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comparison MetaProSIP.xml @ 0:f0e3cb65a6bd draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:39:28 -0500
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-1:000000000000 0:f0e3cb65a6bd
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 CTD2Galaxy.-->
3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="MetaProSIP" name="MetaProSIP" version="2.1.0">
5 <description>Performs proteinSIP on peptide features for elemental flux analysis.</description>
6 <macros>
7 <token name="@EXECUTABLE@">MetaProSIP</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>MetaProSIP
14
15 #if $param_in_mzML:
16 -in_mzML $param_in_mzML
17 #end if
18 #if $param_in_fasta:
19 -in_fasta $param_in_fasta
20 #end if
21 #if $param_out_csv:
22 -out_csv $param_out_csv
23 #end if
24 #if $param_out_peptide_centric_csv:
25 -out_peptide_centric_csv $param_out_peptide_centric_csv
26 #end if
27 #if $param_in_featureXML:
28 -in_featureXML $param_in_featureXML
29 #end if
30 #if $param_r_executable:
31 -r_executable $param_r_executable
32 #end if
33 #if $param_mz_tolerance_ppm:
34 -mz_tolerance_ppm $param_mz_tolerance_ppm
35 #end if
36 #if $param_rt_tolerance_s:
37 -rt_tolerance_s $param_rt_tolerance_s
38 #end if
39 #if $param_intensity_threshold:
40 -intensity_threshold $param_intensity_threshold
41 #end if
42 #if $param_correlation_threshold:
43 -correlation_threshold $param_correlation_threshold
44 #end if
45 #if $param_xic_threshold:
46 -xic_threshold $param_xic_threshold
47 #end if
48 #if $param_decomposition_threshold:
49 -decomposition_threshold $param_decomposition_threshold
50 #end if
51 #if $param_weight_merge_window:
52 -weight_merge_window $param_weight_merge_window
53 #end if
54 #if $param_plot_extension:
55 -plot_extension $param_plot_extension
56 #end if
57 #if $param_qc_output_directory:
58 -qc_output_directory "$param_qc_output_directory"
59 #end if
60 #if $param_labeling_element:
61 -labeling_element $param_labeling_element
62 #end if
63 #if $param_use_unassigned_ids:
64 -use_unassigned_ids
65 #end if
66 #if $param_use_averagine_ids:
67 -use_averagine_ids
68 #end if
69 #if $param_report_natural_peptides:
70 -report_natural_peptides
71 #end if
72 #if $param_filter_monoisotopic:
73 -filter_monoisotopic
74 #end if
75 #if $param_cluster:
76 -cluster
77 #end if
78 #if $adv_opts.adv_opts_selector=='advanced':
79 #if $adv_opts.param_min_correlation_distance_to_averagine:
80 -min_correlation_distance_to_averagine $adv_opts.param_min_correlation_distance_to_averagine
81 #end if
82 #if $adv_opts.param_pattern_15N_TIC_threshold:
83 -pattern_15N_TIC_threshold $adv_opts.param_pattern_15N_TIC_threshold
84 #end if
85 #if $adv_opts.param_pattern_13C_TIC_threshold:
86 -pattern_13C_TIC_threshold $adv_opts.param_pattern_13C_TIC_threshold
87 #end if
88 #if $adv_opts.param_pattern_2H_TIC_threshold:
89 -pattern_2H_TIC_threshold $adv_opts.param_pattern_2H_TIC_threshold
90 #end if
91 #if $adv_opts.param_pattern_18O_TIC_threshold:
92 -pattern_18O_TIC_threshold $adv_opts.param_pattern_18O_TIC_threshold
93 #end if
94 #if $adv_opts.param_heatmap_bins:
95 -heatmap_bins $adv_opts.param_heatmap_bins
96 #end if
97 #if $adv_opts.param_observed_peak_fraction:
98 -observed_peak_fraction $adv_opts.param_observed_peak_fraction
99 #end if
100 #if $adv_opts.param_min_consecutive_isotopes:
101 -min_consecutive_isotopes $adv_opts.param_min_consecutive_isotopes
102 #end if
103 #if $adv_opts.param_score_plot_yaxis_min:
104 -score_plot_yaxis_min $adv_opts.param_score_plot_yaxis_min
105 #end if
106 #if $adv_opts.param_collect_method:
107 -collect_method $adv_opts.param_collect_method
108 #end if
109 #if $adv_opts.param_lowRIA_correlation_threshold:
110 -lowRIA_correlation_threshold $adv_opts.param_lowRIA_correlation_threshold
111 #end if
112 #if $adv_opts.param_force:
113 -force
114 #end if
115 #end if
116 </command>
117 <inputs>
118 <param name="param_in_mzML" type="data" format="mzml" optional="False" label="Centroided MS1 data" help="(-in_mzML) "/>
119 <param name="param_in_fasta" type="data" format="fasta" optional="False" label="Protein sequence database" help="(-in_fasta) "/>
120 <param name="param_in_featureXML" type="data" format="featurexml" optional="False" label="Feature data annotated with identifications (IDMapper)" help="(-in_featureXML) "/>
121 <param name="param_r_executable" type="data" format="text" value="R" label="Path to the R executable (default: 'R')" help="(-r_executable) "/>
122 <param name="param_mz_tolerance_ppm" type="float" value="10.0" label="Tolerance in ppm" help="(-mz_tolerance_ppm) "/>
123 <param name="param_rt_tolerance_s" type="float" value="30.0" label="Rolerance window around feature rt for XIC extraction" help="(-rt_tolerance_s) "/>
124 <param name="param_intensity_threshold" type="float" value="10.0" label="Intensity threshold to collect peaks in the MS1 spectrum" help="(-intensity_threshold) "/>
125 <param name="param_correlation_threshold" type="float" value="0.7" label="Correlation threshold for reporting a RIA" help="(-correlation_threshold) "/>
126 <param name="param_xic_threshold" type="float" value="0.7" label="Minimum correlation to mono-isotopic peak for retaining a higher isotopic peak" help="(-xic_threshold) If featureXML from reference file is used it should be disabled (set to -1) as no mono-isotopic peak is expected to be present"/>
