Mercurial > repos > galaxyp > openms_peakpickerhires
annotate PeakPickerHiRes.xml @ 10:6b01678ec2fc draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
| author | galaxyp |
|---|---|
| date | Thu, 01 Dec 2022 19:20:52 +0000 |
| parents | 146b59d2d3e5 |
| children | 401f500aae50 |
| rev | line source |
|---|---|
|
0
5ae104d0da6e
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'?> |
|
5
d34c1a10e713
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
galaxyp
parents:
1
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
5ae104d0da6e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
3 <!--Proposed Tool Section: [Signal processing and preprocessing]--> |
|
10
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
4 <tool id="PeakPickerHiRes" name="PeakPickerHiRes" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> |
|
0
5ae104d0da6e
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 peaks in profile mass spectra.</description> |
|
5ae104d0da6e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
6 <macros> |
|
5ae104d0da6e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
7 <token name="@EXECUTABLE@">PeakPickerHiRes</token> |
|
5ae104d0da6e
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> |
|
5ae104d0da6e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
9 </macros> |
|
8
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
10 <expand macro="requirements"/> |
|
0
5ae104d0da6e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
11 <expand macro="stdio"/> |
|
8
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
13 @EXT_FOO@ |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
14 #import re |
|
0
5ae104d0da6e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
15 |
|
8
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
16 ## Preprocessing |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
17 mkdir in && |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
19 mkdir out && |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
20 |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
21 ## Main program call |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
22 |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
23 set -o pipefail && |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
24 @EXECUTABLE@ -write_ctd ./ && |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
25 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
26 @EXECUTABLE@ -ini @EXECUTABLE@.ctd |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
27 -in |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
28 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
29 -out |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
30 'out/output.${gxy2omsext("mzml")}' |
|
0
5ae104d0da6e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
31 |
|
8
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
32 ## Postprocessing |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
33 && mv 'out/output.${gxy2omsext("mzml")}' '$out' |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
34 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
35 && mv '@EXECUTABLE@.ctd' '$ctd_out' |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
36 #end if]]></command> |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
37 <configfiles> |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
38 <inputs name="args_json" data_style="paths"/> |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
39 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
40 </configfiles> |
|
0
5ae104d0da6e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
41 <inputs> |
|
10
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
42 <param argument="-in" type="data" format="mzml" optional="false" label="input profile data file" help=" select mzml data sets(s)"/> |
|
8
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
43 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false"> |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
44 <param name="signal_to_noise" argument="-algorithm:signal_to_noise" type="float" optional="true" min="0.0" value="0.0" label="Minimal signal-to-noise ratio for a peak to be picked (0.0 disables SNT estimation!)" help=""/> |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
45 <param name="spacing_difference_gap" argument="-algorithm:spacing_difference_gap" type="float" optional="true" min="0.0" value="4.0" label="The extension of a peak is stopped if the spacing between two subsequent data points exceeds 'spacing_difference_gap * min_spacing'" help="'min_spacing' is the smaller of the two spacings from the peak apex to its two neighboring points. '0' to disable the constraint. Not applicable to chromatograms"/> |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
46 <param name="spacing_difference" argument="-algorithm:spacing_difference" type="float" optional="true" min="0.0" value="1.5" label="Maximum allowed difference between points during peak extension, in multiples of the minimal difference between the peak apex and its two neighboring points" help="If this difference is exceeded a missing point is assumed (see parameter 'missing'). A higher value implies a less stringent peak definition, since individual signals within the peak are allowed to be further apart. '0' to disable the constraint. Not applicable to chromatograms"/> |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
47 <param name="missing" argument="-algorithm:missing" type="integer" optional="true" min="0" value="1" label="Maximum number of missing points allowed when extending a peak to the left or to the right" help="A missing data point occurs if the spacing between two subsequent data points exceeds 'spacing_difference * min_spacing'. 'min_spacing' is the smaller of the two spacings from the peak apex to its two neighboring points. Not applicable to chromatograms"/> |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
48 <param name="ms_levels" argument="-algorithm:ms_levels" type="text" optional="true" value="" label="List of MS levels for which the peak picking is applied" help="If empty, auto mode is enabled, all peaks which aren't picked yet will get picked. Other scans are copied to the output without changes (space separated list, in order to allow for spaces in list items surround them by single quotes)"> |
|
10
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
49 <expand macro="list_integer_valsan" name="ms_levels"> |
|
8
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
50 <validator type="expression" message="a space separated list of integer values in the range 1: is required"><![CDATA[len(value.split(' ')) == len([_ for _ in value.split(' ') if 1 <= int(_)]) |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
51 ]]></validator> |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
52 </expand> |
|
0
5ae104d0da6e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
53 </param> |
|
8
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
54 <param name="report_FWHM" argument="-algorithm:report_FWHM" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add metadata for FWHM (as floatDataArray named 'FWHM' or 'FWHM_ppm', depending on param 'report_FWHM_unit') for each picked peak" help=""/> |
|
10
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
55 <param name="report_FWHM_unit" argument="-algorithm:report_FWHM_unit" type="select" optional="true" label="Unit of FWHM" help="Either absolute in the unit of input, e.g. 'm/z' for spectra, or relative as ppm (only sensible for spectra, not chromatograms)"> |
