Mercurial > repos > galaxyp > openms_idfileconverter

comparison IDFileConverter.xml @ 3:066cf4d993f5 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 09:10:41 -0400
parents 5588e443a7db
children 1dcffdad49c0
comparison
equal deleted inserted replaced
2:5588e443a7db 3:066cf4d993f5
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: [ID Processing]--> 3 <!--Proposed Tool Section: [ID Processing]-->
4 <tool id="IDFileConverter" name="IDFileConverter" version="2.1.0"> 4 <tool id="IDFileConverter" name="IDFileConverter" version="2.2.0">
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
15 ## check input file type
16 #set $in_type = $param_in.ext
17 14
18 ## create the symlinks to set the proper file extension, since IDFileConverter uses them to choose how to handle the input files 15 ## check input file type
19 ln -s '$param_in' 'param_in.${in_type}' && 16 #set $in_type = $param_in.ext
20
21 IDFileConverter
22 17
23 #if $param_in: 18 ## create the symlinks to set the proper file extension, since IDFileConverter uses them to choose how to handle the input files
24 -in 'param_in.${in_type}' 19 ln -s '$param_in' 'param_in.${in_type}' &&
20
21 IDFileConverter
22
23 #if $param_in:
24 -in 'param_in.${in_type}'
25 #end if
26 #if $param_out:
27 -out $param_out
28 #end if
29 #if $param_out_type:
30 -out_type
31 #if " " in str($param_out_type):
32 "$param_out_type"
33 #else
34 $param_out_type
25 #end if 35 #end if
26 #if $param_out: 36 #end if
27 -out $param_out 37 #if $param_mz_file:
38 -mz_file $param_mz_file
39 #end if
40 #if $param_mz_name:
41 -mz_name "$param_mz_name"
42 #end if
43 #if $param_peptideprophet_analyzed:
44 -peptideprophet_analyzed
45 #end if
46 #if $param_score_type:
47 -score_type
48 #if " " in str($param_score_type):
49 "$param_score_type"
50 #else
51 $param_score_type
28 #end if 52 #end if
29 #if $param_out_type: 53 #end if
30 -out_type 54 #if $adv_opts.adv_opts_selector=='advanced':
31 #if " " in str($param_out_type): 55 #if $adv_opts.param_ignore_proteins_per_peptide:
32 "$param_out_type" 56 -ignore_proteins_per_peptide
33 #else 57 #end if
34 $param_out_type 58 #if $adv_opts.param_scan_regex:
35 #end if 59 -scan_regex "$adv_opts.param_scan_regex"
36 #end if 60 #end if
37 #if $param_mz_file: 61 #if $adv_opts.param_no_spectra_data_override:
38 -mz_file $param_mz_file 62 -no_spectra_data_override
39 #end if 63 #end if
40 #if $param_mz_name: 64 #if $adv_opts.param_force:
41 -mz_name "$param_mz_name" 65 -force
42 #end if 66 #end if
43 #if $param_peptideprophet_analyzed: 67 #end if
44 -peptideprophet_analyzed 68 ]]>
45 #end if
46 #if $param_score_type:
47 -score_type
48 #if " " in str($param_score_type):
49 "$param_score_type"
50 #else
51 $param_score_type
52 #end if
53 #end if
54 #if $adv_opts.adv_opts_selector=='advanced':
55 #if $adv_opts.param_ignore_proteins_per_peptide:
56 -ignore_proteins_per_peptide
57 #end if
58 #if $adv_opts.param_scan_regex:
59 -scan_regex "$adv_opts.param_scan_regex"
60 #end if
61 #if $adv_opts.param_force:
62 -force
63 #end if
64 #end if
65 ]]>
66 </command> 69 </command>
67 <inputs> 70 <inputs>
68 <param name="param_in" type="data" format="tabular,mzid,pepxml,idxml" optional="False" label="Input file or directory containing the data to convert" help="(-in) This may be: &lt;br&gt;- a single file in a multi-purpose XML format (pepXML, protXML, idXML, mzid), &lt;br&gt;- a single file in a search engine-specific format (Mascot: mascotXML, OMSSA: omssaXML, X! Tandem: xml, Percolator: psms), &lt;br&gt;- a single text file (tab separated) with one line for all peptide sequences matching a spectrum (top N hits), &lt;br&gt;- for Sequest results, a directory containing .out files. &lt;br&gt;"/> 71 <param name="param_in" type="data" format="pepxml,protXML,mascotXML,omssaXML,xml,psms,tabular,idxml,mzid" optional="False" label="Input file or directory containing the data to convert" help="(-in) This may be: &lt;br&gt;- a single file in a multi-purpose XML format (pepXML, protXML, idXML, mzid), &lt;br&gt;- a single file in a search engine-specific format (Mascot: mascotXML, OMSSA: omssaXML, X! Tandem: xml, Percolator: psms), &lt;br&gt;- a single text file (tab separated) with one line for all peptide sequences matching a spectrum (top N hits), &lt;br&gt;- for Sequest results, a directory containing .out files. &lt;br&gt;"/>
69 <param name="param_out_type" display="radio" type="select" optional="True" label="Output file type (default: determined from file extension)" help="(-out_type) "> 72 <param name="param_out_type" display="radio" type="select" optional="True" label="Output file type (default: determined from file extension)" help="(-out_type) ">
70 <option value="idXML">idXML</option> 73 <option value="idXML">idXML</option>
71 <option value="mzid">mzid</option> 74 <option value="mzid">mzid</option>
72 <option value="pepXML">pepXML</option> 75 <option value="pepXML">pepXML</option>
73 <option value="FASTA">FASTA</option> 76 <option value="FASTA">FASTA</option>
74 </param> 77 </param>
75 <param name="param_mz_file" type="data" format="mzxml,mzml" optional="True" label="[pepXML, Sequest, Mascot, X! Tandem, Percolator only] Retention times will be looked up in this file" help="(-mz_file) "/> 78 <param name="param_mz_file" type="data" format="mzml,mzxml,mzData" optional="True" label="[pepXML, Sequest, Mascot, X! Tandem, mzid, Percolator only] Retention times and native spectrum ids (spectrum_references) will be looked up in this file" help="(-mz_file) "/>
76 <param name="param_mz_name" type="text" size="30" label="[pepXML only] Experiment filename/path (extension will be removed) to match in the pepXML file ('base_name' attribute)" help="(-mz_name) Only necessary if different from 'mz_file'"> 79 <param name="param_mz_name" type="text" size="30" label="[pepXML only] Experiment filename/path (extension will be removed) to match in the pepXML file ('base_name' attribute)" help="(-mz_name) Only necessary if different from 'mz_file'">
77 <sanitizer> 80 <sanitizer>
78 <valid initial="string.printable"> 81 <valid initial="string.printable">
79 <remove value="'"/> 82 <remove value="'"/>
80 <remove value="&quot;"/> 83 <remove value="&quot;"/>
95 <remove value="'"/> 98 <remove value="'"/>
96 <remove value="&quot;"/> 99 <remove value="&quot;"/>
97 </valid> 100 </valid>
98 </sanitizer> 101 </sanitizer>
99 </param> 102 </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"/>
100 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 104 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
101 </expand> 105 </expand>
102 </inputs> 106 </inputs>
103 <outputs> 107 <outputs>
104 <data name="param_out" auto_format="true"/> 108 <data name="param_out" auto_format="true"/>