Mercurial > repos > galaxyp > openms_internalcalibration

annotate InternalCalibration.xml @ 13:f49a58e03ada draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:14:27 +0000
parents 6c58aa0ed5c1
children
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975efdac387b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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1 <?xml version='1.0' encoding='UTF-8'?>
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ed8100768631 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
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975efdac387b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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3 <!--Proposed Tool Section: [Signal processing and preprocessing]-->
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f49a58e03ada planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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4 <tool id="InternalCalibration" name="InternalCalibration" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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975efdac387b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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5 <description>Applies an internal mass recalibration.</description>
975efdac387b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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6 <macros>
975efdac387b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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7 <token name="@EXECUTABLE@">InternalCalibration</token>
975efdac387b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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8 <import>macros.xml</import>
975efdac387b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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9 </macros>
975efdac387b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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10 <expand macro="requirements"/>
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4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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11 <expand macro="stdio"/>
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12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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13 @EXT_FOO@
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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14 #import re
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975efdac387b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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15
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4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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16 ## Preprocessing
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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17 mkdir in &&
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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19 mkdir out &&
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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20 #if $cal.id_in:
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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21 mkdir cal.id_in &&
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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22 ln -s '$cal.id_in' 'cal.id_in/${re.sub("[^\w\-_]", "_", $cal.id_in.element_identifier)}.$gxy2omsext($cal.id_in.ext)' &&
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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23 #end if
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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24 #if $cal.lock_in:
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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25 mkdir cal.lock_in &&
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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26 ln -s '$cal.lock_in' 'cal.lock_in/${re.sub("[^\w\-_]", "_", $cal.lock_in.element_identifier)}.$gxy2omsext($cal.lock_in.ext)' &&
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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27 #end if
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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28 #if "lock_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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29 mkdir cal_lock_out &&
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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30 #end if
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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31 #if "lock_fail_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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32 mkdir cal_lock_fail_out &&
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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33 #end if
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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34 #if "models_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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35 mkdir quality_control_models &&
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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36 #end if
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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37 #if "models_plot_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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38 mkdir quality_control_models_plot &&
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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39 #end if
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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40 #if "residuals_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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41 mkdir quality_control_residuals &&
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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42 #end if
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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43 #if "residuals_plot_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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44 mkdir quality_control_residuals_plot &&
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45 #end if
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4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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46
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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47 ## Main program call
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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48
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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49 set -o pipefail &&
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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50 @EXECUTABLE@ -write_ctd ./ &&
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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51 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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52 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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53 -in
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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54 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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55 -out
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56 'out/output.${gxy2omsext("mzml")}'
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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57 #if $cal.id_in:
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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58 -cal:id_in
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59 'cal.id_in/${re.sub("[^\w\-_]", "_", $cal.id_in.element_identifier)}.$gxy2omsext($cal.id_in.ext)'