127 <param name="param_decomposition_threshold" type="float" value="0.7" label="Minimum R^2 of decomposition that must be achieved for a peptide to be reported" help="(-decomposition_threshold) "/>
128 <param name="param_weight_merge_window" type="float" value="5.0" label="Decomposition coefficients within +- this rate window will be combined" help="(-weight_merge_window) "/>
129 <param name="param_plot_extension" display="radio" type="select" optional="False" value="png" label="Extension used for plots (png|svg|pdf)" help="(-plot_extension) ">
130 <option value="png" selected="true">png</option>
131 <option value="svg">svg</option>
132 <option value="pdf">pdf</option>
133 </param>
134 <param name="param_qc_output_directory" type="text" size="30" label="Output directory for the quality report" help="(-qc_output_directory) ">
135 <sanitizer>
136 <valid initial="string.printable">
137 <remove value="'"/>
138 <remove value="&quot;"/>
139 </valid>
140 </sanitizer>
141 </param>
142 <param name="param_labeling_element" display="radio" type="select" optional="False" value="C" label="Which element (single letter code) is labeled" help="(-labeling_element) ">
143 <option value="C" selected="true">C</option>
144 <option value="N">N</option>
145 <option value="H">H</option>
146 <option value="O">O</option>
147 </param>
148 <param name="param_use_unassigned_ids" display="radio" type="boolean" truevalue="-use_unassigned_ids" falsevalue="" checked="false" optional="True" label="Include identifications not assigned to a feature in pattern detection" help="(-use_unassigned_ids) "/>
149 <param name="param_use_averagine_ids" display="radio" type="boolean" truevalue="-use_averagine_ids" falsevalue="" checked="false" optional="True" label="Use averagine peptides as model to perform pattern detection on unidentified peptides" help="(-use_averagine_ids) "/>
150 <param name="param_report_natural_peptides" display="radio" type="boolean" truevalue="-report_natural_peptides" falsevalue="" checked="false" optional="True" label="Whether purely natural peptides are reported in the quality report" help="(-report_natural_peptides) "/>
151 <param name="param_filter_monoisotopic" display="radio" type="boolean" truevalue="-filter_monoisotopic" falsevalue="" checked="false" optional="True" label="Try to filter out mono-isotopic patterns to improve detection of low RIA patterns" help="(-filter_monoisotopic) "/>
152 <param name="param_cluster" display="radio" type="boolean" truevalue="-cluster" falsevalue="" checked="false" optional="True" label="Perform grouping" help="(-cluster) "/>
153 <expand macro="advanced_options">
154 <param name="param_min_correlation_distance_to_averagine" type="float" value="-1.0" label="Minimum difference in correlation between incorporation pattern and averagine pattern" help="(-min_correlation_distance_to_averagine) 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"/>
155 <param name="param_pattern_15N_TIC_threshold" type="float" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help="(-pattern_15N_TIC_threshold) "/>
156 <param name="param_pattern_13C_TIC_threshold" type="float" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help="(-pattern_13C_TIC_threshold) "/>
157 <param name="param_pattern_2H_TIC_threshold" type="float" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help="(-pattern_2H_TIC_threshold) "/>
158 <param name="param_pattern_18O_TIC_threshold" type="float" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help="(-pattern_18O_TIC_threshold) "/>
159 <param name="param_heatmap_bins" type="integer" value="20" label="Number of RIA bins for heat map generation" help="(-heatmap_bins) "/>
160 <param name="param_observed_peak_fraction" type="float" value="0.5" label="Fraction of observed/expected peaks" help="(-observed_peak_fraction) "/>
161 <param name="param_min_consecutive_isotopes" type="integer" value="2" label="Minimum number of consecutive isotopic intensities needed" help="(-min_consecutive_isotopes) "/>
162 <param name="param_score_plot_yaxis_min" type="float" value="0.0" label="The minimum value of the score axis" help="(-score_plot_yaxis_min) Values smaller than zero usually only make sense if the observed peak fraction is set to 0"/>
163 <param name="param_collect_method" display="radio" type="select" optional="False" value="correlation_maximum" label="How RIAs are collected" help="(-collect_method) ">
164 <option value="correlation_maximum" selected="true">correlation_maximum</option>
165 <option value="decomposition_maximum">decomposition_maximum</option>
166 </param>
167 <param name="param_lowRIA_correlation_threshold" type="float" value="-1.0" label="Correlation threshold for reporting low RIA patterns" help="(-lowRIA_correlation_threshold) Disable and take correlation_threshold value for negative values"/>
168 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
169 </expand>
170 </inputs>
171 <outputs>
172 <data name="param_out_csv" format="tabular"/>
173 <data name="param_out_peptide_centric_csv" format="tabular"/>
174 </outputs>
175 <help>Performs proteinSIP on peptide features for elemental flux analysis.
176
177
178 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/doxygen/parameters/output/UTILS_MetaProSIP.html</help>
179 </tool>