Mercurial > repos > galaxyp > openms_idfileconverter

comparison IDFileConverter.xml @ 11:43a1db77b7a6 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author galaxyp
date Wed, 09 Sep 2020 12:55:15 +0000
parents 83cf7a4cd03c
children 250d6a43f66b
comparison
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10:3baeecbd6e0f 11:43a1db77b7a6
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 CTDConverter.--> 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="2.3.0"> 4 <tool id="IDFileConverter" name="IDFileConverter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
9 </macros> 11 </macros>
10 <expand macro="references"/> 12 <expand macro="requirements"/>
11 <expand macro="stdio"/> 13 <expand macro="stdio"/>
12 <expand macro="requirements"/> 14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
13 <command detect_errors="aggressive"><![CDATA[ 15 @EXT_FOO@
16 #import re
14 17
15 ## check input file type 18 ## Preprocessing
16 #set $in_type = $param_in.ext 19 mkdir in &&
20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
21 mkdir out &&
22 #if $mz_file:
23 mkdir mz_file &&
24 ln -s '$mz_file' 'mz_file/${re.sub("[^\w\-_]", "_", $mz_file.element_identifier)}.$gxy2omsext($mz_file.ext)' &&
25 #end if
17 26
18 ## create the symlinks to set the proper file extension, since IDFileConverter uses them to choose how to handle the input files 27 ## Main program call
19 ln -s '$param_in' 'param_in.${in_type}' &&
20 28
21 IDFileConverter 29 set -o pipefail &&
30 @EXECUTABLE@ -write_ctd ./ &&
31 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
32 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
33 -in
34 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
35 -out
36 'out/output.${out_type}'
37 #if $mz_file:
38 -mz_file
39 'mz_file/${re.sub("[^\w\-_]", "_", $mz_file.element_identifier)}.$gxy2omsext($mz_file.ext)'
40 #end if
22 41
23 #if $param_in: 42 ## Postprocessing
24 -in 'param_in.${in_type}' 43 && mv 'out/output.${out_type}' '$out'
25 #end if 44 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
26 #if $param_out: 45 && mv '@EXECUTABLE@.ctd' '$ctd_out'
27 -out $param_out 46 #end if]]></command>
28 #end if 47 <configfiles>
29 #if $param_out_type: 48 <inputs name="args_json" data_style="paths"/>
30 -out_type 49 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
31 #if " " in str($param_out_type): 50 </configfiles>
32 "$param_out_type"
33 #else
34 $param_out_type
35 #end if
36 #end if
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
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_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
66 #end if
67 #if $adv_opts.param_force:
68 -force
69 #end if
70 #end if
71 ]]>
72 </command>
73 <inputs> 51 <inputs>
74 <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;"/> 52 <param name="in" argument="-in" type="data" format="idxml,mascotxml,mzid,pepxml,protxml,psms,tabular,xml,xquest.xml" optional="false" label="Input file or directory containing the data to convert" help="This may be:. - a single file in a multi-purpose XML format (.pepXML, .protXML, .idXML, .mzid),. - a single file in a search engine-specific format (Mascot: .mascotXML, OMSSA: .omssaXML, X! Tandem: .xml, Percolator: .psms, xQuest: .xquest.xml),. - a single text file (tab separated) with one line for all peptide sequences matching a spectrum (top N hits),. - for Sequest results, a directory containing .out files.. select idxml,mascotxml,mzid,pepxml,protxml,psms,tabular,xml,xquest.xml data sets(s)"/>
75 <param name="param_out_type" display="radio" type="select" optional="True" label="Output file type (default: determined from file extension)" help="(-out_type) "> 53 <param name="out_type" argument="-out_type" type="select" optional="false" label="Output file type (default: determined from file extension)" help="">
76 <option value="idXML">idXML</option> 54 <option value="FASTA">fasta</option>
55 <option value="idXML">idxml</option>
77 <option value="mzid">mzid</option> 56 <option value="mzid">mzid</option>
78 <option value="pepXML">pepXML</option> 57 <option value="pepXML">pepxml</option>
79 <option value="FASTA">FASTA</option> 58 <option value="xquest.xml">xquest.xml</option>
59 <expand macro="list_string_san"/>
80 </param> 60 </param>
81 <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) "/> 61 <param name="mz_file" argument="-mz_file" type="data" format="mzdata,mzml,mzxml" optional="true" label="[pepXML, Sequest, Mascot, X" help="Tandem, mzid, Percolator only] Retention times and native spectrum ids (spectrum_references) will be looked up in this file select mzdata,mzml,mzxml data sets(s)"/>
82 <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'"> 62 <param name="mz_name" argument="-mz_name" type="text" optional="true" value="" label="[pepXML only] Experiment filename/path (extension will be removed) to match in the pepXML file ('base_name' attribute)" help="Only necessary if different from 'mz_file'">
83 <sanitizer> 63 <expand macro="list_string_san"/>
84 <valid initial="string.printable">
85 <remove value="'"/>
86 <remove value="&quot;"/>
87 </valid>
88 </sanitizer>
89 </param> 64 </param>