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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60 #end if
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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61 #if $cal.lock_in:
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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62 -cal:lock_in
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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63 'cal.lock_in/${re.sub("[^\w\-_]", "_", $cal.lock_in.element_identifier)}.$gxy2omsext($cal.lock_in.ext)'
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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64 #end if
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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65 #if "lock_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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66 -cal:lock_out
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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67 'cal_lock_out/output.${gxy2omsext("mzml")}'
0
975efdac387b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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68 #end if
9
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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69 #if "lock_fail_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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70 -cal:lock_fail_out
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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71 'cal_lock_fail_out/output.${gxy2omsext("mzml")}'
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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72 #end if
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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73 #if "models_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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74 -quality_control:models
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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75 'quality_control_models/output.${gxy2omsext("csv")}'
0
975efdac387b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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76 #end if
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77 #if "models_plot_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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78 -quality_control:models_plot
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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79 'quality_control_models_plot/output.${gxy2omsext("png")}'
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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80 #end if
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81 #if "residuals_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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82 -quality_control:residuals
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83 'quality_control_residuals/output.${gxy2omsext("csv")}'
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84 #end if
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85 #if "residuals_plot_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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86 -quality_control:residuals_plot
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87 'quality_control_residuals_plot/output.${gxy2omsext("png")}'
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88 #end if
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89 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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90 | tee '$stdout'
0
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91 #end if
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92
9
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93 ## Postprocessing
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94 && mv 'out/output.${gxy2omsext("mzml")}' '$out'
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95 #if "lock_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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96 && mv 'cal_lock_out/output.${gxy2omsext("mzml")}' '$cal_lock_out'
0
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97 #end if
9
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98 #if "lock_fail_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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99 && mv 'cal_lock_fail_out/output.${gxy2omsext("mzml")}' '$cal_lock_fail_out'
0
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100 #end if
9
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101 #if "models_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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102 && mv 'quality_control_models/output.${gxy2omsext("csv")}' '$quality_control_models'
0
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103 #end if
9
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104 #if "models_plot_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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105 && mv 'quality_control_models_plot/output.${gxy2omsext("png")}' '$quality_control_models_plot'
0
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106 #end if
9
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107 #if "residuals_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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108 && mv 'quality_control_residuals/output.${gxy2omsext("csv")}' '$quality_control_residuals'
0
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109 #end if
9
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110 #if "residuals_plot_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
4682dcff7e2f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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111 && mv 'quality_control_residuals_plot/output.${gxy2omsext("png")}' '$quality_control_residuals_plot'
0
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112 #end if
9
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113 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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114 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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115 #end if]]></command>
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116 <configfiles>
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117 <inputs name="args_json" data_style="paths"/>
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118 <configfile name="hardcoded_json"><![CDATA[{"rscript_executable": "Rscript", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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119 </configfiles>
0
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120 <inputs>
13
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121 <param argument="-in" type="data" format="mzml" optional="false" label="Input peak file" help=" select mzml data sets(s)"/>
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122 <param argument="-ppm_match_tolerance" type="float" optional="true" value="25.0" label="Finding calibrants in raw data uses this tolerance (for lock masses and ID's)" help=""/>
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123 <param argument="-ms_level" type="text" optional="true" value="1 2 3" label="Target MS levels to apply the transformation onto" help="Does not affect calibrant collection (space separated list, in order to allow for spaces in list items surround them by single quotes)">
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124 <expand macro="list_integer_valsan" name="ms_level"/>
9
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125 </param>
13
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126 <param argument="-RT_chunking" type="float" optional="true" value="300.0" label="RT window (one-sided" help="i.e. left-&gt;center, or center-&gt;right) around an MS scan in which calibrants are collected to build a model. Set to -1 to use ALL calibrants for all scans, i.e. a global model"/>
9
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127 <section name="cal" title="Chose one of two optional input files ('id_in' or 'lock_in') to define the calibration masses/function" help="" expanded="false">
