Mercurial > repos > galaxyp > openms_openswathassaygenerator

comparison OpenSwathAssayGenerator.xml @ 9:5848492bfc5a 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 12:44:29 +0000
parents 63a26a130c5d
children a41cd777ced9
comparison
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8:8c01da82292c 9:5848492bfc5a
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="OpenSwathAssayGenerator" name="OpenSwathAssayGenerator" version="2.3.0"> 4 <tool id="OpenSwathAssayGenerator" name="OpenSwathAssayGenerator" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Generates assays according to different models for a specific TraML</description> 5 <description>Generates assays according to different models for a specific TraML</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">OpenSwathAssayGenerator</token> 7 <token name="@EXECUTABLE@">OpenSwathAssayGenerator</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[OpenSwathAssayGenerator 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 mkdir out &&
22 #if $swath_windows_file:
23 mkdir swath_windows_file &&
24 ln -s '$swath_windows_file' 'swath_windows_file/${re.sub("[^\w\-_]", "_", $swath_windows_file.element_identifier)}.$gxy2omsext($swath_windows_file.ext)' &&
17 #end if 25 #end if
18 #if $param_out: 26 #if $unimod_file:
19 -out $param_out 27 mkdir unimod_file &&
28 ln -s '$unimod_file' 'unimod_file/${re.sub("[^\w\-_]", "_", $unimod_file.element_identifier)}.$gxy2omsext($unimod_file.ext)' &&
20 #end if 29 #end if
21 #if $param_min_transitions: 30
22 -min_transitions $param_min_transitions 31 ## Main program call
32
33 set -o pipefail &&
34 @EXECUTABLE@ -write_ctd ./ &&
35 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
36 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
37 -in
38 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
39 -out
40 'out/output.${out_type}'
41 #if $swath_windows_file:
42 -swath_windows_file
43 'swath_windows_file/${re.sub("[^\w\-_]", "_", $swath_windows_file.element_identifier)}.$gxy2omsext($swath_windows_file.ext)'
23 #end if 44 #end if
24 #if $param_max_transitions: 45 #if $unimod_file:
25 -max_transitions $param_max_transitions 46 -unimod_file
47 'unimod_file/${re.sub("[^\w\-_]", "_", $unimod_file.element_identifier)}.$gxy2omsext($unimod_file.ext)'
26 #end if 48 #end if
27 #if $param_allowed_fragment_types: 49
28 -allowed_fragment_types "$param_allowed_fragment_types" 50 ## Postprocessing
29 #end if 51 && mv 'out/output.${out_type}' '$out'
30 #if $param_allowed_fragment_charges: 52 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
31 -allowed_fragment_charges "$param_allowed_fragment_charges" 53 && mv '@EXECUTABLE@.ctd' '$ctd_out'
32 #end if 54 #end if]]></command>
33 #if $param_enable_detection_specific_losses: 55 <configfiles>
34 -enable_detection_specific_losses 56 <inputs name="args_json" data_style="paths"/>
35 #end if 57 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
36 #if $param_enable_detection_unspecific_losses: 58 </configfiles>
37 -enable_detection_unspecific_losses
38 #end if
39 #if $param_enable_identification_specific_losses:
40 -enable_identification_specific_losses
41 #end if
42 #if $param_enable_identification_unspecific_losses:
43 -enable_identification_unspecific_losses
44 #end if
45 #if $param_enable_identification_ms2_precursors:
46 -enable_identification_ms2_precursors
47 #end if
48 #if $param_enable_ms1_uis_scoring:
49 -enable_ms1_uis_scoring
50 #end if
51 #if $param_enable_ms2_uis_scoring:
52 -enable_ms2_uis_scoring
53 #end if
54 #if $param_max_num_alternative_localizations:
55 -max_num_alternative_localizations $param_max_num_alternative_localizations
56 #end if
57 #if $param_enable_reannotation:
58 -enable_reannotation
59 #end if
60 #if $param_precursor_mz_threshold:
61 -precursor_mz_threshold $param_precursor_mz_threshold
62 #end if
63 #if $param_precursor_lower_mz_limit:
64 -precursor_lower_mz_limit $param_precursor_lower_mz_limit
65 #end if
66 #if $param_precursor_upper_mz_limit:
67 -precursor_upper_mz_limit $param_precursor_upper_mz_limit
68 #end if
69 #if $param_product_mz_threshold:
70 -product_mz_threshold $param_product_mz_threshold
71 #end if
72 #if $param_product_lower_mz_limit:
73 -product_lower_mz_limit $param_product_lower_mz_limit
74 #end if
75 #if $param_product_upper_mz_limit:
76 -product_upper_mz_limit $param_product_upper_mz_limit
77 #end if
78 #if $adv_opts.adv_opts_selector=='advanced':
79 #if $adv_opts.param_swath_windows_file:
80 -swath_windows_file $adv_opts.param_swath_windows_file
81 #end if
82 #if $adv_opts.param_force:
83 -force
84 #end if
85 #end if
86 ]]></command>
87 <inputs> 59 <inputs>
88 <param name="param_in" type="data" format="traml" optional="False" label="input file ('traML')" help="(-in) "/> 60 <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)"/>
89 <param name="param_min_transitions" type="integer" value="6" label="minimal number of transitions" help="(-min_transitions) "/> 61 <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="">
90 <param name="param_max_transitions" type="integer" value="6" label="maximal number of transitions" help="(-max_transitions) "/> 62 <option value="TraML">traml</option>
91 <param name="param_allowed_fragment_types" type="text" size="30" value="b,y" label="allowed fragment types" help="(-allowed_fragment_types) "> 63 <option value="pqp">pqp</option>
92 <sanitizer> 64 <option value="tsv">tabular (tsv)</option>
93 <valid initial="string.printable"> 65 <expand macro="list_string_san"/>
94 <remove value="'"/>
95 <remove value="&quot;"/>
96 </valid>
97 </sanitizer>
98 </param> 66 </param>
99 <param name="param_allowed_fragment_charges" type="text" size="30" value="1,2,3,4" label="allowed fragment charge states" help="(-allowed_fragment_charges) "> 67 <param name="min_transitions" argument="-min_transitions" type="integer" optional="true" value="6" label="minimal number of transitions" help=""/>
100 <sanitizer> 68 <param name="max_transitions" argument="-max_transitions" type="integer" optional="true" value="6" label="maximal number of transitions" help=""/>
101 <valid initial="string.printable"> 69 <param name="allowed_fragment_types" argument="-allowed_fragment_types" type="text" optional="true" value="b,y" label="allowed fragment types" help="">
102 <remove value="'"/> 70 <expand macro="list_string_san"/>
103 <remove value="&quot;"/>
104 </valid>
105 </sanitizer>
106 </param> 71 </param>
107 <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) "/> 72 <param name="allowed_fragment_charges" argument="-allowed_fragment_charges" type="text" optional="true" value="1,2,3,4" label="allowed fragment charge states" help="">
108 <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) "/> 73 <expand macro="list_string_san"/>
109 <param name="param_enable_identification_specific_losses" display="radio" type="boolean" truevalue="-enable_identification_specific_losses" falsevalue="" checked="false" optional="True" label="set this flag if specific neutral losses for identification fragment ions should be allowed" help="(-enable_identification_specific_losses) "/> 74 </param>
110 <param name="param_enable_identification_unspecific_losses" display="radio" type="boolean" truevalue="-enable_identification_unspecific_losses" falsevalue="" checked="false" optional="True" label="set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) for identification fragment ions should be allowed" help="(-enable_identification_unspecific_losses) "/> 75 <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=""/>
111 <param name="param_enable_identification_ms2_precursors" display="radio" type="boolean" truevalue="-enable_identification_ms2_precursors" falsevalue="" checked="false" optional="True" label="set this flag if MS2-level precursor ions for identification should be allowed to enable extraction of the precursor signal from the fragment ion data (MS2-level)" help="(-enable_identification_ms2_precursors) This may help in identification if the MS1 signal is weak"/> 76 <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=""/>
112 <param name="param_enable_ms1_uis_scoring" display="radio" type="boolean" truevalue="-enable_ms1_uis_scoring" falsevalue="" checked="false" optional="True" label="set this flag if MS1-UIS assays for UIS scoring should be generated" help="(-enable_ms1_uis_scoring) "/> 77 <param name="precursor_mz_threshold" argument="-precursor_mz_threshold" type="float" optional="true" value="0.025" label="MZ threshold in Thomson for precursor ion selection" help=""/>
113 <param name="param_enable_ms2_uis_scoring" display="radio" type="boolean" truevalue="-enable_ms2_uis_scoring" falsevalue="" checked="false" optional="True" label="set this flag if MS2-UIS assays for UIS scoring should be generated" help="(-enable_ms2_uis_scoring) "/> 78 <param name="precursor_lower_mz_limit" argument="-precursor_lower_mz_limit" type="float" optional="true" value="400.0" label="lower MZ limit for precursor ions" help=""/>
