Mercurial > repos > galaxyp > openms_idfileconverter

comparison IDFileConverter.xml @ 7:1dcffdad49c0 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
author galaxyp
date Mon, 12 Feb 2018 13:07:53 -0500
parents 066cf4d993f5
children 83cf7a4cd03c
comparison
equal deleted inserted replaced
6:e64a9dc50d1c 7:1dcffdad49c0
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 CTDConverter.-->
3 <!--Proposed Tool Section: [ID Processing]--> 3 <!--Proposed Tool Section: [ID Processing]-->
4 <tool id="IDFileConverter" name="IDFileConverter" version="2.2.0"> 4 <tool id="IDFileConverter" name="IDFileConverter" version="2.3.0">
5 <description>Converts identification engine file formats.</description> 5 <description>Converts identification engine file formats.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">IDFileConverter</token> 7 <token name="@EXECUTABLE@">IDFileConverter</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 <command><![CDATA[ 13 <command><![CDATA[
14 14
15 ## check input file type 15 ## check input file type
16 #set $in_type = $param_in.ext 16 #set $in_type = $param_in.ext
17 17
18 ## create the symlinks to set the proper file extension, since IDFileConverter uses them to choose how to handle the input files 18 ## create the symlinks to set the proper file extension, since IDFileConverter uses them to choose how to handle the input files
19 ln -s '$param_in' 'param_in.${in_type}' && 19 ln -s '$param_in' 'param_in.${in_type}' &&
20 20
21 IDFileConverter 21 IDFileConverter
22 22
23 #if $param_in: 23 #if $param_in:
24 -in 'param_in.${in_type}' 24 -in 'param_in.${in_type}'
25 #end if 25 #end if
26 #if $param_out: 26 #if $param_out:
27 -out $param_out 27 -out $param_out
28 #end if 28 #end if
29 #if $param_out_type: 29 #if $param_out_type:
30 -out_type 30 -out_type
58 #if $adv_opts.param_scan_regex: 58 #if $adv_opts.param_scan_regex:
59 -scan_regex "$adv_opts.param_scan_regex" 59 -scan_regex "$adv_opts.param_scan_regex"
60 #end if 60 #end if
61 #if $adv_opts.param_no_spectra_data_override: 61 #if $adv_opts.param_no_spectra_data_override:
62 -no_spectra_data_override 62 -no_spectra_data_override
63 #end if
64 #if $adv_opts.param_add_ionmatch_annotation:
65 -add_ionmatch_annotation $adv_opts.param_add_ionmatch_annotation
63 #end if 66 #end if
64 #if $adv_opts.param_force: 67 #if $adv_opts.param_force:
65 -force 68 -force
66 #end if 69 #end if
67 #end if 70 #end if
99 <remove value="&quot;"/> 102 <remove value="&quot;"/>
100 </valid> 103 </valid>
101 </sanitizer> 104 </sanitizer>
102 </param> 105 </param>
103 <param name="param_no_spectra_data_override" display="radio" type="boolean" truevalue="-no_spectra_data_override" falsevalue="" checked="false" optional="True" label="[+mz_file only] Setting this flag will avoid overriding 'spectra_data' in ProteinIdentifications if mz_file is given and 'spectrum_reference's are added/updated" help="(-no_spectra_data_override) Use only if you are sure it is absolutely the same mz_file as used for identification"/> 106 <param name="param_no_spectra_data_override" display="radio" type="boolean" truevalue="-no_spectra_data_override" falsevalue="" checked="false" optional="True" label="[+mz_file only] Setting this flag will avoid overriding 'spectra_data' in ProteinIdentifications if mz_file is given and 'spectrum_reference's are added/updated" help="(-no_spectra_data_override) Use only if you are sure it is absolutely the same mz_file as used for identification"/>
107 <param name="param_add_ionmatch_annotation" type="float" value="0.0" label="[+mz_file only] Will annotate the contained identifications with their matches in the given mz_file" help="(-add_ionmatch_annotation) Will take quite some while. Match tolerance is .4"/>
104 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 108 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
105 </expand> 109 </expand>
106 </inputs> 110 </inputs>
107 <outputs> 111 <outputs>
108 <data name="param_out" auto_format="true"/> 112 <data name="param_out" auto_format="true"/>