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128 <param name="id_in" argument="-cal:id_in" type="data" format="featurexml,idxml" optional="true" label="Identifications or features whose peptide ID's serve as calibration masses" help=" select featurexml,idxml data sets(s)"/>
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129 <param name="lock_in" argument="-cal:lock_in" type="data" format="csv" optional="true" label="Input file containing reference m/z values (text file with each line as: m/z ms-level charge) which occur in all scans" help=" select csv data sets(s)"/>
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130 <param name="lock_require_mono" argument="-cal:lock_require_mono" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Require all lock masses to be monoisotopic" help="i.e. not the iso1, iso2 etc ('charge' column is used to determine the spacing). Peaks which are not mono-isotopic are not used"/>
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131 <param name="lock_require_iso" argument="-cal:lock_require_iso" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Require all lock masses to have at least the +1 isotope" help="Peaks without isotope pattern are not used"/>
13
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132 <param name="model_type" argument="-cal:model_type" type="select" optional="true" label="Type of function to be fitted to the calibration points" help="">
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133 <option value="linear">linear</option>
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134 <option value="linear_weighted" selected="true">linear_weighted</option>
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135 <option value="quadratic">quadratic</option>
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136 <option value="quadratic_weighted">quadratic_weighted</option>
13
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137 <expand macro="list_string_san" name="model_type"/>
0
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138 </param>
9
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139 </section>
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140 <section name="RANSAC" title="Robust outlier removal using RANSAC" help="" expanded="false">
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141 <param name="enabled" argument="-RANSAC:enabled" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply RANSAC to calibration points to remove outliers before fitting a model" help=""/>
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142 <param name="threshold" argument="-RANSAC:threshold" type="float" optional="true" value="10.0" label="Threshold for accepting inliers (instrument precision (not accuracy!) as ppm^2 distance)" help=""/>
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143 <param name="pc_inliers" argument="-RANSAC:pc_inliers" type="integer" optional="true" min="1" max="99" value="30" label="Minimum percentage (of available data) of inliers (&lt;threshold away from model) to accept the model" help=""/>
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144 <param name="iter" argument="-RANSAC:iter" type="integer" optional="true" value="70" label="Maximal # iterations" help=""/>
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145 </section>
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146 <section name="goodness" title="Thresholds for accepting calibration success" help="" expanded="false">
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147 <param name="median" argument="-goodness:median" type="float" optional="true" value="4.0" label="The median ppm error of calibrated masses must be smaller than this threshold" help=""/>
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148 <param name="MAD" argument="-goodness:MAD" type="float" optional="true" value="2.0" label="The median absolute deviation of the ppm error of calibrated masses must be smaller than this threshold" help=""/>
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149 </section>
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150 <expand macro="adv_opts_macro">
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151 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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152 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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153 <expand macro="list_string_san" name="test"/>
9
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154 </param>
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155 </expand>
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156 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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157 <option value="lock_out_FLAG">lock_out (Optional output file containing peaks from 'in' which were matched to reference m/z values)</option>
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158 <option value="lock_fail_out_FLAG">lock_fail_out (Optional output file containing lock masses which were NOT found or accepted(!) in data from 'in')</option>
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159 <option value="models_FLAG">models (Table of model parameters for each spectrum)</option>
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160 <option value="models_plot_FLAG">models_plot (Plot image of model parameters for each spectrum)</option>
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161 <option value="residuals_FLAG">residuals (Table of pre- and post calibration errors)</option>
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162 <option value="residuals_plot_FLAG">residuals_plot (Plot image of pre- and post calibration errors)</option>
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163 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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164 </param>
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165 </inputs>
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166 <outputs>
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167 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
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168 <data name="cal_lock_out" label="${tool.name} on ${on_string}: cal:lock_out" format="mzml">
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169 <filter>OPTIONAL_OUTPUTS is not None and "lock_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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170 </data>
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171 <data name="cal_lock_fail_out" label="${tool.name} on ${on_string}: cal:lock_fail_out" format="mzml">
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172 <filter>OPTIONAL_OUTPUTS is not None and "lock_fail_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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173 </data>
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174 <data name="quality_control_models" label="${tool.name} on ${on_string}: quality_control:models" format="csv">
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175 <filter>OPTIONAL_OUTPUTS is not None and "models_FLAG" in OPTIONAL_OUTPUTS</filter>
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176 </data>
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177 <data name="quality_control_models_plot" label="${tool.name} on ${on_string}: quality_control:models_plot" format="png">
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178 <filter>OPTIONAL_OUTPUTS is not None and "models_plot_FLAG" in OPTIONAL_OUTPUTS</filter>
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179 </data>
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180 <data name="quality_control_residuals" label="${tool.name} on ${on_string}: quality_control:residuals" format="csv">
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181 <filter>OPTIONAL_OUTPUTS is not None and "residuals_FLAG" in OPTIONAL_OUTPUTS</filter>
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182 </data>
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183 <data name="quality_control_residuals_plot" label="${tool.name} on ${on_string}: quality_control:residuals_plot" format="png">
