Mercurial > repos > galaxyp > openms_idmassaccuracy
comparison IDMassAccuracy.xml @ 11:65be0674bb70 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author | galaxyp |
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date | Wed, 09 Sep 2020 20:06:18 +0000 |
parents | 86f5365280dd |
children | 31bc4129f589 |
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10:fe66116dfd0b | 11:65be0674bb70 |
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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 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: [Utilities]--> | 3 <!--Proposed Tool Section: [Utilities]--> |
4 <tool id="IDMassAccuracy" name="IDMassAccuracy" version="2.3.0"> | 4 <tool id="IDMassAccuracy" name="IDMassAccuracy" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> |
5 <description>Calculates a distribution of the mass error from given mass spectra and IDs.</description> | 5 <description>Calculates a distribution of the mass error from given mass spectra and IDs.</description> |
6 <macros> | 6 <macros> |
7 <token name="@EXECUTABLE@">IDMassAccuracy</token> | 7 <token name="@EXECUTABLE@">IDMassAccuracy</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[IDMassAccuracy | 15 @EXT_FOO@ |
16 #import re | |
14 | 17 |
15 -in | 18 ## Preprocessing |
16 #for token in $param_in: | 19 mkdir in && |
17 $token | 20 ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) } |
18 #end for | 21 mkdir id_in && |
19 -id_in | 22 ${ ' '.join(["ln -s '%s' 'id_in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $id_in if _]) } |
20 #for token in $param_id_in: | 23 #if "out_precursor_FLAG" in str($OPTIONAL_OUTPUTS).split(',') |
21 $token | 24 mkdir out_precursor && |
22 #end for | 25 #end if |
23 #if $param_precursor_out: | 26 #if "out_fragment_FLAG" in str($OPTIONAL_OUTPUTS).split(',') |
24 -precursor_out $param_precursor_out | 27 mkdir out_fragment && |
28 #end if | |
29 #if "out_precursor_fit_FLAG" in str($OPTIONAL_OUTPUTS).split(',') | |
30 mkdir out_precursor_fit && | |
31 #end if | |
32 #if "out_fragment_fit_FLAG" in str($OPTIONAL_OUTPUTS).split(',') | |
33 mkdir out_fragment_fit && | |
25 #end if | 34 #end if |
26 | 35 |
27 #if $rep_param_precursor_columns: | 36 ## Main program call |
28 -precursor_columns | 37 |
29 #for token in $rep_param_precursor_columns: | 38 set -o pipefail && |
30 #if " " in str(token): | 39 @EXECUTABLE@ -write_ctd ./ && |
31 "$token.param_precursor_columns" | 40 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && |
32 #else | 41 @EXECUTABLE@ -ini @EXECUTABLE@.ctd |
33 $token.param_precursor_columns | 42 -in |
34 #end if | 43 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} |
35 #end for | 44 -id_in |
45 ${' '.join(["'id_in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $id_in if _])} | |
46 #if "out_precursor_FLAG" in str($OPTIONAL_OUTPUTS).split(',') | |
47 -out_precursor | |
48 'out_precursor/output.${gxy2omsext("tabular")}' | |
36 #end if | 49 #end if |
37 #if $param_precursor_error_ppm: | 50 #if "out_fragment_FLAG" in str($OPTIONAL_OUTPUTS).split(',') |
38 -precursor_error_ppm | 51 -out_fragment |
52 'out_fragment/output.${gxy2omsext("tabular")}' | |
39 #end if | 53 #end if |
40 #if $param_fragment_out: | 54 #if "out_precursor_fit_FLAG" in str($OPTIONAL_OUTPUTS).split(',') |
41 -fragment_out $param_fragment_out | 55 -out_precursor_fit |
56 'out_precursor_fit/output.${gxy2omsext("tabular")}' | |
57 #end if | |
58 #if "out_fragment_fit_FLAG" in str($OPTIONAL_OUTPUTS).split(',') | |
59 -out_fragment_fit | |
60 'out_fragment_fit/output.${gxy2omsext("tabular")}' | |
61 #end if | |
62 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 | |
63 | tee '$stdout' | |
42 #end if | 64 #end if |
43 | 65 |
44 #if $rep_param_fragment_columns: | 66 ## Postprocessing |
45 -fragment_columns | 67 #if "out_precursor_FLAG" in str($OPTIONAL_OUTPUTS).split(',') |
46 #for token in $rep_param_fragment_columns: | 68 && mv 'out_precursor/output.${gxy2omsext("tabular")}' '$out_precursor' |
47 #if " " in str(token): | |
48 "$token.param_fragment_columns" | |
49 #else | |
50 $token.param_fragment_columns | |
51 #end if | |
52 #end for | |
53 #end if | 69 #end if |
54 #if $param_fragment_error_ppm: | 70 #if "out_fragment_FLAG" in str($OPTIONAL_OUTPUTS).split(',') |
55 -fragment_error_ppm | 71 && mv 'out_fragment/output.${gxy2omsext("tabular")}' '$out_fragment' |