|
8
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
56 <option value="relative" selected="true">relative</option> |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
57 <option value="absolute">absolute</option> |
|
10
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
58 <expand macro="list_string_san" name="report_FWHM_unit"/> |
|
8
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
59 </param> |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
60 <section name="SignalToNoise" title="" help="" expanded="false"> |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
61 <param name="max_intensity" argument="-algorithm:SignalToNoise:max_intensity" type="integer" optional="true" min="-1" value="-1" label="maximal intensity considered for histogram construction" help="By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will be added to the LAST histogram bin. If you choose 'max_intensity' too small, the noise estimate might be too small as well. If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime). In general, the Median-S/N estimator is more robust to a manual max_intensity than the MeanIterative-S/N"/> |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
62 <param name="auto_max_stdev_factor" argument="-algorithm:SignalToNoise:auto_max_stdev_factor" type="float" optional="true" min="0.0" max="999.0" value="3.0" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" help=""/> |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
63 <param name="auto_max_percentile" argument="-algorithm:SignalToNoise:auto_max_percentile" type="integer" optional="true" min="0" max="100" value="95" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile" help=""/> |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
64 <param name="auto_mode" argument="-algorithm:SignalToNoise:auto_mode" type="integer" optional="true" min="-1" max="1" value="0" label="method to use to determine maximal intensity: -1 --> use 'max_intensity'; 0 --> 'auto_max_stdev_factor' method (default); 1 --> 'auto_max_percentile' method" help=""/> |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
65 <param name="win_len" argument="-algorithm:SignalToNoise:win_len" type="float" optional="true" min="1.0" value="200.0" label="window length in Thomson" help=""/> |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
66 <param name="bin_count" argument="-algorithm:SignalToNoise:bin_count" type="integer" optional="true" min="3" value="30" label="number of bins for intensity values" help=""/> |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
67 <param name="min_required_elements" argument="-algorithm:SignalToNoise:min_required_elements" type="integer" optional="true" min="1" value="10" label="minimum number of elements required in a window (otherwise it is considered sparse)" help=""/> |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
68 <param name="noise_for_empty_window" argument="-algorithm:SignalToNoise:noise_for_empty_window" type="float" optional="true" value="1e+20" label="noise value used for sparse windows" help=""/> |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
69 <param name="write_log_messages" argument="-algorithm:SignalToNoise:write_log_messages" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Write out log messages in case of sparse windows or median in rightmost histogram bin" help=""/> |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
70 </section> |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
71 </section> |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
72 <expand macro="adv_opts_macro"> |
|
10
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
73 <param argument="-processOption" type="select" optional="true" label="Whether to load all data and process them in-memory or whether to process the data on the fly (lowmemory) without loading the whole file into memory first" help=""> |
|
0
5ae104d0da6e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
74 <option value="inmemory" selected="true">inmemory</option> |
|
5ae104d0da6e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
75 <option value="lowmemory">lowmemory</option> |
|
10
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
76 <expand macro="list_string_san" name="processOption"/> |
|
0
5ae104d0da6e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
77 </param> |
|
10
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
78 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
79 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
80 <expand macro="list_string_san" name="test"/> |
|
8
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
81 </param> |
|
0
5ae104d0da6e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
82 </expand> |
|
8
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
83 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
84 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
85 </param> |
|
0
5ae104d0da6e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
86 </inputs> |
|
5ae104d0da6e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
87 <outputs> |
|
8
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
88 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
89 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
90 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
91 </data> |
|
0
5ae104d0da6e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
92 </outputs> |
|
10
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
93 <tests><!-- TOPP_PeakPickerHiRes_1 --> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
94 <test expect_num_outputs="2"> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
95 <section name="adv_opts"> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
96 <param name="processOption" value="inmemory"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
97 <param name="force" value="false"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
98 <param name="test" value="true"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
99 </section> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
100 <param name="in" value="PeakPickerHiRes_input.mzML"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
101 <output name="out" file="PeakPickerHiRes_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
102 <section name="algorithm"> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
103 <param name="signal_to_noise" value="1.0"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
104 <param name="spacing_difference_gap" value="4.0"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
105 <param name="spacing_difference" value="1.5"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
106 <param name="missing" value="1"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
107 <param name="ms_levels" value="1"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
108 <param name="report_FWHM" value="true"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
109 <param name="report_FWHM_unit" value="relative"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
110 <section name="SignalToNoise"> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
111 <param name="max_intensity" value="-1"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
112 <param name="auto_max_stdev_factor" value="3.0"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
