Mercurial > repos > galaxyp > openms_metaprosip

annotate MetaProSIP.xml @ 11:c18e6eb07aa9 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 20:29:53 +0000
parents 73c1493ac4c2
children 819ed5aae76f
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f0e3cb65a6bd 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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fdb3fbfef4cc 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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3 <!--Proposed Tool Section: [Utilities]-->
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4 <tool id="MetaProSIP" name="MetaProSIP" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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5 <description>Performs proteinSIP on peptide features for elemental flux analysis.</description>
f0e3cb65a6bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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6 <macros>
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7 <token name="@EXECUTABLE@">MetaProSIP</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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96cc79adfadb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
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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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73c1493ac4c2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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18 ## Preprocessing
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19 mkdir in_mzML &&
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20 ln -s '$in_mzML' 'in_mzML/${re.sub("[^\w\-_]", "_", $in_mzML.element_identifier)}.$gxy2omsext($in_mzML.ext)' &&
73c1493ac4c2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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21 mkdir in_fasta &&
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22 ln -s '$in_fasta' 'in_fasta/${re.sub("[^\w\-_]", "_", $in_fasta.element_identifier)}.$gxy2omsext($in_fasta.ext)' &&
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23 mkdir out_csv &&
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24 mkdir out_peptide_centric_csv &&
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25 mkdir in_featureXML &&
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26 ln -s '$in_featureXML' 'in_featureXML/${re.sub("[^\w\-_]", "_", $in_featureXML.element_identifier)}.$gxy2omsext($in_featureXML.ext)' &&
73c1493ac4c2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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73c1493ac4c2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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28 ## Main program call
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29
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73c1493ac4c2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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30 set -o pipefail &&
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31 @EXECUTABLE@ -write_ctd ./ &&
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32 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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33 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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34 -in_mzML
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35 'in_mzML/${re.sub("[^\w\-_]", "_", $in_mzML.element_identifier)}.$gxy2omsext($in_mzML.ext)'
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36 -in_fasta
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37 'in_fasta/${re.sub("[^\w\-_]", "_", $in_fasta.element_identifier)}.$gxy2omsext($in_fasta.ext)'
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38 -out_csv
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39 'out_csv/output.${gxy2omsext("csv")}'
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40 -out_peptide_centric_csv
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41 'out_peptide_centric_csv/output.${gxy2omsext("csv")}'
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42 -in_featureXML
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43 'in_featureXML/${re.sub("[^\w\-_]", "_", $in_featureXML.element_identifier)}.$gxy2omsext($in_featureXML.ext)'
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44
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45 ## Postprocessing
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46 && mv 'out_csv/output.${gxy2omsext("csv")}' '$out_csv'
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47 && mv 'out_peptide_centric_csv/output.${gxy2omsext("csv")}' '$out_peptide_centric_csv'
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48 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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49 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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50 #end if]]></command>
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51 <configfiles>
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52 <inputs name="args_json" data_style="paths"/>
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53 <configfile name="hardcoded_json"><![CDATA[{"r_executable": "R", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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54 </configfiles>
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55 <inputs>
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56 <param name="in_mzML" argument="-in_mzML" type="data" format="mzml" optional="false" label="Centroided MS1 data" help=" select mzml data sets(s)"/>
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57 <param name="in_fasta" argument="-in_fasta" type="data" format="fasta" optional="false" label="Protein sequence database" help=" select fasta data sets(s)"/>
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58 <param name="in_featureXML" argument="-in_featureXML" type="data" format="featurexml" optional="false" label="Feature data annotated with identifications (IDMapper)" help=" select featurexml data sets(s)"/>
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59 <param name="mz_tolerance_ppm" argument="-mz_tolerance_ppm" type="float" optional="true" value="10.0" label="Tolerance in ppm" help=""/>
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60 <param name="rt_tolerance_s" argument="-rt_tolerance_s" type="float" optional="true" value="30.0" label="Rolerance window around feature rt for XIC extraction" help=""/>
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61 <param name="intensity_threshold" argument="-intensity_threshold" type="float" optional="true" value="10.0" label="Intensity threshold to collect peaks in the MS1 spectrum" help=""/>
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62 <param name="correlation_threshold" argument="-correlation_threshold" type="float" optional="true" value="0.7" label="Correlation threshold for reporting a RIA" help=""/>
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63 <param name="xic_threshold" argument="-xic_threshold" type="float" optional="true" value="0.7" label="Minimum correlation to mono-isotopic peak for retaining a higher isotopic peak" help="If featureXML from reference file is used it should be disabled (set to -1) as no mono-isotopic peak is expected to be present"/>
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64 <param name="decomposition_threshold" argument="-decomposition_threshold" type="float" optional="true" value="0.7" label="Minimum R-squared of decomposition that must be achieved for a peptide to be reported" help=""/>
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65 <param name="weight_merge_window" argument="-weight_merge_window" type="float" optional="true" value="5.0" label="Decomposition coefficients within +- this rate window will be combined" help=""/>
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66 <param name="plot_extension" argument="-plot_extension" display="radio" type="select" optional="false" label="Extension used for plots (png|svg|pdf)" help="">
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67 <option value="png" selected="true">png</option>
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68 <option value="svg">svg</option>
