Mercurial > repos > galaxyp > openms_textexporter
comparison TextExporter.xml @ 9:27aeff17fd2e draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author | galaxyp |
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date | Thu, 27 Aug 2020 19:45:29 -0400 |
parents | 3a2a31d4032c |
children | 1c596fdaf34a |
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8:1294873c8d1d | 9:27aeff17fd2e |
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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: [File Handling]--> | 3 <!--Proposed Tool Section: [File Handling]--> |
4 <tool id="TextExporter" name="TextExporter" version="2.3.0"> | 4 <tool id="TextExporter" name="TextExporter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> |
5 <description>Exports various XML formats to a text file.</description> | 5 <description>Exports various XML formats to a text file.</description> |
6 <macros> | 6 <macros> |
7 <token name="@EXECUTABLE@">TextExporter</token> | 7 <token name="@EXECUTABLE@">TextExporter</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[TextExporter | 15 @EXT_FOO@ |
16 #import re | |
14 | 17 |
15 #if $param_in: | 18 ## Preprocessing |
16 -in $param_in | 19 mkdir in && |
20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && | |
21 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') | |
22 mkdir out && | |
17 #end if | 23 #end if |
18 #if $param_out: | 24 #if "centroids_FLAG" in str($OPTIONAL_OUTPUTS).split(',') |
19 -out $param_out | 25 mkdir consensus_centroids && |
20 #end if | 26 #end if |
21 #if $param_separator: | 27 #if "elements_FLAG" in str($OPTIONAL_OUTPUTS).split(',') |
22 -separator "$param_separator" | 28 mkdir consensus_elements && |
23 #end if | 29 #end if |
24 #if $param_replacement: | 30 #if "features_FLAG" in str($OPTIONAL_OUTPUTS).split(',') |
25 -replacement "$param_replacement" | 31 mkdir consensus_features && |
26 #end if | 32 #end if |
27 #if $param_quoting: | 33 |
28 -quoting | 34 ## Main program call |
29 #if " " in str($param_quoting): | 35 |
30 "$param_quoting" | 36 set -o pipefail && |
31 #else | 37 @EXECUTABLE@ -write_ctd ./ && |
32 $param_quoting | 38 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && |
33 #end if | 39 @EXECUTABLE@ -ini @EXECUTABLE@.ctd |
40 -in | |
41 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' | |
42 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') | |
43 -out | |
44 'out/output.${gxy2omsext("csv")}' | |
34 #end if | 45 #end if |
35 #if $param_no_ids: | 46 #if "centroids_FLAG" in str($OPTIONAL_OUTPUTS).split(',') |
36 -no_ids | 47 -consensus:centroids |
48 'consensus_centroids/output.${gxy2omsext("csv")}' | |
37 #end if | 49 #end if |
38 #if $param_feature_minimal: | 50 #if "elements_FLAG" in str($OPTIONAL_OUTPUTS).split(',') |
39 -feature:minimal | 51 -consensus:elements |
52 'consensus_elements/output.${gxy2omsext("csv")}' | |
40 #end if | 53 #end if |
41 #if $param_feature_add_metavalues: | 54 #if "features_FLAG" in str($OPTIONAL_OUTPUTS).split(',') |
42 -feature:add_metavalues $param_feature_add_metavalues | 55 -consensus:features |
56 'consensus_features/output.${gxy2omsext("csv")}' | |
43 #end if | 57 #end if |
44 #if $param_id_proteins_only: | 58 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 |
45 -id:proteins_only | 59 | tee '$stdout' |
46 #end if | 60 #end if |
47 #if $param_id_peptides_only: | 61 |
48 -id:peptides_only | 62 ## Postprocessing |
63 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') | |
64 && mv 'out/output.${gxy2omsext("csv")}' '$out' | |
49 #end if | 65 #end if |
50 #if $param_id_first_dim_rt: | 66 #if "centroids_FLAG" in str($OPTIONAL_OUTPUTS).split(',') |
51 -id:first_dim_rt | 67 && mv 'consensus_centroids/output.${gxy2omsext("csv")}' '$consensus_centroids' |
52 #end if | 68 #end if |
53 #if $param_id_add_metavalues: | 69 #if "elements_FLAG" in str($OPTIONAL_OUTPUTS).split(',') |
54 -id:add_metavalues $param_id_add_metavalues | 70 && mv 'consensus_elements/output.${gxy2omsext("csv")}' '$consensus_elements' |
55 #end if | 71 #end if |
56 #if $param_id_add_hit_metavalues: | 72 #if "features_FLAG" in str($OPTIONAL_OUTPUTS).split(',') |
57 -id:add_hit_metavalues $param_id_add_hit_metavalues | 73 && mv 'consensus_features/output.${gxy2omsext("csv")}' '$consensus_features' |
58 #end if | 74 #end if |
59 #if $param_consensus_centroids: | 75 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS |
