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comparison MetaProSIP.xml @ 13:819ed5aae76f draft

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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 18:58:27 +0000
parents c18e6eb07aa9
children 5f72a8fa935d
comparison
equal deleted inserted replaced
12:41a21bbf40d8 13:819ed5aae76f
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [Utilities]--> 3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="MetaProSIP" name="MetaProSIP" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="MetaProSIP" name="MetaProSIP" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Performs proteinSIP on peptide features for elemental flux analysis.</description> 5 <description>Performs proteinSIP on peptide features for elemental flux analysis.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">MetaProSIP</token> 7 <token name="@EXECUTABLE@">MetaProSIP</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
11 </macros> 9 </macros>
12 <expand macro="requirements"/> 10 <expand macro="requirements"/>
13 <expand macro="stdio"/> 11 <expand macro="stdio"/>
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ 12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
15 @EXT_FOO@ 13 @EXT_FOO@
51 <configfiles> 49 <configfiles>
52 <inputs name="args_json" data_style="paths"/> 50 <inputs name="args_json" data_style="paths"/>
53 <configfile name="hardcoded_json"><![CDATA[{"r_executable": "R", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 51 <configfile name="hardcoded_json"><![CDATA[{"r_executable": "R", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
54 </configfiles> 52 </configfiles>
55 <inputs> 53 <inputs>
56 <param name="in_mzML" argument="-in_mzML" type="data" format="mzml" optional="false" label="Centroided MS1 data" help=" select mzml data sets(s)"/> 54 <param argument="-in_mzML" type="data" format="mzml" optional="false" label="Centroided MS1 data" help=" select mzml data sets(s)"/>
57 <param name="in_fasta" argument="-in_fasta" type="data" format="fasta" optional="false" label="Protein sequence database" help=" select fasta data sets(s)"/> 55 <param argument="-in_fasta" type="data" format="fasta" optional="false" label="Protein sequence database" help=" select fasta data sets(s)"/>
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)"/> 56 <param argument="-in_featureXML" type="data" format="featurexml" optional="false" label="Feature data annotated with identifications (IDMapper)" help=" select featurexml data sets(s)"/>
59 <param name="mz_tolerance_ppm" argument="-mz_tolerance_ppm" type="float" optional="true" value="10.0" label="Tolerance in ppm" help=""/> 57 <param argument="-mz_tolerance_ppm" type="float" optional="true" value="10.0" label="Tolerance in ppm" help=""/>
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=""/> 58 <param argument="-rt_tolerance_s" type="float" optional="true" value="30.0" label="Rolerance window around feature rt for XIC extraction" help=""/>
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=""/> 59 <param argument="-intensity_threshold" type="float" optional="true" value="10.0" label="Intensity threshold to collect peaks in the MS1 spectrum" help=""/>
62 <param name="correlation_threshold" argument="-correlation_threshold" type="float" optional="true" value="0.7" label="Correlation threshold for reporting a RIA" help=""/> 60 <param argument="-correlation_threshold" type="float" optional="true" value="0.7" label="Correlation threshold for reporting a RIA" help=""/>
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"/> 61 <param 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"/>
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=""/> 62 <param 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=""/>
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=""/> 63 <param argument="-weight_merge_window" type="float" optional="true" value="5.0" label="Decomposition coefficients within +- this rate window will be combined" help=""/>
66 <param name="plot_extension" argument="-plot_extension" display="radio" type="select" optional="false" label="Extension used for plots (png|svg|pdf)" help=""> 64 <param argument="-plot_extension" type="select" optional="true" label="Extension used for plots (png|svg|pdf)" help="">
67 <option value="png" selected="true">png</option> 65 <option value="png" selected="true">png</option>
68 <option value="svg">svg</option> 66 <option value="svg">svg</option>
69 <option value="pdf">pdf</option> 67 <option value="pdf">pdf</option>
70 <expand macro="list_string_san"/> 68 <expand macro="list_string_san" name="plot_extension"/>
71 </param> 69 </param>
72 <param name="qc_output_directory" argument="-qc_output_directory" type="text" optional="true" value="" label="Output directory for the quality report" help=""> 70 <param argument="-qc_output_directory" type="text" optional="true" value="" label="Output directory for the quality report" help="">
73 <expand macro="list_string_san"/> 71 <expand macro="list_string_san" name="qc_output_directory"/>
74 </param> 72 </param>
75 <param name="labeling_element" argument="-labeling_element" display="radio" type="select" optional="false" label="Which element (single letter code) is labeled" help=""> 73 <param argument="-labeling_element" type="select" optional="true" label="Which element (single letter code) is labeled" help="">
76 <option value="C" selected="true">C</option> 74 <option value="C" selected="true">C</option>
77 <option value="N">N</option> 75 <option value="N">N</option>
78 <option value="H">H</option> 76 <option value="H">H</option>
79 <option value="O">O</option> 77 <option value="O">O</option>
80 <expand macro="list_string_san"/> 78 <expand macro="list_string_san" name="labeling_element"/>
81 </param> 79 </param>
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=""/> 80 <param argument="-use_unassigned_ids" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Include identifications not assigned to a feature in pattern detection" help=""/>
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=""/> 81 <param 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=""/>
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=""/> 82 <param argument="-report_natural_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether purely natural peptides are reported in the quality report" help=""/>
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=""/> 83 <param 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=""/>
