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comparison IDFileConverter.xml @ 4:6ead64a594bd draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
parents 3d84209d3178
children
comparison
equal deleted inserted replaced
3:ec62782f6c68 4:6ead64a594bd
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="IDFileConverter" name="IDFileConverter" version="1.12.0"> 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 <description>Converts identification engine file formats.</description> 3 <!--Proposed Tool Section: [ID Processing]-->
4 <macros> 4 <tool id="IDFileConverter" name="IDFileConverter" version="2.0.0">
5 <token name="@EXECUTABLE@">IDFileConverter</token> 5 <description>Converts identification engine file formats.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">IDFileConverter</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>IDFileConverter 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>IDFileConverter
11 14
12 -in ${param_in} 15 #if $param_in:
13 -out ${param_out} 16 -in $param_in
14 -out_type ${param_out_type} 17 #end if
15 -mz_file ${param_mz_file} 18 #if $param_out:
16 -mz_name ${param_mz_name} 19 -out $param_out
17 ${param_use_precursor_data} 20 #end if
18 ${param_peptideprophet_analyzed} 21 #if $param_out_type:
19 -threads \${GALAXY_SLOTS:-24} 22 -out_type
23 #if &quot; &quot; in str($param_out_type):
24 &quot;$param_out_type&quot;
25 #else
26 $param_out_type
27 #end if
28 #end if
29 #if $param_mz_file:
30 -mz_file $param_mz_file
31 #end if
32 #if $param_mz_name:
33 -mz_name &quot;$param_mz_name&quot;
34 #end if
35 #if $param_use_precursor_data:
36 -use_precursor_data
37 #end if
38 #if $param_peptideprophet_analyzed:
39 -peptideprophet_analyzed
40 #end if
41 #if $param_score_type:
42 -score_type
43 #if &quot; &quot; in str($param_score_type):
44 &quot;$param_score_type&quot;
45 #else
46 $param_score_type
47 #end if
48 #end if
49 -threads \${GALAXY_SLOTS:-24}
20 #if $adv_opts.adv_opts_selector=='advanced': 50 #if $adv_opts.adv_opts_selector=='advanced':
21 ${adv_opts.param_ignore_proteins_per_peptide} 51 #if $adv_opts.param_ignore_proteins_per_peptide:
22 -scan_regex ${adv_opts.param_scan_regex} 52 -ignore_proteins_per_peptide
53 #end if
54 #if $adv_opts.param_scan_regex:
55 -scan_regex &quot;$adv_opts.param_scan_regex&quot;
56 #end if
57 #if $adv_opts.param_count_from_zero:
58 -count_from_zero
59 #end if
60 #if $adv_opts.param_force:
61 -force
62 #end if
23 #end if 63 #end if
24 </command> 64 </command>
25 <inputs> 65 <inputs>
26 <param name="param_in" type="data" format="pepXML,idXML" optional="False" label="Input file or directory containing the output of the search engine.#br#Sequest: Directory containing the .out files#br#pepXML: Single pepXML file.#br#protXML: Single protXML file.#br#mascotXML: Single Mascot XML file.#br#omssaXML: Single OMSSA XML file.#br#XTandem: Single XML file.#br#idXML: Single idXML file.#br#" help="(-in)"/> 66 <param format="tabular,xml,txt,pepxml" 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;" label="Input file or directory containing the data to convert" name="param_in" optional="False" type="data"/>
27 <param name="param_out_type" type="select" optional="True" label="output file type -- default: determined from file extension or content#br#" help="(-out_type)"> 67 <param help="(-out_type) " label="Output file type (default: determined from file extension)" name="param_out_type" optional="True" type="select">
28 <option value="idXML">idXML</option> 68 <option value="idXML">idXML</option>
29 <option value="mzid">mzid</option> 69 <option value="mzid">mzid</option>
30 <option value="pepXML">pepXML</option> 70 <option value="pepXML">pepXML</option>
31 <option value="FASTA">FASTA</option> 71 <option value="FASTA">FASTA</option>
32 </param> 72 </param>
33 <param name="param_mz_file" type="data" format="mzML,mzXML" optional="True" label="[Sequest, pepXML, mascotXML, XTandem only] Retention times will be looked up in this file" help="(-mz_file)"/> 73 <param format="xml,mzxml,mzml" help="(-mz_file) " label="[pepXML, Sequest, Mascot, X! Tandem, Percolator only] Retention times will be looked up in this file" name="param_mz_file" optional="True" type="data"/>
34 <param name="param_mz_name" type="text" size="20" label="[pepXML only] Experiment filename/path (extension will be removed) to match in the pepXML file ('base_name' attribute). Only necessary if different from 'mz_file'." help="(-mz_name)"/> 74 <param help="(-mz_name) Only necessary if different from 'mz_file'" label="[pepXML only] Experiment filename/path (extension will be removed) to match in the pepXML file ('base_name' attribute)" name="param_mz_name" size="30" type="text">