113 <param name="auto_max_percentile" value="95"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
114 <param name="auto_mode" value="0"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
115 <param name="win_len" value="200.0"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
116 <param name="bin_count" value="30"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
117 <param name="min_required_elements" value="10"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
118 <param name="noise_for_empty_window" value="1e+20"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
119 <param name="write_log_messages" value="true"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
120 </section> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
121 </section> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
122 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
123 <output name="ctd_out" ftype="xml"> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
124 <assert_contents> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
125 <is_valid_xml/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
126 </assert_contents> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
127 </output> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
128 </test> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
129 <!-- TOPP_PeakPickerHiRes_2 --> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
130 <test expect_num_outputs="2"> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
131 <section name="adv_opts"> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
132 <param name="processOption" value="inmemory"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
133 <param name="force" value="false"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
134 <param name="test" value="true"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
135 </section> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
136 <param name="in" value="PeakPickerHiRes_2_input.mzML"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
137 <output name="out" file="PeakPickerHiRes_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
138 <section name="algorithm"> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
139 <param name="signal_to_noise" value="1.0"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
140 <param name="spacing_difference_gap" value="4.0"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
141 <param name="spacing_difference" value="1.5"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
142 <param name="missing" value="1"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
143 <param name="ms_levels" value="1"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
144 <param name="report_FWHM" value="true"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
145 <param name="report_FWHM_unit" value="relative"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
146 <section name="SignalToNoise"> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
147 <param name="max_intensity" value="-1"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
148 <param name="auto_max_stdev_factor" value="3.0"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
149 <param name="auto_max_percentile" value="95"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
150 <param name="auto_mode" value="0"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
151 <param name="win_len" value="200.0"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
152 <param name="bin_count" value="30"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
153 <param name="min_required_elements" value="10"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
154 <param name="noise_for_empty_window" value="1e+20"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
155 <param name="write_log_messages" value="true"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
156 </section> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
157 </section> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
158 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
159 <output name="ctd_out" ftype="xml"> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
160 <assert_contents> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
161 <is_valid_xml/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
162 </assert_contents> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
163 </output> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
164 </test> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
165 <!-- TOPP_PeakPickerHiRes_3 --> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
166 <test expect_num_outputs="2"> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
167 <section name="adv_opts"> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
168 <param name="processOption" value="lowmemory"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
169 <param name="force" value="false"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
170 <param name="test" value="true"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
171 </section> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
172 <param name="in" value="PeakPickerHiRes_input.mzML"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
173 <output name="out" file="PeakPickerHiRes_output_lowMem.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
174 <section name="algorithm"> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
175 <param name="signal_to_noise" value="1.0"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
176 <param name="spacing_difference_gap" value="4.0"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
177 <param name="spacing_difference" value="1.5"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
178 <param name="missing" value="1"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
179 <param name="ms_levels" value="1"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
180 <param name="report_FWHM" value="true"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
181 <param name="report_FWHM_unit" value="relative"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
182 <section name="SignalToNoise"> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
183 <param name="max_intensity" value="-1"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
184 <param name="auto_max_stdev_factor" value="3.0"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
185 <param name="auto_max_percentile" value="95"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
186 <param name="auto_mode" value="0"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
187 <param name="win_len" value="200.0"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
188 <param name="bin_count" value="30"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
189 <param name="min_required_elements" value="10"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
190 <param name="noise_for_empty_window" value="1e+20"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
191 <param name="write_log_messages" value="true"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
192 </section> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
193 </section> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
194 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
195 <output name="ctd_out" ftype="xml"> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
