 <expand macro="adv_opts_macro"> |
|
13
6b6f5338c01c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
galaxyp
parents:
12
diff
changeset
|
86 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> |
|
11
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
87 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
88 <expand macro="list_string_san"/> |
|
0
048af24c0e2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
89 </param> |
|
11
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
90 </expand> |
|
13
6b6f5338c01c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
galaxyp
parents:
12
diff
changeset
|
91 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> |
|
11
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
92 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> |
|
0
048af24c0e2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
93 </param> |
|
048af24c0e2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
94 </inputs> |
|
048af24c0e2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
95 <outputs> |
|
11
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
96 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
97 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
98 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
99 </data> |
|
0
048af24c0e2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
100 </outputs> |
|
11
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
101 <tests> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
102 <expand macro="autotest_FeatureFinderSuperHirn"/> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
103 <expand macro="manutest_FeatureFinderSuperHirn"/> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
104 </tests> |
|
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
105 <help><![CDATA[Finds mass spectrometric features in mass spectra. |
|
13
6b6f5338c01c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
galaxyp
parents:
12
diff
changeset
|
106 |
|
6b6f5338c01c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
galaxyp
parents:
12
diff
changeset
|
107 |
|
6b6f5338c01c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
galaxyp
parents:
12
diff
changeset
|
108 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.6.0/html/UTILS_FeatureFinderSuperHirn.html]]></help> |
|
11
c42075bb5123
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
9
diff
changeset
|
109 <expand macro="references"/> |
|
0
048af24c0e2b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
110 </tool> |