Mercurial > repos > galaxyp > openms_highresprecursormasscorrector
annotate HighResPrecursorMassCorrector.xml @ 16:b606d4a12558 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author | galaxyp |
---|---|
date | Fri, 14 Jun 2024 21:40:04 +0000 |
parents | d3546bb9fd8e |
children |
rev | line source |
---|---|
7
26304be6f0a6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
galaxyp
parents:
3
diff
changeset
|
1 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> |
16
b606d4a12558
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
2 <!--Proposed Tool Section: [Mass Correction and Calibration]--> |
15
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
3 <tool id="HighResPrecursorMassCorrector" name="HighResPrecursorMassCorrector" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> |
16
b606d4a12558
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
4 <description>Corrects the precursor mass and charge determined by the instrument software</description> |
0
e37289d08990
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
5 <macros> |
e37289d08990
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
6 <token name="@EXECUTABLE@">HighResPrecursorMassCorrector</token> |
e37289d08990
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
7 <import>macros.xml</import> |
e37289d08990
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
8 </macros> |
e37289d08990
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
9 <expand macro="requirements"/> |
11
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
10 <expand macro="stdio"/> |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
11 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
12 @EXT_FOO@ |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
13 #import re |
0
e37289d08990
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
14 |
11
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
15 ## Preprocessing |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
16 mkdir in && |
16
b606d4a12558
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && |
11
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
18 mkdir out && |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
19 #if "out_csv_FLAG" in str($OPTIONAL_OUTPUTS).split(',') |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
20 mkdir out_csv && |
0
e37289d08990
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
21 #end if |
11
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
22 #if $feature.in: |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
23 mkdir feature.in && |
16
b606d4a12558
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
24 cp '$feature.in' 'feature.in/${re.sub("[^\w\-_]", "_", $feature.in.element_identifier)}.$gxy2omsext($feature.in.ext)' && |
0
e37289d08990
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
25 #end if |
11
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
26 |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
27 ## Main program call |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
28 |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
29 set -o pipefail && |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
30 @EXECUTABLE@ -write_ctd ./ && |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
31 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
32 @EXECUTABLE@ -ini @EXECUTABLE@.ctd |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
33 -in |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
34 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
35 -out |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
36 'out/output.${gxy2omsext("mzml")}' |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
37 #if "out_csv_FLAG" in str($OPTIONAL_OUTPUTS).split(',') |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
38 -out_csv |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
39 'out_csv/output.${gxy2omsext("csv")}' |
0
e37289d08990
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
40 #end if |
11
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
41 #if $feature.in: |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
42 -feature:in |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
43 'feature.in/${re.sub("[^\w\-_]", "_", $feature.in.element_identifier)}.$gxy2omsext($feature.in.ext)' |
0
e37289d08990
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
44 #end if |
11
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
45 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
46 | tee '$stdout' |
0
e37289d08990
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
47 #end if |
11
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
48 |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
49 ## Postprocessing |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
50 && mv 'out/output.${gxy2omsext("mzml")}' '$out' |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
51 #if "out_csv_FLAG" in str($OPTIONAL_OUTPUTS).split(',') |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
52 && mv 'out_csv/output.${gxy2omsext("csv")}' '$out_csv' |
0
e37289d08990
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
53 #end if |
11
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
54 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
55 && mv '@EXECUTABLE@.ctd' '$ctd_out' |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
56 #end if]]></command> |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
57 <configfiles> |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
58 <inputs name="args_json" data_style="paths"/> |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
59 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
60 </configfiles> |
0
e37289d08990
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
61 <inputs> |
16
b606d4a12558
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
62 <param argument="-in" type="data" format="mzml" label="Input file (centroided data)" help=" select mzml data sets(s)"/> |
11
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
63 <section name="feature" title="Use features for precursor mass correction" help="" expanded="false"> |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
64 <param name="in" argument="-feature:in" type="data" format="featurexml" optional="true" label="Features used to correct precursor masses" help=" select featurexml data sets(s)"/> |
16
b606d4a12558
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
65 <param name="mz_tolerance" argument="-feature:mz_tolerance" type="float" value="5.0" label="The precursor mass tolerance" help="Used to determine matching to feature mass traces"/> |
b606d4a12558
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
66 <param name="mz_tolerance_unit" argument="-feature:mz_tolerance_unit" type="select" label="Unit of precursor mass tolerance" help=""> |
11
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
67 <option value="Da">Da</option> |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
68 <option value="ppm" selected="true">ppm</option> |
15
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
69 <expand macro="list_string_san" name="mz_tolerance_unit"/> |
11
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
70 </param> |
16
b606d4a12558
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
71 <param name="rt_tolerance" argument="-feature:rt_tolerance" type="float" value="0.0" label="Additional retention time tolerance added to feature boundaries" help=""/> |
b606d4a12558
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
72 <param name="max_trace" argument="-feature:max_trace" type="integer" value="2" label="Maximum isotopic trace considered in matching a precursor to a feature" help=""/> |
