Mercurial > repos > galaxyp > openms_idfileconverter
comparison IDFileConverter.xml @ 7:1dcffdad49c0 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
author | galaxyp |
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date | Mon, 12 Feb 2018 13:07:53 -0500 |
parents | 066cf4d993f5 |
children | 83cf7a4cd03c |
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6:e64a9dc50d1c | 7:1dcffdad49c0 |
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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="""/> | 102 <remove value="""/> |
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"/> |