Mercurial > repos > galaxyp > openms_eicextractor

annotate EICExtractor.xml @ 11:2bd3c83eed94 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author galaxyp
date Wed, 09 Sep 2020 12:58:22 +0000
parents e8a9dc186db5
children 0546885ddaf9
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1 <?xml version='1.0' encoding='UTF-8'?>
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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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3 <!--Proposed Tool Section: [Quantitation]-->
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4 <tool id="EICExtractor" name="EICExtractor" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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5 <description>Extracts intensities from dedicates positions in a LC/MS map</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">EICExtractor</token>
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8 <import>macros.xml</import>
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9 <import>macros_autotest.xml</import>
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10 <import>macros_test.xml</import>
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11 </macros>
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12 <expand macro="requirements"/>
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13 <expand macro="stdio"/>
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14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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15 @EXT_FOO@
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16 #import re
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17
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18 ## Preprocessing
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19 mkdir in &&
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20 ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
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21 #if $in_header:
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22 mkdir in_header &&
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23 ${ ' '.join(["ln -s '%s' 'in_header/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_header if _]) }
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24 #end if
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25 mkdir pos &&
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26 ln -s '$pos' 'pos/${re.sub("[^\w\-_]", "_", $pos.element_identifier)}.$gxy2omsext($pos.ext)' &&
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27 mkdir out &&
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28 #if "out_debug_TIC_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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29 mkdir auto_rt_out_debug_TIC &&
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30 #end if
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32 ## Main program call
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34 set -o pipefail &&
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35 @EXECUTABLE@ -write_ctd ./ &&
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36 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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37 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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38 -in
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39 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
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40 #if $in_header:
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41 -in_header
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42 ${' '.join(["'in_header/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_header if _])}
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43 #end if
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44 -pos
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45 'pos/${re.sub("[^\w\-_]", "_", $pos.element_identifier)}.$gxy2omsext($pos.ext)'
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46 -out
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47 'out/output.${gxy2omsext("csv")}'
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48 #if "out_debug_TIC_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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49 -auto_rt:out_debug_TIC
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50 'auto_rt_out_debug_TIC/output.${gxy2omsext("mzml")}'
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51 #end if
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52 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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53 | tee '$stdout'
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54 #end if
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55
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56 ## Postprocessing
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57 && mv 'out/output.${gxy2omsext("csv")}' '$out'
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58 #if "out_debug_TIC_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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59 && mv 'auto_rt_out_debug_TIC/output.${gxy2omsext("mzml")}' '$auto_rt_out_debug_TIC'
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60 #end if
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61 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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62 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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63 #end if]]></command>
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64 <configfiles>
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65 <inputs name="args_json" data_style="paths"/>
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66 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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67 </configfiles>
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68 <inputs>
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69 <param name="in" argument="-in" type="data" format="mzml" multiple="true" optional="false" label="Input raw data file" help=" select mzml data sets(s)"/>
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70 <param name="in_header" argument="-in_header" type="data" format="txt" multiple="true" optional="true" label="[for Waters data only] Read additional information from _HEADER.TXT" help="Provide one for each raw input file select txt data sets(s)"/>
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71 <param name="pos" argument="-pos" type="data" format="edta" optional="false" label="Input config file stating where to find signal" help=" select edta data sets(s)"/>
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72 <param name="rt_tol" argument="-rt_tol" type="float" optional="true" value="3.0" label="RT tolerance in [s] for finding max peak (whole RT range around RT middle)" help=""/>
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73 <param name="mz_tol" argument="-mz_tol" type="float" optional="true" value="10.0" label="m/z tolerance in [ppm] for finding a peak" help=""/>
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74 <param name="rt_collect" argument="-rt_collect" type="integer" optional="true" value="1" label="# of scans up &amp; down in RT from highest point for ppm estimation in result" help=""/>
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75 <section name="auto_rt" title="Parameters for automatic detection of injection RT peaks (no need to specify them in 'pos' input file)" help="" expanded="false">
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76 <param name="enabled" argument="-auto_rt:enabled" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Automatically detect injection peaks from TIC and quantify all m/z x RT combinations" help=""/>
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77 <param name="FHWM" argument="-auto_rt:FHWM" type="float" optional="true" value="5.0" label="Expected full width at half-maximum of each raw RT peak in [s]" help="Gaussian smoothing filter with this width is applied to TIC"/>
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78 <param name="SNThreshold" argument="-auto_rt:SNThreshold" type="float" optional="true" value="5.0" label="S/N threshold for a smoothed raw peak to pass peak picking" help="Higher thesholds will result in less peaks"/>
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79 </section>
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80 <expand macro="adv_opts_macro">
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81 <param name="out_separator" argument="-out_separator" type="text" optional="true" value="," label="Separator character for output CSV file" help="">
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82 <expand macro="list_string_san"/>
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83 </param>
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84 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
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85 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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86 <expand macro="list_string_san"/>
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87 </param>
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88 </expand>
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89 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
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90 <option value="out_debug_TIC_FLAG">out_debug_TIC (Optional output file (for first input) containing the smoothed TIC, S/N levels and picked RT positions)</option>
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91 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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92 </param>
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93 </inputs>
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94 <outputs>
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95 <data name="out" label="${tool.name} on ${on_string}: out" format="csv"/>
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96 <data name="auto_rt_out_debug_TIC" label="${tool.name} on ${on_string}: auto_rt:out_debug_TIC" format="mzml">
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97 <filter>OPTIONAL_OUTPUTS is not None and "out_debug_TIC_FLAG" in OPTIONAL_OUTPUTS</filter>
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98 </data>
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99 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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100 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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101 </data>
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102 </outputs>
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103 <tests>
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104 <expand macro="autotest_EICExtractor"/>
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105 <expand macro="manutest_EICExtractor"/>
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106 </tests>
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107 <help><![CDATA[Extracts intensities from dedicates positions in a LC/MS map
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108
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109
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110 For more information, visit http://www.openms.de/documentation/TOPP_EICExtractor.html]]></help>
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111 <expand macro="references"/>
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112 </tool>