11
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
73 <param name="believe_charge" argument="-feature:believe_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Assume precursor charge to be correct" help=""/> |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
74 <param name="keep_original" argument="-feature:keep_original" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Make a copy of the precursor and MS2 (true) or discard the original (false)" help=""/> |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
75 <param name="assign_all_matching" argument="-feature:assign_all_matching" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Correct a precursor using all matching features (true) or only the nearest (false)" help="Only evaluated if copies are created (feature:keep_original)"/> |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
76 </section> |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
77 <section name="nearest_peak" title="Use nearest centroided MS1 peak for precursor mass correction" help="" expanded="false"> |
16
b606d4a12558
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
78 <param name="mz_tolerance" argument="-nearest_peak:mz_tolerance" type="float" value="0.0" label="The precursor mass tolerance to find the closest MS1 peak" help="(Disable method by setting value to 0.0)"/> |
b606d4a12558
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
79 <param name="mz_tolerance_unit" argument="-nearest_peak:mz_tolerance_unit" type="select" label="Unit of precursor mass tolerance" help=""> |
11
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
80 <option value="Da">Da</option> |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
81 <option value="ppm" selected="true">ppm</option> |
15
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
82 <expand macro="list_string_san" name="mz_tolerance_unit"/> |
11
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
83 </param> |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
84 </section> |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
85 <section name="highest_intensity_peak" title="Use centroided MS1 peak with the highest intensity in a certrain mass range - for precursor mass correction" help="" expanded="false"> |
16
b606d4a12558
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
86 <param name="mz_tolerance" argument="-highest_intensity_peak:mz_tolerance" type="float" value="0.0" label="The precursor mass tolerance to find the highest intensity MS1 peak" help="Suggested value 1/max. expected charge. (Disable method by setting value to 0.0)"/> |
b606d4a12558
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
87 <param name="mz_tolerance_unit" argument="-highest_intensity_peak:mz_tolerance_unit" type="select" label="Unit of precursor mass tolerance" help=""> |
11
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
88 <option value="Da">Da</option> |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
89 <option value="ppm" selected="true">ppm</option> |
15
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
90 <expand macro="list_string_san" name="mz_tolerance_unit"/> |
11
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
91 </param> |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
92 </section> |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
93 <expand macro="adv_opts_macro"> |
15
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
94 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> |
16
b606d4a12558
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
95 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true"> |
15
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
96 <expand macro="list_string_san" name="test"/> |
11
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
97 </param> |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
98 </expand> |
13
cdbd06d8cbd5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
galaxyp
parents:
11
diff
changeset
|
99 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> |
cdbd06d8cbd5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
galaxyp
parents:
11
diff
changeset
|
100 <option value="out_csv_FLAG">out_csv (Optional CSV output file for results on 'nearest_peak' or 'highest_intensity_peak' algorithm (see corresponding subsection) containing columns: RT, uncorrectedMZ, correctedMZ, deltaMZ)</option> |
11
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
101 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> |
0
e37289d08990
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
102 </param> |
e37289d08990
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
103 </inputs> |
e37289d08990
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
104 <outputs> |
11
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
105 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
106 <data name="out_csv" label="${tool.name} on ${on_string}: out_csv" format="csv"> |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
107 <filter>OPTIONAL_OUTPUTS is not None and "out_csv_FLAG" in OPTIONAL_OUTPUTS</filter> |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
108 </data> |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
109 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
110 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
111 </data> |
0
e37289d08990
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
112 </outputs> |
16
b606d4a12558
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
113 <tests> |
b606d4a12558
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
114 <!-- TOPP_HighResPrecursorMassCorrector_1 --> |
15
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
115 <test expect_num_outputs="2"> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
116 <section name="adv_opts"> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
117 <param name="force" value="false"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
118 <param name="test" value="true"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
119 </section> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
120 <param name="in" value="HighResPrecursorMassCorrector_2860_1103_3.mzML"/> |
16
b606d4a12558
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
121 <output name="out" value="HighResPrecursorMassCorrector_2860_1103_3_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
15
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
122 <section name="feature"> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
123 <param name="in" value="HighResPrecursorMassCorrector_2860_1103_3.featureXML"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
124 <param name="mz_tolerance" value="5.0"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
125 <param name="mz_tolerance_unit" value="ppm"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
126 <param name="rt_tolerance" value="0.0"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
127 <param name="max_trace" value="2"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
128 <param name="believe_charge" value="false"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
129 <param name="keep_original" value="false"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
130 <param name="assign_all_matching" value="false"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
131 </section> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
132 <section name="nearest_peak"> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
133 <param name="mz_tolerance" value="0.0"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