60 -consensus:centroids $param_consensus_centroids | 76 && mv '@EXECUTABLE@.ctd' '$ctd_out' |
61 #end if | 77 #end if]]></command> |
62 #if $param_consensus_elements: | 78 <configfiles> |
63 -consensus:elements $param_consensus_elements | 79 <inputs name="args_json" data_style="paths"/> |
64 #end if | 80 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
65 #if $param_consensus_features: | 81 </configfiles> |
66 -consensus:features $param_consensus_features | |
67 #end if | |
68 #if $param_consensus_sorting_method: | |
69 -consensus:sorting_method | |
70 #if " " in str($param_consensus_sorting_method): | |
71 "$param_consensus_sorting_method" | |
72 #else | |
73 $param_consensus_sorting_method | |
74 #end if | |
75 #end if | |
76 #if $param_consensus_sort_by_maps: | |
77 -consensus:sort_by_maps | |
78 #end if | |
79 #if $param_consensus_sort_by_size: | |
80 -consensus:sort_by_size | |
81 #end if | |
82 #if $adv_opts.adv_opts_selector=='advanced': | |
83 #if $adv_opts.param_force: | |
84 -force | |
85 #end if | |
86 #end if | |
87 ]]></command> | |
88 <inputs> | 82 <inputs> |
89 <param name="param_in" type="data" format="featurexml,consensusxml,idxml,mzml" optional="False" label="Input file" help="(-in) "/> | 83 <param name="in" argument="-in" type="data" format="consensusxml,featurexml,idxml,mzml" optional="false" label="Input file" help=" select consensusxml,featurexml,idxml,mzml data sets(s)"/> |
90 <param name="param_separator" type="text" size="30" label="The used separator character(s); if not set the 'tab' character is used" help="(-separator) "> | 84 <param name="separator" argument="-separator" type="text" optional="true" value="" label="The used separator character(s); if not set the 'tab' character is used" help=""> |
91 <sanitizer> | 85 <expand macro="list_string_san"/> |
92 <valid initial="string.printable"> | |
93 <remove value="'"/> | |
94 <remove value="""/> | |
95 </valid> | |
96 </sanitizer> | |
97 </param> | 86 </param> |
98 <param name="param_replacement" type="text" size="30" value="_" label="Used to replace occurrences of the separator in strings before writing, if 'quoting' is 'none'" help="(-replacement) "> | 87 <param name="replacement" argument="-replacement" type="text" optional="true" value="_" label="Used to replace occurrences of the separator in strings before writing, if 'quoting' is 'none'" help=""> |
99 <sanitizer> | 88 <expand macro="list_string_san"/> |
100 <valid initial="string.printable"> | |
101 <remove value="'"/> | |
102 <remove value="""/> | |
103 </valid> | |
104 </sanitizer> | |
105 </param> | 89 </param> |
106 <param name="param_quoting" display="radio" type="select" optional="False" value="none" label="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes, <br>'escape' for quoting with backslash-escaping of embedded quotes" help="(-quoting) "> | 90 <param name="quoting" argument="-quoting" display="radio" type="select" optional="false" label="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes" help="'escape' for quoting with backslash-escaping of embedded quotes"> |
107 <option value="none" selected="true">none</option> | 91 <option value="none" selected="true">none</option> |
108 <option value="double">double</option> | 92 <option value="double">double</option> |
109 <option value="escape">escape</option> | 93 <option value="escape">escape</option> |
94 <expand macro="list_string_san"/> | |
110 </param> | 95 </param> |
111 <param name="param_no_ids" display="radio" type="boolean" truevalue="-no_ids" falsevalue="" checked="false" optional="True" label="Suppresses output of identification data" help="(-no_ids) "/> | 96 <param name="no_ids" argument="-no_ids" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Suppresses output of identification data" help=""/> |
112 <param name="param_feature_minimal" display="radio" type="boolean" truevalue="-feature:minimal" falsevalue="" checked="false" optional="True" label="Set this flag to write only three attributes: RT, m/z, and intensity" help="(-minimal) "/> | 97 <section name="feature" title="Options for featureXML input files" help="" expanded="false"> |
