Mercurial > repos > galaxyp > openms_metaprosip

comparison MetaProSIP.xml @ 2:21644dec106d draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 1e51bed3a1c10c67ef0404216608e9333db04c64
author galaxyp
date Wed, 18 Oct 2017 15:29:01 -0400
parents a25d96e0d837
children fdb3fbfef4cc
comparison
equal deleted inserted replaced
1:a25d96e0d837 2:21644dec106d
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>
10 <expand macro="references"/> 10 <expand macro="references"/>
11 <expand macro="stdio"/> 11 <expand macro="stdio"/>
12 <expand macro="requirements"/> 12 <expand macro="requirements">
13 <requirement type="package" version="3.3.1">r-base</requirement>
14 </expand>
13 <command>MetaProSIP 15 <command>MetaProSIP
14 16
15 #if $param_in_mzML: 17 #if $param_in_mzML:
16 -in_mzML $param_in_mzML 18 -in_mzML $param_in_mzML
17 #end if 19 #end if
25 -out_peptide_centric_csv $param_out_peptide_centric_csv 27 -out_peptide_centric_csv $param_out_peptide_centric_csv
26 #end if 28 #end if
27 #if $param_in_featureXML: 29 #if $param_in_featureXML:
28 -in_featureXML $param_in_featureXML 30 -in_featureXML $param_in_featureXML
29 #end if 31 #end if
30 #if $param_r_executable: 32
31 -r_executable $param_r_executable 33 -r_executable 'R'
32 #end if 34
33 #if $param_mz_tolerance_ppm: 35 #if $param_mz_tolerance_ppm:
34 -mz_tolerance_ppm $param_mz_tolerance_ppm 36 -mz_tolerance_ppm $param_mz_tolerance_ppm
35 #end if 37 #end if
36 #if $param_rt_tolerance_s: 38 #if $param_rt_tolerance_s:
37 -rt_tolerance_s $param_rt_tolerance_s 39 -rt_tolerance_s $param_rt_tolerance_s
131 </command> 133 </command>
132 <inputs> 134 <inputs>
133 <param name="param_in_mzML" type="data" format="mzml" optional="False" label="Centroided MS1 data" help="(-in_mzML) "/> 135 <param name="param_in_mzML" type="data" format="mzml" optional="False" label="Centroided MS1 data" help="(-in_mzML) "/>
134 <param name="param_in_fasta" type="data" format="fasta" optional="False" label="Protein sequence database" help="(-in_fasta) "/> 136 <param name="param_in_fasta" type="data" format="fasta" optional="False" label="Protein sequence database" help="(-in_fasta) "/>
135 <param name="param_in_featureXML" type="data" format="featurexml" optional="False" label="Feature data annotated with identifications (IDMapper)" help="(-in_featureXML) "/> 137 <param name="param_in_featureXML" type="data" format="featurexml" optional="False" label="Feature data annotated with identifications (IDMapper)" help="(-in_featureXML) "/>
136 <param name="param_r_executable" type="data" format="txt" value="R" label="Path to the R executable (default: 'R')" help="(-r_executable) "/>
137 <param name="param_mz_tolerance_ppm" type="float" value="10.0" label="Tolerance in ppm" help="(-mz_tolerance_ppm) "/> 138 <param name="param_mz_tolerance_ppm" type="float" value="10.0" label="Tolerance in ppm" help="(-mz_tolerance_ppm) "/>
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) "/> 139 <param name="param_rt_tolerance_s" type="float" value="30.0" label="Rolerance window around feature rt for XIC extraction" help="(-rt_tolerance_s) "/>
139 <param name="param_intensity_threshold" type="float" value="10.0" label="Intensity threshold to collect peaks in the MS1 spectrum" help="(-intensity_threshold) "/> 140 <param name="param_intensity_threshold" type="float" value="10.0" label="Intensity threshold to collect peaks in the MS1 spectrum" help="(-intensity_threshold) "/>
140 <param name="param_correlation_threshold" type="float" value="0.7" label="Correlation threshold for reporting a RIA" help="(-correlation_threshold) "/> 141 <param name="param_correlation_threshold" type="float" value="0.7" label="Correlation threshold for reporting a RIA" help="(-correlation_threshold) "/>
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"/> 142 <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"/>