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184 <filter>OPTIONAL_OUTPUTS is not None and "residuals_plot_FLAG" in OPTIONAL_OUTPUTS</filter>
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185 </data>
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186 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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187 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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188 </data>
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189 </outputs>
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190 <tests><!-- TOPP_InternalCalibration_1 -->
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191 <test expect_num_outputs="4">
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192 <section name="adv_opts">
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193 <param name="force" value="false"/>
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194 <param name="test" value="true"/>
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195 </section>
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196 <param name="in" value="InternalCalibration_1_BSA1.mzML"/>
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197 <output name="out" file="InternalCalibration_1_BSA1_out.mzML.tmp" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
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198 <param name="ppm_match_tolerance" value="25.0"/>
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199 <param name="ms_level" value="1"/>
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200 <param name="RT_chunking" value="-1.0"/>
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201 <section name="cal">
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202 <param name="id_in" value="InternalCalibration_1_BSA1_OMSSA.idXML"/>
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203 <param name="lock_require_mono" value="false"/>
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204 <param name="lock_require_iso" value="false"/>
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205 <param name="model_type" value="linear"/>
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206 </section>
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207 <section name="RANSAC">
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208 <param name="enabled" value="true"/>
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209 <param name="threshold" value="1.0"/>
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210 <param name="pc_inliers" value="30"/>
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211 <param name="iter" value="500"/>
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212 </section>
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213 <section name="goodness">
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214 <param name="median" value="4.0"/>
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215 <param name="MAD" value="2.0"/>
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216 </section>
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217 <section name="quality_control"/>
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218 <output name="quality_control_models" file="InternalCalibration_1_models.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
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219 <output name="quality_control_residuals" file="InternalCalibration_1_residuals.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
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220 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,models_FLAG,residuals_FLAG"/>
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221 <output name="ctd_out" ftype="xml">
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222 <assert_contents>
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223 <is_valid_xml/>
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224 </assert_contents>
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225 </output>
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226 </test>
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227 <!-- TOPP_InternalCalibration_2 -->
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228 <test expect_num_outputs="4">
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229 <section name="adv_opts">
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230 <param name="force" value="false"/>
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231 <param name="test" value="true"/>
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232 </section>
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233 <param name="in" value="InternalCalibration_2_lockmass.mzML.gz"/>
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234 <output name="out" file="InternalCalibration_2_lockmass.mzML.tmp" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
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235 <param name="ppm_match_tolerance" value="25.0"/>
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236 <param name="ms_level" value="1 2 3"/>
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237 <param name="RT_chunking" value="60.0"/>
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238 <section name="cal">
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239 <param name="lock_in" value="InternalCalibration_2_lock.csv" ftype="csv"/>
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240 <param name="lock_require_mono" value="true"/>
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241 <param name="lock_require_iso" value="false"/>
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242 <param name="model_type" value="linear"/>
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243 </section>
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244 <section name="RANSAC">
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245 <param name="enabled" value="false"/>
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246 <param name="threshold" value="10.0"/>
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247 <param name="pc_inliers" value="30"/>
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248 <param name="iter" value="70"/>
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249 </section>
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250 <section name="goodness">
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251 <param name="median" value="4.0"/>
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252 <param name="MAD" value="2.0"/>
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253 </section>
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254 <section name="quality_control"/>
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255 <output name="quality_control_models" file="InternalCalibration_2_models.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
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256 <output name="quality_control_residuals" file="InternalCalibration_2_residuals.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
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257 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,models_FLAG,residuals_FLAG"/>
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258 <output name="ctd_out" ftype="xml">
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259 <assert_contents>
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260 <is_valid_xml/>
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261 </assert_contents>
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262 </output>
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263 </test>
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264 </tests>
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265 <help><![CDATA[Applies an internal mass recalibration.
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266
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267
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268 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_InternalCalibration.html]]></help>
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269 <expand macro="references"/>
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270 </tool>