90 <param name="param_peptideprophet_analyzed" display="radio" type="boolean" truevalue="-peptideprophet_analyzed" falsevalue="" checked="false" optional="True" label="[pepXML output only] Write output in the format of a PeptideProphet analysis result" help="(-peptideprophet_analyzed) By default a 'raw' pepXML is produced that contains only search engine results"/> 65 <param name="peptideprophet_analyzed" argument="-peptideprophet_analyzed" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[pepXML output only] Write output in the format of a PeptideProphet analysis result" help="By default a 'raw' pepXML is produced that contains only search engine results"/>
91 <param name="param_score_type" display="radio" type="select" optional="False" value="qvalue" label="[Percolator only] Which of the Percolator scores to report as 'the' score for a peptide hit" help="(-score_type) "> 66 <param name="score_type" argument="-score_type" display="radio" type="select" optional="false" label="[Percolator only] Which of the Percolator scores to report as 'the' score for a peptide hit" help="">
92 <option value="qvalue" selected="true">qvalue</option> 67 <option value="qvalue" selected="true">qvalue</option>
93 <option value="PEP">PEP</option> 68 <option value="PEP">PEP</option>
94 <option value="score">score</option> 69 <option value="score">score</option>
70 <expand macro="list_string_san"/>
95 </param> 71 </param>
96 <expand macro="advanced_options"> 72 <expand macro="adv_opts_macro">
97 <param name="param_ignore_proteins_per_peptide" display="radio" type="boolean" truevalue="-ignore_proteins_per_peptide" falsevalue="" checked="false" optional="True" label="[Sequest only] Workaround to deal with .out files that contain" 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)"/> 73 <param name="ignore_proteins_per_peptide" argument="-ignore_proteins_per_peptide" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[Sequest only] Workaround to deal with .out files that contain" help="e.g. &quot;+1&quot; in references column,. but do not list extra references in subsequent lines (try -debug 3 or 4)"/>
98 <param name="param_scan_regex" type="text" size="30" label="[Mascot, pepXML, Percolator only] Regular expression used to extract the scan number or retention time" help="(-scan_regex) See documentation for details"> 74 <param name="scan_regex" argument="-scan_regex" type="text" optional="true" value="" label="[Mascot, pepXML, Percolator only] Regular expression used to extract the scan number or retention time" help="See documentation for details">
99 <sanitizer> 75 <expand macro="list_string_san"/>
100 <valid initial="string.printable">
101 <remove value="'"/>
102 <remove value="&quot;"/>
103 </valid>
104 </sanitizer>
105 </param> 76 </param>
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"/> 77 <param name="no_spectra_data_override" argument="-no_spectra_data_override" type="boolean" truevalue="true" falsevalue="false" checked="false" 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="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"/> 78 <param name="no_spectra_references_override" argument="-no_spectra_references_override" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[+mz_file only] Setting this flag will avoid overriding 'spectrum_reference' in PeptideIdentifications if mz_file is given and a 'spectrum_reference' is already present" help=""/>
108 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 79 <param name="add_ionmatch_annotation" argument="-add_ionmatch_annotation" type="float" optional="true" value="0.0" label="[+mz_file only] Will annotate the contained identifications with their matches in the given mz_file" help="Will take quite some while. Match tolerance is .4"/>
80 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
81 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
82 <expand macro="list_string_san"/>
83 </param>
109 </expand> 84 </expand>
85 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
86 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
87 </param>
110 </inputs> 88 </inputs>
111 <outputs> 89 <outputs>
112 <data name="param_out" auto_format="true"/> 90 <data name="out" label="${tool.name} on ${on_string}: out">
91 <change_format>
92 <when input="out_type" value="FASTA" format="fasta"/>
93 <when input="out_type" value="idXML" format="idxml"/>
94 <when input="out_type" value="mzid" format="mzid"/>
95 <when input="out_type" value="pepXML" format="pepxml"/>
96 <when input="out_type" value="xquest.xml" format="xquest.xml"/>
97 </change_format>
98 </data>
99 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
100 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
101 </data>
113 </outputs> 102 </outputs>
114 <help>Converts identification engine file formats. 103 <tests>
104 <expand macro="autotest_IDFileConverter"/>
105 <expand macro="manutest_IDFileConverter"/>
106 </tests>
107 <help><![CDATA[Converts identification engine file formats.
115 108
116 109
117 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_IDFileConverter.html</help> 110 For more information, visit http://www.openms.de/documentation/TOPP_IDFileConverter.html]]></help>
111 <expand macro="references"/>
118 </tool> 112 </tool>