196 <assert_contents> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
197 <is_valid_xml/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
198 </assert_contents> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
199 </output> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
200 </test> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
201 <!-- TOPP_PeakPickerHiRes_4 --> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
202 <test expect_num_outputs="2"> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
203 <section name="adv_opts"> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
204 <param name="processOption" value="lowmemory"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
205 <param name="force" value="false"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
206 <param name="test" value="true"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
207 </section> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
208 <param name="in" value="PeakPickerHiRes_2_input.mzML"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
209 <output name="out" file="PeakPickerHiRes_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
210 <section name="algorithm"> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
211 <param name="signal_to_noise" value="1.0"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
212 <param name="spacing_difference_gap" value="4.0"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
213 <param name="spacing_difference" value="1.5"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
214 <param name="missing" value="1"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
215 <param name="ms_levels" value="1"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
216 <param name="report_FWHM" value="true"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
217 <param name="report_FWHM_unit" value="relative"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
218 <section name="SignalToNoise"> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
219 <param name="max_intensity" value="-1"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
220 <param name="auto_max_stdev_factor" value="3.0"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
221 <param name="auto_max_percentile" value="95"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
222 <param name="auto_mode" value="0"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
223 <param name="win_len" value="200.0"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
224 <param name="bin_count" value="30"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
225 <param name="min_required_elements" value="10"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
226 <param name="noise_for_empty_window" value="1e+20"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
227 <param name="write_log_messages" value="true"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
228 </section> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
229 </section> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
230 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
231 <output name="ctd_out" ftype="xml"> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
232 <assert_contents> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
233 <is_valid_xml/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
234 </assert_contents> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
235 </output> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
236 </test> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
237 <!-- TOPP_PeakPickerHiRes_5 --> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
238 <test expect_num_outputs="2"> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
239 <section name="adv_opts"> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
240 <param name="processOption" value="inmemory"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
241 <param name="force" value="false"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
242 <param name="test" value="true"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
243 </section> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
244 <param name="in" value="PeakPickerHiRes_5_input.mzML"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
245 <output name="out" file="PeakPickerHiRes_5_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
246 <section name="algorithm"> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
247 <param name="signal_to_noise" value="0.0"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
248 <param name="spacing_difference_gap" value="4.0"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
249 <param name="spacing_difference" value="1.5"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
250 <param name="missing" value="1"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
251 <param name="ms_levels" value=""/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
252 <param name="report_FWHM" value="false"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
253 <param name="report_FWHM_unit" value="relative"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
254 <section name="SignalToNoise"> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
255 <param name="max_intensity" value="-1"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
256 <param name="auto_max_stdev_factor" value="3.0"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
257 <param name="auto_max_percentile" value="95"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
258 <param name="auto_mode" value="0"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
259 <param name="win_len" value="200.0"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
260 <param name="bin_count" value="30"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
261 <param name="min_required_elements" value="10"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
262 <param name="noise_for_empty_window" value="1e+20"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
263 <param name="write_log_messages" value="true"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
264 </section> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
265 </section> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
266 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
267 <output name="ctd_out" ftype="xml"> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
268 <assert_contents> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
269 <is_valid_xml/> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
270 </assert_contents> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
271 </output> |
|
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
272 </test> |
|
8
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
273 </tests> |
|
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
274 <help><![CDATA[Finds mass spectrometric peaks in profile mass spectra. |
|
0
5ae104d0da6e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
275 |
|
5ae104d0da6e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
276 |
|
10
6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
8
diff
changeset
|
277 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_PeakPickerHiRes.html]]></help> |
|
8
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
galaxyp
parents:
7
diff
changeset
|
278 <expand macro="references"/> |
|
0
5ae104d0da6e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
279 </tool> |