134 <param name="mz_tolerance_unit" value="ppm"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
135 </section> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
136 <section name="highest_intensity_peak"> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
137 <param name="mz_tolerance" value="0.0"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
138 <param name="mz_tolerance_unit" value="ppm"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
139 </section> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
140 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
141 <output name="ctd_out" ftype="xml"> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
142 <assert_contents> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
143 <is_valid_xml/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
144 </assert_contents> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
145 </output> |
16
b606d4a12558
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
146 <assert_stdout> |
b606d4a12558
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
147 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
b606d4a12558
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
148 </assert_stdout> |
15
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
149 </test> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
150 <!-- TOPP_HighResPrecursorMassCorrector_3 --> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
151 <test expect_num_outputs="2"> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
152 <section name="adv_opts"> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
153 <param name="force" value="false"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
154 <param name="test" value="true"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
155 </section> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
156 <param name="in" value="HighResPrecursorMassCorrector_2538_1091_2.mzML"/> |
16
b606d4a12558
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
157 <output name="out" value="HighResPrecursorMassCorrector_2538_1091_2_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
15
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
158 <section name="feature"> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
159 <param name="in" value="HighResPrecursorMassCorrector_2538_1091_2.featureXML"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
160 <param name="mz_tolerance" value="5.0"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
161 <param name="mz_tolerance_unit" value="ppm"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
162 <param name="rt_tolerance" value="0.0"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
163 <param name="max_trace" value="2"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
164 <param name="believe_charge" value="false"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
165 <param name="keep_original" value="false"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
166 <param name="assign_all_matching" value="false"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
167 </section> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
168 <section name="nearest_peak"> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
169 <param name="mz_tolerance" value="0.0"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
170 <param name="mz_tolerance_unit" value="ppm"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
171 </section> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
172 <section name="highest_intensity_peak"> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
173 <param name="mz_tolerance" value="0.0"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
174 <param name="mz_tolerance_unit" value="ppm"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
175 </section> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
176 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
177 <output name="ctd_out" ftype="xml"> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
178 <assert_contents> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
179 <is_valid_xml/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
180 </assert_contents> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
181 </output> |
16
b606d4a12558
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
182 <assert_stdout> |
b606d4a12558
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
183 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
b606d4a12558
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
184 </assert_stdout> |
15
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
185 </test> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
186 <!-- TOPP_HighResPrecursorMassCorrector_4 --> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
187 <test expect_num_outputs="2"> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
188 <section name="adv_opts"> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
189 <param name="force" value="false"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
190 <param name="test" value="true"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
191 </section> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
192 <param name="in" value="HighResPrecursorMassCorrector_2810_1091_3.mzML"/> |
16
b606d4a12558
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
193 <output name="out" value="HighResPrecursorMassCorrector_2810_1091_3_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
15
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
194 <section name="feature"> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
195 <param name="in" value="HighResPrecursorMassCorrector_2810_1091_3.featureXML"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
196 <param name="mz_tolerance" value="5.0"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
197 <param name="mz_tolerance_unit" value="ppm"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
198 <param name="rt_tolerance" value="0.0"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
199 <param name="max_trace" value="2"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
200 <param name="believe_charge" value="false"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
201 <param name="keep_original" value="false"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
202 <param name="assign_all_matching" value="false"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
203 </section> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
204 <section name="nearest_peak"> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
205 <param name="mz_tolerance" value="0.0"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
206 <param name="mz_tolerance_unit" value="ppm"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
207 </section> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
208 <section name="highest_intensity_peak"> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
209 <param name="mz_tolerance" value="0.0"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
210 <param name="mz_tolerance_unit" value="ppm"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
211 </section> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
212 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
213 <output name="ctd_out" ftype="xml"> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
214 <assert_contents> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
215 <is_valid_xml/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
216 </assert_contents> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
217 </output> |
16
b606d4a12558
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
218 <assert_stdout> |