113 <param name="param_feature_add_metavalues" type="integer" min="-1" max="100" optional="True" value="-1" label="Add columns for meta values which occur with a certain frequency (0-100%)" help="(-add_metavalues) Set to -1 to omit meta values (default)"/> | 98 <param name="minimal" argument="-feature:minimal" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag to write only three attributes: RT, m/z, and intensity" help=""/> |
114 <param name="param_id_proteins_only" display="radio" type="boolean" truevalue="-id:proteins_only" falsevalue="" checked="false" optional="True" label="Set this flag if you want only protein information from an idXML file" help="(-proteins_only) "/> | 99 <param name="add_metavalues" argument="-feature:add_metavalues" type="integer" optional="true" min="-1" max="100" value="-1" label="Add columns for meta values which occur with a certain frequency (0-100%)" help="Set to -1 to omit meta values (default)"/> |
115 <param name="param_id_peptides_only" display="radio" type="boolean" truevalue="-id:peptides_only" falsevalue="" checked="false" optional="True" label="Set this flag if you want only peptide information from an idXML file" help="(-peptides_only) "/> | 100 </section> |
116 <param name="param_id_first_dim_rt" display="radio" type="boolean" truevalue="-id:first_dim_rt" falsevalue="" checked="false" optional="True" label="If this flag is set the first_dim RT of the peptide hits will also be printed (if present)" help="(-first_dim_rt) "/> | 101 <section name="id" title="Options for idXML input files" help="" expanded="false"> |
117 <param name="param_id_add_metavalues" type="integer" min="-1" max="100" optional="True" value="-1" label="Add columns for meta values which occur with a certain frequency (0-100%)" help="(-add_metavalues) Set to -1 to omit meta values (default)"/> | 102 <param name="proteins_only" argument="-id:proteins_only" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag if you want only protein information from an idXML file" help=""/> |
118 <param name="param_id_add_hit_metavalues" type="integer" min="-1" max="100" optional="True" value="-1" label="Add columns for meta values which occur with a certain frequency (0-100%)" help="(-add_hit_metavalues) Set to -1 to omit meta values (default)"/> | 103 <param name="peptides_only" argument="-id:peptides_only" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag if you want only peptide information from an idXML file" help=""/> |
119 <param name="param_consensus_sorting_method" type="select" optional="False" value="none" label="Sorting options can be combined" help="(-sorting_method) The precedence is: sort_by_size, sort_by_maps, sorting_method"> | 104 <param name="protein_groups" argument="-id:protein_groups" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag if you want to also write indist" help="group information from an idXML file"/> |
120 <option value="none" selected="true">none</option> | 105 <param name="first_dim_rt" argument="-id:first_dim_rt" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this flag is set the first_dim RT of the peptide hits will also be printed (if present)" help=""/> |
121 <option value="RT">RT</option> | 106 <param name="add_metavalues" argument="-id:add_metavalues" type="integer" optional="true" min="-1" max="100" value="-1" label="Add columns for meta values of PeptideID (=spectrum) entries which occur with a certain frequency (0-100%)" help="Set to -1 to omit meta values (default)"/> |
122 <option value="MZ">MZ</option> | 107 <param name="add_hit_metavalues" argument="-id:add_hit_metavalues" type="integer" optional="true" min="-1" max="100" value="-1" label="Add columns for meta values of PeptideHit (=PSM) entries which occur with a certain frequency (0-100%)" help="Set to -1 to omit meta values (default)"/> |
123 <option value="RT_then_MZ">RT_then_MZ</option> | 108 <param name="add_protein_hit_metavalues" argument="-id:add_protein_hit_metavalues" type="integer" optional="true" min="-1" max="100" value="-1" label="Add columns for meta values on protein level which occur with a certain frequency (0-100%)" help="Set to -1 to omit meta values (default)"/> |
124 <option value="intensity">intensity</option> | 109 </section> |
125 <option value="quality_decreasing">quality_decreasing</option> | 110 <section name="consensus" title="Options for consensusXML input files" help="" expanded="false"> |
126 <option value="quality_increasing">quality_increasing</option> | 111 <param name="sorting_method" argument="-consensus:sorting_method" type="select" optional="false" label="Sorting options can be combined" help="The precedence is: sort_by_size, sort_by_maps, sorting_method"> |