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69 <option value="pdf">pdf</option>
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70 <expand macro="list_string_san"/>
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71 </param>
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72 <param name="qc_output_directory" argument="-qc_output_directory" type="text" optional="true" value="" label="Output directory for the quality report" help="">
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73 <expand macro="list_string_san"/>
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74 </param>
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75 <param name="labeling_element" argument="-labeling_element" display="radio" type="select" optional="false" label="Which element (single letter code) is labeled" help="">
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76 <option value="C" selected="true">C</option>
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77 <option value="N">N</option>
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78 <option value="H">H</option>
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79 <option value="O">O</option>
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80 <expand macro="list_string_san"/>
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81 </param>
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82 <param name="use_unassigned_ids" argument="-use_unassigned_ids" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Include identifications not assigned to a feature in pattern detection" help=""/>
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83 <param name="use_averagine_ids" argument="-use_averagine_ids" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use averagine peptides as model to perform pattern detection on unidentified peptides" help=""/>
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84 <param name="report_natural_peptides" argument="-report_natural_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether purely natural peptides are reported in the quality report" help=""/>
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85 <param name="filter_monoisotopic" argument="-filter_monoisotopic" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Try to filter out mono-isotopic patterns to improve detection of low RIA patterns" help=""/>
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86 <param name="cluster" argument="-cluster" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Perform grouping" help=""/>
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87 <expand macro="adv_opts_macro">
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88 <param name="min_correlation_distance_to_averagine" argument="-min_correlation_distance_to_averagine" type="float" optional="true" value="-1.0" label="Minimum difference in correlation between incorporation pattern and averagine pattern" help="Positive values filter all RIAs passing the correlation threshold but that also show a better correlation to an averagine peptide. Disabled for values &lt;= -1"/>
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89 <param name="pattern_15N_TIC_threshold" argument="-pattern_15N_TIC_threshold" type="float" optional="true" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help=""/>
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90 <param name="pattern_13C_TIC_threshold" argument="-pattern_13C_TIC_threshold" type="float" optional="true" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help=""/>
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91 <param name="pattern_2H_TIC_threshold" argument="-pattern_2H_TIC_threshold" type="float" optional="true" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help=""/>
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92 <param name="pattern_18O_TIC_threshold" argument="-pattern_18O_TIC_threshold" type="float" optional="true" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help=""/>
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93 <param name="heatmap_bins" argument="-heatmap_bins" type="integer" optional="true" value="20" label="Number of RIA bins for heat map generation" help=""/>
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94 <param name="observed_peak_fraction" argument="-observed_peak_fraction" type="float" optional="true" value="0.5" label="Fraction of observed/expected peaks" help=""/>
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95 <param name="min_consecutive_isotopes" argument="-min_consecutive_isotopes" type="integer" optional="true" value="2" label="Minimum number of consecutive isotopic intensities needed" help=""/>
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96 <param name="score_plot_yaxis_min" argument="-score_plot_yaxis_min" type="float" optional="true" value="0.0" label="The minimum value of the score axis" help="Values smaller than zero usually only make sense if the observed peak fraction is set to 0"/>
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97 <param name="collect_method" argument="-collect_method" display="radio" type="select" optional="false" label="How RIAs are collected" help="">
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98 <option value="correlation_maximum" selected="true">correlation_maximum</option>
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99 <option value="decomposition_maximum">decomposition_maximum</option>
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100 <expand macro="list_string_san"/>
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101 </param>
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102 <param name="lowRIA_correlation_threshold" argument="-lowRIA_correlation_threshold" type="float" optional="true" value="-1.0" label="Correlation threshold for reporting low RIA patterns" help="Disable and take correlation_threshold value for negative values"/>
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103 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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104 <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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105 <expand macro="list_string_san"/>
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106 </param>
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107 </expand>
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108 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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109 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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110 </param>
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111 </inputs>
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112 <outputs>
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113 <data name="out_csv" label="${tool.name} on ${on_string}: out_csv" format="csv"/>
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114 <data name="out_peptide_centric_csv" label="${tool.name} on ${on_string}: out_peptide_centric_csv" format="csv"/>
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115 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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116 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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117 </data>
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118 </outputs>
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119 <tests>
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120 <expand macro="autotest_MetaProSIP"/>
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121 <expand macro="manutest_MetaProSIP"/>
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122 </tests>
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123 <help><![CDATA[Performs proteinSIP on peptide features for elemental flux analysis.
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124
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125
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126 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_MetaProSIP.html]]></help>
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127 <expand macro="references"/>
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128 </tool>