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comparison OpenSwathDecoyGenerator.xml @ 9:1814187218fe 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 20:15:46 +0000
parents 5cc0f0e55785
children 3769d3a7e9ba
comparison
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8:9f505cd4428f 9:1814187218fe
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: [Targeted Experiments]--> 3 <!--Proposed Tool Section: [Targeted Experiments]-->
4 <tool id="OpenSwathDecoyGenerator" name="OpenSwathDecoyGenerator" version="2.3.0"> 4 <tool id="OpenSwathDecoyGenerator" name="OpenSwathDecoyGenerator" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Generates decoys according to different models for a specific TraML</description> 5 <description>Generates decoys according to different models for a specific TraML</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">OpenSwathDecoyGenerator</token> 7 <token name="@EXECUTABLE@">OpenSwathDecoyGenerator</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[OpenSwathDecoyGenerator 15 @EXT_FOO@
16 #import re
14 17
15 #if $param_in: 18 ## Preprocessing
16 -in $param_in 19 mkdir in &&
17 #end if 20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
18 #if $param_out: 21 mkdir out &&
19 -out $param_out 22
20 #end if 23 ## Main program call
21 #if $param_method: 24
22 -method "$param_method" 25 set -o pipefail &&
23 #end if 26 @EXECUTABLE@ -write_ctd ./ &&
24 #if $param_decoy_tag: 27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
25 -decoy_tag "$param_decoy_tag" 28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
26 #end if 29 -in
27 #if $param_mz_threshold: 30 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
28 -mz_threshold $param_mz_threshold 31 -out
29 #end if 32 'out/output.${out_type}'
30 #if $param_exclude_similar: 33
31 -exclude_similar 34 ## Postprocessing
32 #end if 35 && mv 'out/output.${out_type}' '$out'
33 #if $param_similarity_threshold: 36 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
34 -similarity_threshold $param_similarity_threshold 37 && mv '@EXECUTABLE@.ctd' '$ctd_out'
35 #end if 38 #end if]]></command>
36 #if $param_append: 39 <configfiles>
37 -append 40 <inputs name="args_json" data_style="paths"/>
38 #end if 41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
39 #if $param_remove_CNterm_mods: 42 </configfiles>
40 -remove_CNterm_mods
41 #end if
42 #if $param_remove_unannotated:
43 -remove_unannotated
44 #end if
45 #if $param_identity_threshold:
46 -identity_threshold $param_identity_threshold
47 #end if
48 #if $param_max_attempts:
49 -max_attempts $param_max_attempts
50 #end if
51 #if $param_mz_shift:
52 -mz_shift $param_mz_shift
53 #end if
54 #if $param_precursor_mass_shift:
55 -precursor_mass_shift $param_precursor_mass_shift
56 #end if
57 #if $param_allowed_fragment_types:
58 -allowed_fragment_types "$param_allowed_fragment_types"
59 #end if
60 #if $param_allowed_fragment_charges:
61 -allowed_fragment_charges "$param_allowed_fragment_charges"
62 #end if
63 #if $param_enable_detection_specific_losses:
64 -enable_detection_specific_losses
65 #end if
66 #if $param_enable_detection_unspecific_losses:
67 -enable_detection_unspecific_losses
68 #end if
69 #if $adv_opts.adv_opts_selector=='advanced':
70 #if $adv_opts.param_force:
71 -force
72 #end if
73 #end if
74 ]]></command>
75 <inputs> 43 <inputs>
76 <param name="param_in" type="data" format="traml" optional="False" label="input file ('traML')" help="(-in) "/> 44 <param name="in" argument="-in" type="data" format="mrm,pqp,tabular,traml" optional="false" label="Input file" help=" select mrm,pqp,tabular,traml data sets(s)"/>
77 <param name="param_method" type="text" size="30" value="shuffle" label="decoy generation method ('shuffle','pseudo-reverse','reverse','shift')" help="(-method) "> 45 <param name="out_type" argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="">
78 <sanitizer> 46 <option value="TraML">traml</option>
79 <valid initial="string.printable"> 47 <option value="pqp">pqp</option>
80 <remove value="'"/> 48 <option value="tsv">tabular (tsv)</option>
81 <remove value="&quot;"/> 49 <expand macro="list_string_san"/>
82 </valid>
83 </sanitizer>
84 </param> 50 </param>
