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comparison MetaProSIP.xml @ 1:a25d96e0d837 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
author galaxyp
date Wed, 09 Aug 2017 09:29:30 -0400
parents f0e3cb65a6bd
children 21644dec106d
comparison
equal deleted inserted replaced
0:f0e3cb65a6bd 1:a25d96e0d837
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 CTD2Galaxy.--> 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]--> 3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="MetaProSIP" name="MetaProSIP" version="2.1.0"> 4 <tool id="MetaProSIP" name="MetaProSIP" version="2.2.0.1">
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 </macros> 9 </macros>
50 #end if 50 #end if
51 #if $param_weight_merge_window: 51 #if $param_weight_merge_window:
52 -weight_merge_window $param_weight_merge_window 52 -weight_merge_window $param_weight_merge_window
53 #end if 53 #end if
54 #if $param_plot_extension: 54 #if $param_plot_extension:
55 -plot_extension $param_plot_extension 55 -plot_extension
56 #if " " in str($param_plot_extension):
57 "$param_plot_extension"
58 #else
59 $param_plot_extension
60 #end if
56 #end if 61 #end if
57 #if $param_qc_output_directory: 62 #if $param_qc_output_directory:
58 -qc_output_directory "$param_qc_output_directory" 63 -qc_output_directory "$param_qc_output_directory"
59 #end if 64 #end if
60 #if $param_labeling_element: 65 #if $param_labeling_element:
61 -labeling_element $param_labeling_element 66 -labeling_element
67 #if " " in str($param_labeling_element):
68 "$param_labeling_element"
69 #else
70 $param_labeling_element
71 #end if
62 #end if 72 #end if
63 #if $param_use_unassigned_ids: 73 #if $param_use_unassigned_ids:
64 -use_unassigned_ids 74 -use_unassigned_ids
65 #end if 75 #end if
66 #if $param_use_averagine_ids: 76 #if $param_use_averagine_ids:
102 #end if 112 #end if
103 #if $adv_opts.param_score_plot_yaxis_min: 113 #if $adv_opts.param_score_plot_yaxis_min:
104 -score_plot_yaxis_min $adv_opts.param_score_plot_yaxis_min 114 -score_plot_yaxis_min $adv_opts.param_score_plot_yaxis_min
105 #end if 115 #end if
106 #if $adv_opts.param_collect_method: 116 #if $adv_opts.param_collect_method:
107 -collect_method $adv_opts.param_collect_method 117 -collect_method
118 #if " " in str($adv_opts.param_collect_method):
119 "$adv_opts.param_collect_method"
120 #else
121 $adv_opts.param_collect_method
122 #end if
108 #end if 123 #end if
109 #if $adv_opts.param_lowRIA_correlation_threshold: 124 #if $adv_opts.param_lowRIA_correlation_threshold:
110 -lowRIA_correlation_threshold $adv_opts.param_lowRIA_correlation_threshold 125 -lowRIA_correlation_threshold $adv_opts.param_lowRIA_correlation_threshold
111 #end if 126 #end if
112 #if $adv_opts.param_force: 127 #if $adv_opts.param_force:
116 </command> 131 </command>
117 <inputs> 132 <inputs>
118 <param name="param_in_mzML" type="data" format="mzml" optional="False" label="Centroided MS1 data" help="(-in_mzML) "/> 133 <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) "/> 134 <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) "/> 135 <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) "/> 136 <param name="param_r_executable" type="data" format="txt" 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) "/> 137 <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) "/> 138 <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) "/> 139 <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) "/> 140 <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"/> 141 <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"/>
173 <data name="param_out_peptide_centric_csv" format="tabular"/> 188 <data name="param_out_peptide_centric_csv" format="tabular"/>
174 </outputs> 189 </outputs>
175 <help>Performs proteinSIP on peptide features for elemental flux analysis. 190 <help>Performs proteinSIP on peptide features for elemental flux analysis.
176 191
177 192
178 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/doxygen/parameters/output/UTILS_MetaProSIP.html</help> 193 For more information, visit http://www.openms.de/comp/metaprosip/</help>
179 </tool> 194 </tool>