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comparison CruxAdapter.xml @ 0:a8dd6f1257ab 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 12:57:00 +0000
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children aed7aeb6feec
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-1:000000000000 0:a8dd6f1257ab
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.-->
3 <!--Proposed Tool Section: [Identification]-->
4 <tool id="CruxAdapter" name="CruxAdapter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Identifies MS/MS spectra using Crux.</description>
6 <macros>
7 <token name="@EXECUTABLE@">CruxAdapter</token>
8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
11 </macros>
12 <expand macro="requirements"/>
13 <expand macro="stdio"/>
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
15 @EXT_FOO@
16 #import re
17
18 ## Preprocessing
19 mkdir in &&
20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
21 mkdir out &&
22 mkdir database &&
23 ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
24
25 ## Main program call
26
27 set -o pipefail &&
28 @EXECUTABLE@ -write_ctd ./ &&
29 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
30 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
31 -in
32 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
33 -out
34 'out/output.${gxy2omsext("idxml")}'
35 -database
36 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)'
37
38 ## Postprocessing
39 && mv 'out/output.${gxy2omsext("idxml")}' '$out'
40 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
41 && mv '@EXECUTABLE@.ctd' '$ctd_out'
42 #end if]]></command>
43 <configfiles>
44 <inputs name="args_json" data_style="paths"/>
45 <configfile name="hardcoded_json"><![CDATA[{"crux_executable": "crux", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
46 </configfiles>
47 <inputs>
48 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="Input file" help=" select mzml data sets(s)"/>
49 <param name="database" argument="-database" type="data" format="fasta" optional="false" label="FASTA file" help=" select fasta data sets(s)"/>
50 <param name="extra_index_args" argument="-extra_index_args" type="text" optional="true" value="" label="Extra arguments to be passed to tide-index" help="">
51 <expand macro="list_string_san"/>
52 </param>
53 <param name="extra_search_args" argument="-extra_search_args" type="text" optional="true" value="" label="Extra arguments to be passed to tide-search" help="">
54 <expand macro="list_string_san"/>
55 </param>
56 <param name="extra_percolator_args" argument="-extra_percolator_args" type="text" optional="true" value="" label="Extra arguments to be passed to percolato" help="">
57 <expand macro="list_string_san"/>
58 </param>
59 <param name="precursor_mass_tolerance" argument="-precursor_mass_tolerance" type="float" optional="true" value="10.0" label="Precursor monoisotopic mass tolerance (Crux parameter: peptide_mass_tolerance)" help=""/>
60 <param name="precursor_mass_units" argument="-precursor_mass_units" display="radio" type="select" optional="false" label="Unit of precursor mass tolerance (amu, m/z or ppm)" help="">
61 <option value="mass">mass</option>
62 <option value="mz">mz</option>
63 <option value="ppm" selected="true">ppm</option>
64 <expand macro="list_string_san"/>
65 </param>
66 <param name="fragment_bin_offset" argument="-fragment_bin_offset" type="float" optional="true" value="0.0" label="In the discretization of the m/z axes of the observed and theoretical spectra, this parameter specifies the location of the left edge of the first bin, relative to mass = 0" help="(i.e., mz-bin-offset = 0.xx means the left edge of the first bin will be located at +0.xx Da)"/>
67 <param name="fragment_bin_width" argument="-fragment_bin_width" type="float" optional="true" value="0.02" label="Before calculation of the XCorr score, the m/z axes of the observed and theoretical spectra are discretized" help="This parameter specifies the size of each bin. The exact formula for computing the discretized m/z value is floor((x/mz-bin-width) + 1.0 - mz-bin-offset), where x is the observed m/z value. For low resolution ion trap ms/ms data 1.0005079 and for high resolution ms/ms 0.02 is recommended"/>
68 <param name="isotope_error" argument="-isotope_error" type="text" optional="true" value="" label="List of positive, non-zero integers" help="">
69 <expand macro="list_string_san"/>
70 </param>
71 <param name="run_percolator" argument="-run_percolator" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Whether to run percolator after tide-search" help=""/>
72 <param name="enzyme" argument="-enzyme" type="select" optional="false" label="The enzyme used for peptide digestion" help="">
73 <option value="custom-enzyme">custom-enzyme</option>
74 <option value="glu-c">glu-c</option>
75 <option value="pepsin-a">pepsin-a</option>
76 <option value="cyanogen-bromide">cyanogen-bromide</option>
77 <option value="clostripain">clostripain</option>
78 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
79 <option value="arg-c">arg-c</option>
80 <option value="asp-n">asp-n</option>
81 <option value="no-enzyme">no-enzyme</option>
82 <option value="iodosobenzoate">iodosobenzoate</option>
83 <option value="staph-protease">staph-protease</option>
84 <option value="proline-endopeptidase">proline-endopeptidase</option>