85 <param name="param_decoy_tag" type="text" size="30" value="DECOY_" label="decoy tag" help="(-decoy_tag) "> 51 <param name="method" argument="-method" display="radio" type="select" optional="false" label="decoy generation method ('shuffle','pseudo-reverse','reverse','shift')" help="">
86 <sanitizer> 52 <option value="shuffle" selected="true">shuffle</option>
87 <valid initial="string.printable"> 53 <option value="pseudo-reverse">pseudo-reverse</option>
88 <remove value="'"/> 54 <option value="reverse">reverse</option>
89 <remove value="&quot;"/> 55 <option value="shift">shift</option>
90 </valid> 56 <expand macro="list_string_san"/>
91 </sanitizer>
92 </param> 57 </param>
93 <param name="param_mz_threshold" type="float" value="0.05" label="MZ threshold in Thomson for fragment ion annotation" help="(-mz_threshold) "/> 58 <param name="decoy_tag" argument="-decoy_tag" type="text" optional="true" value="DECOY_" label="decoy tag" help="">
94 <param name="param_exclude_similar" display="radio" type="boolean" truevalue="-exclude_similar" falsevalue="" checked="false" optional="True" label="set this flag if decoy assays with similarity of the peptide sequence to the target assays higher than the identity_threshold should be excluded" help="(-exclude_similar) If similarity_threshold is over 0, decoy assays with an absolute difference of the decoy and target product mz smaller than similarity_threshold are further excluded"/> 59 <expand macro="list_string_san"/>
95 <param name="param_similarity_threshold" type="float" value="-1.0" label="Similarity threshold for absolute difference of the product mz of target and decoy assays for exclusion in Dalton" help="(-similarity_threshold) Suggested value: 0.05"/>
96 <param name="param_append" display="radio" type="boolean" truevalue="-append" falsevalue="" checked="false" optional="True" label="set this flag if non-decoy TraML should be appended to the output" help="(-append) "/>
97 <param name="param_remove_CNterm_mods" display="radio" type="boolean" truevalue="-remove_CNterm_mods" falsevalue="" checked="false" optional="True" label="set this flag to remove decoy peptides with C/N terminal modifications (may be necessary depending on the decoy generation method)" help="(-remove_CNterm_mods) "/>
98 <param name="param_remove_unannotated" display="radio" type="boolean" truevalue="-remove_unannotated" falsevalue="" checked="false" optional="True" label="set this flag if target assays with unannotated ions should be ignored from decoy generation" help="(-remove_unannotated) "/>
99 <param name="param_identity_threshold" type="float" value="0.7" label="shuffle: identity threshold for the shuffle algorithm" help="(-identity_threshold) "/>
100 <param name="param_max_attempts" type="integer" value="10" label="shuffle: maximum attempts to lower the sequence identity between target and decoy for the shuffle algorithm" help="(-max_attempts) "/>
101 <param name="param_mz_shift" type="float" value="20.0" label="shift: MZ shift in Thomson for shift decoy method" help="(-mz_shift) "/>
102 <param name="param_precursor_mass_shift" type="float" value="0.0" label="Mass shift to apply to the precursor ion" help="(-precursor_mass_shift) "/>
103 <param name="param_allowed_fragment_types" type="text" size="30" value="b,y" label="allowed fragment types" help="(-allowed_fragment_types) ">
104 <sanitizer>
105 <valid initial="string.printable">
106 <remove value="'"/>
107 <remove value="&quot;"/>
108 </valid>
109 </sanitizer>
110 </param> 60 </param>
111 <param name="param_allowed_fragment_charges" type="text" size="30" value="1,2,3,4" label="allowed fragment charge states" help="(-allowed_fragment_charges) "> 61 <param name="switchKR" argument="-switchKR" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Whether to switch terminal K and R (to achieve different precursor mass)" help=""/>
112 <sanitizer> 62 <expand macro="adv_opts_macro">
113 <valid initial="string.printable"> 63 <param name="min_decoy_fraction" argument="-min_decoy_fraction" type="float" optional="true" value="0.8" label="Minimum fraction of decoy / target peptides and proteins" help=""/>
114 <remove value="'"/> 64 <param name="aim_decoy_fraction" argument="-aim_decoy_fraction" type="float" optional="true" value="1.0" label="Number of decoys the algorithm should generate (if unequal to 1, the algorithm will randomly select N peptides for decoy generation)" help=""/>