56 #end if | 72 #end if |
57 #if $param_fragment_mass_tolerance: | 73 #if "out_precursor_fit_FLAG" in str($OPTIONAL_OUTPUTS).split(',') |
58 -fragment_mass_tolerance $param_fragment_mass_tolerance | 74 && mv 'out_precursor_fit/output.${gxy2omsext("tabular")}' '$out_precursor_fit' |
59 #end if | 75 #end if |
60 #if $param_separator: | 76 #if "out_fragment_fit_FLAG" in str($OPTIONAL_OUTPUTS).split(',') |
61 -separator "$param_separator" | 77 && mv 'out_fragment_fit/output.${gxy2omsext("tabular")}' '$out_fragment_fit' |
62 #end if | 78 #end if |
63 #if $adv_opts.adv_opts_selector=='advanced': | 79 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS |
64 #if $adv_opts.param_number_of_bins: | 80 && mv '@EXECUTABLE@.ctd' '$ctd_out' |
65 -number_of_bins $adv_opts.param_number_of_bins | 81 #end if]]></command> |
66 #end if | 82 <configfiles> |
67 #if $adv_opts.param_generate_gnuplot_scripts: | 83 <inputs name="args_json" data_style="paths"/> |
68 -generate_gnuplot_scripts | 84 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
69 #end if | 85 </configfiles> |
70 #if $adv_opts.param_force: | |
71 -force | |
72 #end if | |
73 #end if | |
74 ]]></command> | |
75 <inputs> | 86 <inputs> |
76 <param name="param_in" type="data" format="mzml" multiple="true" optional="False" size="30" label="Input mzML file list, containing the spectra" help="(-in) "> | 87 <param name="in" argument="-in" type="data" format="mzml" multiple="true" optional="false" label="Input mzML file list, containing the spectra" help=" select mzml data sets(s)"/> |
77 <sanitizer> | 88 <param name="id_in" argument="-id_in" type="data" format="idxml" multiple="true" optional="false" label="Input idXML file list, containing the identifications" help=" select idxml data sets(s)"/> |
78 <valid initial="string.printable"> | 89 <param name="precursor_error_ppm" argument="-precursor_error_ppm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this flag is used, the precursor mass tolerances are estimated in ppm instead of Da" help=""/> |
79 <remove value="'"/> | 90 <param name="fragment_error_ppm" argument="-fragment_error_ppm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this flag is used, the fragment mass tolerances are estimated in ppm instead of Da" help=""/> |
80 <remove value="""/> | 91 <param name="fragment_mass_tolerance" argument="-fragment_mass_tolerance" type="float" optional="true" value="0.5" label="Maximal fragment mass tolerance which is allowed for MS/MS spectra, used for the calculation of matching ions" help=""/> |
81 </valid> | 92 <expand macro="adv_opts_macro"> |
82 </sanitizer> | 93 <param name="number_of_bins" argument="-number_of_bins" type="integer" optional="true" min="10" value="100" label="Number of bins that should be used to calculate the histograms for the fitting" help=""/> |
94 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> | |
95 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> | |
96 <expand macro="list_string_san"/> | |
97 </param> | |
98 </expand> | |
99 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="false"> | |
100 <option value="out_precursor_FLAG">out_precursor (Enables the test mode (needed for internal use only))</option> | |
101 <option value="out_fragment_FLAG">out_fragment (Enables the test mode (needed for internal use only))</option> | |
102 <option value="out_precursor_fit_FLAG">out_precursor_fit (Enables the test mode (needed for internal use only))</option> | |
103 <option value="out_fragment_fit_FLAG">out_fragment_fit (Enables the test mode (needed for internal use only))</option> | |
104 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> | |
83 </param> | 105 </param> |
84 <param name="param_id_in" type="data" format="idxml" multiple="true" optional="False" size="30" label="Input idXML file list, containing the identifications" help="(-id_in) "> | |
85 <sanitizer> | |
86 <valid initial="string.printable"> | |
87 <remove value="'"/> | |
88 <remove value="""/> | |
89 </valid> | |
90 </sanitizer> | |
91 </param> | |
92 <repeat name="rep_param_precursor_columns" min="0" max="1" title="param_precursor_columns"> | |
93 <param name="param_precursor_columns" display="radio" type="select" optional="True" value="MassDifference" label="Columns which will be written to the output file" help="(-precursor_columns) "> | |