85 <option value="elastase">elastase</option>
86 <option value="chymotrypsin">chymotrypsin</option>
87 <option value="lys-c">lys-c</option>
88 <option value="lys-n">lys-n</option>
89 <option value="trypsin/p">trypsin/p</option>
90 <option value="trypsin" selected="true">trypsin</option>
91 <expand macro="list_string_san"/>
92 </param>
93 <param name="digestion" argument="-digestion" display="radio" type="select" optional="false" label="Full, partial or non specific digestion" help="">
94 <option value="full-digest" selected="true">full-digest</option>
95 <option value="partial-digest">partial-digest</option>
96 <option value="non-specific-digest">non-specific-digest</option>
97 <expand macro="list_string_san"/>
98 </param>
99 <param name="allowed_missed_cleavages" argument="-allowed_missed_cleavages" type="integer" optional="true" value="0" label="Number of possible cleavage sites missed by the enzyme, maximum value is 5; for enzyme search" help=""/>
100 <param name="decoy_format" argument="-decoy-format" display="radio" type="select" optional="false" label="Decoy generation method either by reversing the sequence or shuffling it" help="">
101 <option value="none">none</option>
102 <option value="shuffle" selected="true">shuffle</option>
103 <option value="peptide-reverse">peptide-reverse</option>
104 <option value="protein-reverse">protein-reverse</option>
105 <expand macro="list_string_san"/>
106 </param>
107 <param name="keep_terminal_aminos" argument="-keep-terminal-aminos" display="radio" type="select" optional="false" label="Whether to keep N and C terminal in place or also shuffled / reversed" help="">
108 <option value="N">N</option>
109 <option value="C">C</option>
110 <option value="NC" selected="true">NC</option>
111 <option value="none">none</option>
112 <expand macro="list_string_san"/>
113 </param>
114 <param name="cterm_modifications" argument="-cterm_modifications" type="text" optional="true" value="" label="Specifies C-terminal static and variable mass modifications on peptides" help="Specify a comma-separated list of C-terminal modification sequences of the form: X+21.9819 Default = &lt;empty&gt;">
115 <expand macro="list_string_san"/>
116 </param>
117 <param name="nterm_modifications" argument="-nterm_modifications" type="text" optional="true" value="" label="Specifies N-terminal static and variable mass modifications on peptides" help="Specify a comma-separated list of N-terminal modification sequences of the form: 1E-18.0106,C-17.0265 Default = &lt;empty&gt;">
118 <expand macro="list_string_san"/>
119 </param>
120 <param name="modifications" argument="-modifications" type="text" optional="true" value="" label="Expression for static and variable mass modifications to include" help="Specify a comma-separated list of modification sequences of the form: C+57.02146,2M+15.9949,1STY+79.966331,... Default = C+57.02146">
121 <expand macro="list_string_san"/>
122 </param>
123 <param name="test_fdr" argument="-test_fdr" type="float" optional="true" value="0.01" label="False discovery rate threshold used in selecting hyperparameters during internal cross-validation and for reporting the final results" help=""/>
124 <param name="train_fdr" argument="-train_fdr" type="float" optional="true" value="0.01" label="False discovery rate threshold to define positive examples in training" help=""/>
125 <expand macro="adv_opts_macro">
126 <param name="custom_enzyme" argument="-custom_enzyme" type="text" optional="true" value="" label="Specify rules for in silico digestion of protein sequences" help="Overrides the enzyme option. Two lists of residues are given enclosed in square brackets or curly braces and separated by a |. The first list contains residues required/prohibited before the cleavage site and the second list is residues after the cleavage site. ">
127 <expand macro="list_string_san"/>
128 </param>
129 <param name="decoy_prefix" argument="-decoy_prefix" type="text" optional="true" value="decoy_" label="Specifies the prefix of the protein names that indicate a decoy" help="">
130 <expand macro="list_string_san"/>
131 </param>
132 <param name="deisotope" argument="-deisotope" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Deisotope spectra before searching" help=""/>
133 <param name="report_decoys" argument="-report_decoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Include decoys in the final reported dataset" help=""/>
134 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
135 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
136 <expand macro="list_string_san"/>
137 </param>
138 </expand>
139 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
140 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
141 </param>
142 </inputs>
143 <outputs>
144 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
145 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
146 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
147 </data>
148 </outputs>
149 <tests>
150 <expand macro="autotest_CruxAdapter"/>
151 <expand macro="manutest_CruxAdapter"/>
152 </tests>
153 <help><![CDATA[Identifies MS/MS spectra using Crux.
154
155
156 For more information, visit http://www.openms.de/documentation/TOPP_CruxAdapter.html]]></help>
157 <expand macro="references"/>
158 </tool>