86 <param name="cluster" argument="-cluster" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Perform grouping" help=""/> 84 <param argument="-cluster" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Perform grouping" help=""/>
87 <expand macro="adv_opts_macro"> 85 <expand macro="adv_opts_macro">
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"/> 86 <param 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"/>
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=""/> 87 <param 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=""/>
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=""/> 88 <param 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=""/>
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=""/> 89 <param 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=""/>
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=""/> 90 <param 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=""/>
93 <param name="heatmap_bins" argument="-heatmap_bins" type="integer" optional="true" value="20" label="Number of RIA bins for heat map generation" help=""/> 91 <param argument="-heatmap_bins" type="integer" optional="true" value="20" label="Number of RIA bins for heat map generation" help=""/>
94 <param name="observed_peak_fraction" argument="-observed_peak_fraction" type="float" optional="true" value="0.5" label="Fraction of observed/expected peaks" help=""/> 92 <param argument="-observed_peak_fraction" type="float" optional="true" value="0.5" label="Fraction of observed/expected peaks" help=""/>
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=""/> 93 <param argument="-min_consecutive_isotopes" type="integer" optional="true" value="2" label="Minimum number of consecutive isotopic intensities needed" help=""/>
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"/> 94 <param 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"/>
97 <param name="collect_method" argument="-collect_method" display="radio" type="select" optional="false" label="How RIAs are collected" help=""> 95 <param argument="-collect_method" type="select" optional="true" label="How RIAs are collected" help="">
98 <option value="correlation_maximum" selected="true">correlation_maximum</option> 96 <option value="correlation_maximum" selected="true">correlation_maximum</option>
99 <option value="decomposition_maximum">decomposition_maximum</option> 97 <option value="decomposition_maximum">decomposition_maximum</option>
100 <expand macro="list_string_san"/> 98 <expand macro="list_string_san" name="collect_method"/>
101 </param> 99 </param>
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"/> 100 <param 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"/>
103 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 101 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
104 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 102 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
105 <expand macro="list_string_san"/> 103 <expand macro="list_string_san" name="test"/>
106 </param> 104 </param>
107 </expand> 105 </expand>
108 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 106 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
109 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 107 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
110 </param> 108 </param>
114 <data name="out_peptide_centric_csv" label="${tool.name} on ${on_string}: out_peptide_centric_csv" format="csv"/> 112 <data name="out_peptide_centric_csv" label="${tool.name} on ${on_string}: out_peptide_centric_csv" format="csv"/>
115 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 113 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
116 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 114 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
117 </data> 115 </data>
118 </outputs> 116 </outputs>
119 <tests> 117 <tests><!-- TOPP_MetaProSIP_1 -->
120 <expand macro="autotest_MetaProSIP"/> 118 <test expect_num_outputs="3">
121 <expand macro="manutest_MetaProSIP"/> 119 <section name="adv_opts">
120 <param name="min_correlation_distance_to_averagine" value="-1.0"/>
121 <param name="pattern_15N_TIC_threshold" value="0.95"/>
122 <param name="pattern_13C_TIC_threshold" value="0.95"/>
123 <param name="pattern_2H_TIC_threshold" value="0.95"/>
124 <param name="pattern_18O_TIC_threshold" value="0.95"/>
125 <param name="heatmap_bins" value="20"/>
126 <param name="observed_peak_fraction" value="0.5"/>
127 <param name="min_consecutive_isotopes" value="2"/>
128 <param name="score_plot_yaxis_min" value="0.0"/>
129 <param name="collect_method" value="correlation_maximum"/>
130 <param name="lowRIA_correlation_threshold" value="-1.0"/>
131 <param name="force" value="false"/>
132 <param name="test" value="true"/>
133 </section>
134 <param name="in_mzML" value="MetaProSIP_1_input.mzML"/>
135 <param name="in_fasta" value="MetaProSIP_1_input.fasta"/>
136 <output name="out_csv" file="MetaProSIP_1_output_1.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
137 <output name="out_peptide_centric_csv" file="MetaProSIP_1_output_2.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
138 <param name="in_featureXML" value="MetaProSIP_1_input.featureXML"/>
139 <param name="mz_tolerance_ppm" value="10.0"/>
140 <param name="rt_tolerance_s" value="30.0"/>
141 <param name="intensity_threshold" value="10.0"/>
142 <param name="correlation_threshold" value="0.7"/>
143 <param name="xic_threshold" value="0.7"/>
144 <param name="decomposition_threshold" value="0.7"/>
145 <param name="weight_merge_window" value="5.0"/>
146 <param name="plot_extension" value="png"/>
147 <param name="qc_output_directory" value=""/>
148 <param name="labeling_element" value="C"/>
149 <param name="use_unassigned_ids" value="false"/>
150 <param name="use_averagine_ids" value="false"/>
151 <param name="report_natural_peptides" value="false"/>
152 <param name="filter_monoisotopic" value="false"/>
153 <param name="cluster" value="false"/>
154 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
155 <output name="ctd_out" ftype="xml">
156 <assert_contents>
157 <is_valid_xml/>
158 </assert_contents>
159 </output>
160 </test>
122 </tests> 161 </tests>
123 <help><![CDATA[Performs proteinSIP on peptide features for elemental flux analysis. 162 <help><![CDATA[Performs proteinSIP on peptide features for elemental flux analysis.
124 163
125 164
126 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_MetaProSIP.html]]></help> 165 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_MetaProSIP.html]]></help>
127 <expand macro="references"/> 166 <expand macro="references"/>
128 </tool> 167 </tool>