b606d4a12558
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
219 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
b606d4a12558
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
220 </assert_stdout> |
15
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
221 </test> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
222 <!-- TOPP_HighResPrecursorMassCorrector_5 --> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
223 <test expect_num_outputs="2"> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
224 <section name="adv_opts"> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
225 <param name="force" value="false"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
226 <param name="test" value="true"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
227 </section> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
228 <param name="in" value="HighResPrecursorMassCorrector_3070_1191_3.mzML"/> |
16
b606d4a12558
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
229 <output name="out" value="HighResPrecursorMassCorrector_3070_1191_3_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
15
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
230 <section name="feature"> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
231 <param name="in" value="HighResPrecursorMassCorrector_3070_1191_3.featureXML"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
232 <param name="mz_tolerance" value="5.0"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
233 <param name="mz_tolerance_unit" value="ppm"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
234 <param name="rt_tolerance" value="0.0"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
235 <param name="max_trace" value="2"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
236 <param name="believe_charge" value="false"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
237 <param name="keep_original" value="false"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
238 <param name="assign_all_matching" value="false"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
239 </section> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
240 <section name="nearest_peak"> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
241 <param name="mz_tolerance" value="0.0"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
242 <param name="mz_tolerance_unit" value="ppm"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
243 </section> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
244 <section name="highest_intensity_peak"> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
245 <param name="mz_tolerance" value="0.0"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
246 <param name="mz_tolerance_unit" value="ppm"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
247 </section> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
248 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
249 <output name="ctd_out" ftype="xml"> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
250 <assert_contents> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
251 <is_valid_xml/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
252 </assert_contents> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
253 </output> |
16
b606d4a12558
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
254 <assert_stdout> |
b606d4a12558
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
255 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
b606d4a12558
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
256 </assert_stdout> |
15
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
257 </test> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
258 <!-- TOPP_HighResPrecursorMassCorrector_6 --> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
259 <test expect_num_outputs="2"> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
260 <section name="adv_opts"> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
261 <param name="force" value="false"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
262 <param name="test" value="true"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
263 </section> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
264 <param name="in" value="HighResPrecursorMassCorrector_6.mzML"/> |
16
b606d4a12558
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
265 <output name="out" value="HighResPrecursorMassCorrector_6_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
15
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
266 <section name="feature"> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
267 <param name="mz_tolerance" value="5.0"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
268 <param name="mz_tolerance_unit" value="ppm"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
269 <param name="rt_tolerance" value="0.0"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
270 <param name="max_trace" value="2"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
271 <param name="believe_charge" value="false"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
272 <param name="keep_original" value="false"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
273 <param name="assign_all_matching" value="false"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
274 </section> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
275 <section name="nearest_peak"> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
276 <param name="mz_tolerance" value="0.0"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
277 <param name="mz_tolerance_unit" value="ppm"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
278 </section> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
279 <section name="highest_intensity_peak"> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
280 <param name="mz_tolerance" value="0.2"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
281 <param name="mz_tolerance_unit" value="ppm"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
282 </section> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
283 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
284 <output name="ctd_out" ftype="xml"> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
285 <assert_contents> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
286 <is_valid_xml/> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
287 </assert_contents> |
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
288 </output> |
16
b606d4a12558
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
289 <assert_stdout> |
b606d4a12558
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
290 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
b606d4a12558
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
291 </assert_stdout> |
15
d3546bb9fd8e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents:
13
diff
changeset
|
292 </test> |
11
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
293 </tests> |
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
294 <help><![CDATA[Corrects the precursor mass and charge determined by the instrument software. |
0
e37289d08990
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
295 |
e37289d08990
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
296 |
16
b606d4a12558
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents:
15
diff
changeset
|
297 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_HighResPrecursorMassCorrector.html]]></help> |
11
8962ca0b2456
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
9
diff
changeset
|
298 <expand macro="references"/> |
0
e37289d08990
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
299 </tool> |