35 <param name="param_use_precursor_data" type="boolean" truevalue="-use_precursor_data true" falsevalue="-use_precursor_data false" checked="false" optional="True" label="[pepXML only] Use precursor RTs (and m/z values) from 'mz_file' for the generated peptide identifications, instead of the RTs of MS2 spectra." help="(-use_precursor_data)"/> 75 <sanitizer>
36 <param name="param_peptideprophet_analyzed" type="boolean" truevalue="-peptideprophet_analyzed true" falsevalue="-peptideprophet_analyzed false" checked="false" optional="True" label="[pepXML output only] Write output in the format of a PeptideProphet analysis result. By default a 'raw' pepXML is produced that contains only search engine results." help="(-peptideprophet_analyzed)"/> 76 <valid initial="string.printable">
37 <expand macro="advanced_options"> 77 <remove value="'"/>
38 <param name="param_ignore_proteins_per_peptide" type="boolean" truevalue="-ignore_proteins_per_peptide true" falsevalue="-ignore_proteins_per_peptide false" checked="false" optional="True" label="[Sequest only] Workaround to deal with .out files that contain e.g. &quot;+1&quot; in references column,#br#but do not list extra references in subsequent lines (try -debug 3 or 4)" help="(-ignore_proteins_per_peptide)"/> 78 <remove value="&quot;"/>
39 <param name="param_scan_regex" type="text" size="20" label="[mascotXML only] Regular expression used to extract the scan number or retention time. See documentation for details." help="(-scan_regex)"/> 79 </valid>
40 </expand> 80 </sanitizer>
41 </inputs> 81 </param>
42 <outputs> 82 <param checked="false" falsevalue="" help="(-use_precursor_data) " label="[pepXML only] Use precursor RTs (and m/z values) from 'mz_file' for the generated peptide identifications, instead of the RTs of MS2 spectra" name="param_use_precursor_data" optional="True" truevalue="-use_precursor_data" type="boolean"/>
43 <data name="param_out" label="Output file" format="pepXML"> 83 <param checked="false" falsevalue="" help="(-peptideprophet_analyzed) By default a 'raw' pepXML is produced that contains only search engine results" label="[pepXML output only] Write output in the format of a PeptideProphet analysis result" name="param_peptideprophet_analyzed" optional="True" truevalue="-peptideprophet_analyzed" type="boolean"/>
44 <change_format> 84 <param help="(-score_type) " label="[Percolator only] Which of the Percolator scores to report as 'the' score for a peptide hit" name="param_score_type" optional="True" type="select" value="qvalue">
45 <when input="param_out_type" value="idXML" format="idXML"/> 85 <option value="qvalue">qvalue</option>
46 </change_format> 86 <option value="PEP">PEP</option>
47 </data> 87 <option value="score">score</option>
48 </outputs> 88 </param>
49 <help>**What it does** 89 <expand macro="advanced_options">
50 90 <param checked="false" falsevalue="" help="(-ignore_proteins_per_peptide) e.g. &quot;+1&quot; in references column, &lt;br&gt;but do not list extra references in subsequent lines (try -debug 3 or 4)" label="[Sequest only] Workaround to deal with .out files that contain" name="param_ignore_proteins_per_peptide" optional="True" truevalue="-ignore_proteins_per_peptide" type="boolean"/>
51 Converts identification engine file formats. 91 <param help="(-scan_regex) See documentation for details" label="[Mascot, Percolator only] Regular expression used to extract the scan number or retention time" name="param_scan_regex" size="30" type="text">
92 <sanitizer>
93 <valid initial="string.printable">
94 <remove value="'"/>
95 <remove value="&quot;"/>
96 </valid>
97 </sanitizer>
98 </param>
99 <param checked="false" falsevalue="" help="(-count_from_zero) " label="[Percolator only] Scan numbers extracted by 'scan_regex' start counting at zero (default: start at one)" name="param_count_from_zero" optional="True" truevalue="-count_from_zero" type="boolean"/>
100 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
101 </expand>
102 </inputs>
103 <outputs>
104 <data format="xml" name="param_out"/>
105 </outputs>
106 <help>Converts identification engine file formats.
52 107
53 108
54 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDFileConverter.html 109 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDFileConverter.html</help>
55 110 </tool>
56 @REFERENCES@
57 </help>
58 </tool>