94 <option value="MassDifference">MassDifference</option> | |
95 </param> | |
96 </repeat> | |
97 <param name="param_precursor_error_ppm" display="radio" type="boolean" truevalue="-precursor_error_ppm" falsevalue="" checked="false" optional="True" label="If this flag is used, the precursor mass tolerances are estimated in ppm instead of Da" help="(-precursor_error_ppm) "/> | |
98 <repeat name="rep_param_fragment_columns" min="0" max="1" title="param_fragment_columns"> | |
99 <param name="param_fragment_columns" display="radio" type="select" optional="True" value="MassDifference" label="Columns which will be written to the output file" help="(-fragment_columns) "> | |
100 <option value="MassDifference">MassDifference</option> | |
101 </param> | |
102 </repeat> | |
103 <param name="param_fragment_error_ppm" display="radio" type="boolean" truevalue="-fragment_error_ppm" falsevalue="" checked="false" optional="True" label="If this flag is used, the fragment mass tolerances are estimated in ppm instead of Da" help="(-fragment_error_ppm) "/> | |
104 <param name="param_fragment_mass_tolerance" type="float" value="0.5" label="Maximal fragment mass tolerance which is allowed for MS/MS spectra, used for the calculation of matching ions" help="(-fragment_mass_tolerance) "/> | |
105 <param name="param_separator" type="text" size="30" value=" " label="character which should be used to separate the columns in the output files" help="(-separator) "> | |
106 <sanitizer> | |
107 <valid initial="string.printable"> | |
108 <remove value="'"/> | |
109 <remove value="""/> | |
110 </valid> | |
111 </sanitizer> | |
112 </param> | |
113 <expand macro="advanced_options"> | |
114 <param name="param_number_of_bins" type="integer" min="10" optional="True" value="100" label="Number of bins that should be used to calculate the histograms for the fitting" help="(-number_of_bins) "/> | |
115 <param name="param_generate_gnuplot_scripts" display="radio" type="boolean" truevalue="-generate_gnuplot_scripts" falsevalue="" checked="false" optional="True" label="If this option is set to true, the distributions and the fits are used to generate a gnuplot script, that can be used to generate plots" help="(-generate_gnuplot_scripts) The options 'precursor_out' and 'fragment_out' must be set to take this effect"/> | |
116 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> | |
117 </expand> | |
118 </inputs> | 106 </inputs> |
119 <outputs> | 107 <outputs> |
120 <data name="param_precursor_out" format="tabular"/> | 108 <data name="out_precursor" label="${tool.name} on ${on_string}: out_precursor" format="tabular"> |
121 <data name="param_fragment_out" format="tabular"/> | 109 <filter>OPTIONAL_OUTPUTS is not None and "out_precursor_FLAG" in OPTIONAL_OUTPUTS</filter> |
110 </data> | |
111 <data name="out_fragment" label="${tool.name} on ${on_string}: out_fragment" format="tabular"> | |
112 <filter>OPTIONAL_OUTPUTS is not None and "out_fragment_FLAG" in OPTIONAL_OUTPUTS</filter> | |
113 </data> | |
114 <data name="out_precursor_fit" label="${tool.name} on ${on_string}: out_precursor_fit" format="tabular"> | |
115 <filter>OPTIONAL_OUTPUTS is not None and "out_precursor_fit_FLAG" in OPTIONAL_OUTPUTS</filter> | |
116 </data> | |
117 <data name="out_fragment_fit" label="${tool.name} on ${on_string}: out_fragment_fit" format="tabular"> | |
118 <filter>OPTIONAL_OUTPUTS is not None and "out_fragment_fit_FLAG" in OPTIONAL_OUTPUTS</filter> | |
119 </data> | |
120 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout"> | |
121 <filter>OPTIONAL_OUTPUTS is None</filter> | |
122 </data> | |
123 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | |
124 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | |
125 </data> | |
122 </outputs> | 126 </outputs> |
123 <help>Calculates a distribution of the mass error from given mass spectra and IDs. | 127 <tests> |
128 <expand macro="autotest_IDMassAccuracy"/> | |
129 <expand macro="manutest_IDMassAccuracy"/> | |
130 </tests> | |
131 <help><![CDATA[Calculates a distribution of the mass error from given mass spectra and IDs. | |
124 | 132 |
125 | 133 |
126 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_IDMassAccuracy.html</help> | 134 For more information, visit http://www.openms.de/documentation/UTILS_IDMassAccuracy.html]]></help> |
135 <expand macro="references"/> | |
127 </tool> | 136 </tool> |