112 <option value="none" selected="true">none</option> | |
113 <option value="RT">RT</option> | |
114 <option value="MZ">MZ</option> | |
115 <option value="RT_then_MZ">RT_then_MZ</option> | |
116 <option value="intensity">intensity</option> | |
117 <option value="quality_decreasing">quality_decreasing</option> | |
118 <option value="quality_increasing">quality_increasing</option> | |
119 <expand macro="list_string_san"/> | |
120 </param> | |
121 <param name="sort_by_maps" argument="-consensus:sort_by_maps" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply a stable sort by the covered maps, lexicographically" help=""/> | |
122 <param name="sort_by_size" argument="-consensus:sort_by_size" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply a stable sort by decreasing size" help="(i.e., the number of elements)"/> | |
123 </section> | |
124 <expand macro="adv_opts_macro"> | |
125 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> | |
126 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> | |
127 <expand macro="list_string_san"/> | |
128 </param> | |
129 </expand> | |
130 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="false"> | |
131 <option value="out_FLAG">out (Apply a stable sort by decreasing size)</option> | |
132 <option value="centroids_FLAG">centroids (Apply a stable sort by decreasing size)</option> | |
133 <option value="elements_FLAG">elements (Apply a stable sort by decreasing size)</option> | |
134 <option value="features_FLAG">features (Apply a stable sort by decreasing size)</option> | |
135 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> | |
127 </param> | 136 </param> |
128 <param name="param_consensus_sort_by_maps" display="radio" type="boolean" truevalue="-consensus:sort_by_maps" falsevalue="" checked="false" optional="True" label="Apply a stable sort by the covered maps, lexicographically" help="(-sort_by_maps) "/> | |
129 <param name="param_consensus_sort_by_size" display="radio" type="boolean" truevalue="-consensus:sort_by_size" falsevalue="" checked="false" optional="True" label="Apply a stable sort by decreasing size (i.e., the number of elements)" help="(-sort_by_size) "/> | |
130 <expand macro="advanced_options"> | |
131 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> | |
132 </expand> | |
133 </inputs> | 137 </inputs> |
134 <outputs> | 138 <outputs> |
135 <data name="param_out" format="tabular"/> | 139 <data name="out" label="${tool.name} on ${on_string}: out" format="csv"> |
136 <data name="param_consensus_centroids" format="tabular"/> | 140 <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter> |
137 <data name="param_consensus_elements" format="tabular"/> | 141 </data> |
138 <data name="param_consensus_features" format="tabular"/> | 142 <data name="consensus_centroids" label="${tool.name} on ${on_string}: consensus:centroids" format="csv"> |
143 <filter>OPTIONAL_OUTPUTS is not None and "centroids_FLAG" in OPTIONAL_OUTPUTS</filter> | |
144 </data> | |
145 <data name="consensus_elements" label="${tool.name} on ${on_string}: consensus:elements" format="csv"> | |
146 <filter>OPTIONAL_OUTPUTS is not None and "elements_FLAG" in OPTIONAL_OUTPUTS</filter> | |
147 </data> | |
148 <data name="consensus_features" label="${tool.name} on ${on_string}: consensus:features" format="csv"> | |
149 <filter>OPTIONAL_OUTPUTS is not None and "features_FLAG" in OPTIONAL_OUTPUTS</filter> | |
150 </data> | |
151 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout"> | |
152 <filter>OPTIONAL_OUTPUTS is None</filter> | |
153 </data> | |
154 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | |
155 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | |
156 </data> | |
139 </outputs> | 157 </outputs> |
140 <help>Exports various XML formats to a text file. | 158 <tests> |
159 <expand macro="autotest_TextExporter"/> | |
160 <expand macro="manutest_TextExporter"/> | |
161 </tests> | |
162 <help><![CDATA[Exports various XML formats to a text file. | |
141 | 163 |
142 | 164 |
143 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_TextExporter.html</help> | 165 For more information, visit http://www.openms.de/documentation/TOPP_TextExporter.html]]></help> |
166 <expand macro="references"/> | |
144 </tool> | 167 </tool> |