115 <remove value="&quot;"/> 65 <param name="shuffle_max_attempts" argument="-shuffle_max_attempts" type="integer" optional="true" value="30" label="shuffle: maximum attempts to lower the amino acid sequence identity between target and decoy for the shuffle algorithm" help=""/>
116 </valid> 66 <param name="shuffle_sequence_identity_threshold" argument="-shuffle_sequence_identity_threshold" type="float" optional="true" value="0.5" label="shuffle: target-decoy amino acid sequence identity threshold for the shuffle algorithm" help=""/>
117 </sanitizer> 67 <param name="shift_precursor_mz_shift" argument="-shift_precursor_mz_shift" type="float" optional="true" value="0.0" label="shift: precursor ion MZ shift in Thomson for shift decoy method" help=""/>
68 <param name="shift_product_mz_shift" argument="-shift_product_mz_shift" type="float" optional="true" value="20.0" label="shift: fragment ion MZ shift in Thomson for shift decoy method" help=""/>
69 <param name="product_mz_threshold" argument="-product_mz_threshold" type="float" optional="true" value="0.025" label="MZ threshold in Thomson for fragment ion annotation" help=""/>
70 <param name="allowed_fragment_types" argument="-allowed_fragment_types" type="text" optional="true" value="b,y" label="allowed fragment types" help="">
71 <expand macro="list_string_san"/>
72 </param>
73 <param name="allowed_fragment_charges" argument="-allowed_fragment_charges" type="text" optional="true" value="1,2,3,4" label="allowed fragment charge states" help="">
74 <expand macro="list_string_san"/>
75 </param>
76 <param name="enable_detection_specific_losses" argument="-enable_detection_specific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag if specific neutral losses for detection fragment ions should be allowed" help=""/>
77 <param name="enable_detection_unspecific_losses" argument="-enable_detection_unspecific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) for detection fragment ions should be allowed" help=""/>
78 <param name="separate" argument="-separate" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag if decoys should not be appended to targets" help=""/>
79 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
80 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
81 <expand macro="list_string_san"/>
82 </param>
83 </expand>
84 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
85 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
118 </param> 86 </param>
119 <param name="param_enable_detection_specific_losses" display="radio" type="boolean" truevalue="-enable_detection_specific_losses" falsevalue="" checked="false" optional="True" label="set this flag if specific neutral losses for detection fragment ions should be allowed" help="(-enable_detection_specific_losses) "/>
120 <param name="param_enable_detection_unspecific_losses" display="radio" type="boolean" truevalue="-enable_detection_unspecific_losses" falsevalue="" checked="false" optional="True" label="set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) for detection fragment ions should be allowed" help="(-enable_detection_unspecific_losses) "/>
121 <expand macro="advanced_options">
122 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
123 </expand>
124 </inputs> 87 </inputs>
125 <outputs> 88 <outputs>
126 <data name="param_out" format="traml"/> 89 <data name="out" label="${tool.name} on ${on_string}: out">
90 <change_format>
91 <when input="out_type" value="TraML" format="traml"/>
92 <when input="out_type" value="pqp" format="pqp"/>
93 <when input="out_type" value="tsv" format="tabular"/>
94 </change_format>
95 </data>
96 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
97 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
98 </data>
127 </outputs> 99 </outputs>
128 <help>Generates decoys according to different models for a specific TraML 100 <tests>
101 <expand macro="autotest_OpenSwathDecoyGenerator"/>
102 <expand macro="manutest_OpenSwathDecoyGenerator"/>
103 </tests>
104 <help><![CDATA[Generates decoys according to different models for a specific TraML
129 105
130 106
131 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_OpenSwathDecoyGenerator.html</help> 107 For more information, visit http://www.openms.de/documentation/TOPP_OpenSwathDecoyGenerator.html]]></help>
108 <expand macro="references"/>
132 </tool> 109 </tool>