114 <param name="param_max_num_alternative_localizations" type="integer" value="20" label="maximum number of site-localization permutations" help="(-max_num_alternative_localizations) "/> 79 <param name="precursor_upper_mz_limit" argument="-precursor_upper_mz_limit" type="float" optional="true" value="1200.0" label="upper MZ limit for precursor ions" help=""/>
115 <param name="param_enable_reannotation" display="radio" type="boolean" truevalue="-enable_reannotation" falsevalue="" checked="false" optional="True" label="set this flag if reannotation of fragment ions should be allowed" help="(-enable_reannotation) "/> 80 <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=""/>
116 <param name="param_precursor_mz_threshold" type="float" value="0.025" label="MZ threshold in Thomson for precursor ion selection" help="(-precursor_mz_threshold) "/> 81 <param name="product_lower_mz_limit" argument="-product_lower_mz_limit" type="float" optional="true" value="350.0" label="lower MZ limit for fragment ions" help=""/>
117 <param name="param_precursor_lower_mz_limit" type="float" value="400.0" label="lower MZ limit for precursor ions" help="(-precursor_lower_mz_limit) "/> 82 <param name="product_upper_mz_limit" argument="-product_upper_mz_limit" type="float" optional="true" value="2000.0" label="upper MZ limit for fragment ions" help=""/>
118 <param name="param_precursor_upper_mz_limit" type="float" value="1200.0" label="upper MZ limit for precursor ions" help="(-precursor_upper_mz_limit) "/> 83 <param name="swath_windows_file" argument="-swath_windows_file" type="data" format="txt" optional="true" label="Tab separated file containing the SWATH windows for exclusion of fragment ions falling into the precursor isolation window: lower_offset upper_offset \newline 400 425 \newline" help="Note that the first line is a header and will be skipped select txt data sets(s)"/>
119 <param name="param_product_mz_threshold" type="float" value="0.025" label="MZ threshold in Thomson for fragment ion annotation" help="(-product_mz_threshold) "/> 84 <param name="unimod_file" argument="-unimod_file" type="data" format="xml" optional="true" label="(Modified) Unimod XML file (http://www.unimod.org/xml/unimod.xml) describing residue modifiability" help=" select xml data sets(s)"/>
120 <param name="param_product_lower_mz_limit" type="float" value="350.0" label="lower MZ limit for fragment ions" help="(-product_lower_mz_limit) "/> 85 <param name="enable_ipf" argument="-enable_ipf" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if identification transitions should be generated for IPF" help="Note: Requires setting 'unimod_file'"/>
121 <param name="param_product_upper_mz_limit" type="float" value="2000.0" label="upper MZ limit for fragment ions" help="(-product_upper_mz_limit) "/> 86 <expand macro="adv_opts_macro">
122 <expand macro="advanced_options"> 87 <param name="max_num_alternative_localizations" argument="-max_num_alternative_localizations" type="integer" optional="true" value="10000" label="IPF: maximum number of site-localization permutations" help=""/>
123 <param name="param_swath_windows_file" type="data" format="txt" optional="True" label="Tab separated file containing the SWATH windows for exclusion of fragment ions falling into the precursor isolation window: lower_offset upper_offset \newline 400 425 \newline .." help="(-swath_windows_file) Note that the first line is a header and will be skipped"/> 88 <param name="disable_identification_ms2_precursors" argument="-disable_identification_ms2_precursors" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if MS2-level precursor ions for identification should not be allowed for extraction of the precursor signal from the fragment ion data (MS2-level)" help=""/>
124 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 89 <param name="disable_identification_specific_losses" argument="-disable_identification_specific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if specific neutral losses for identification fragment ions should not be allowed" help=""/>
90 <param name="enable_identification_unspecific_losses" argument="-enable_identification_unspecific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) for identification fragment ions should be allowed" help=""/>
91 <param name="enable_swath_specifity" argument="-enable_swath_specifity" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if identification transitions without precursor specificity" help="(i.e. across whole precursor isolation window instead of precursor MZ) should be generated"/>
92 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
93 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
94 <expand macro="list_string_san"/>
95 </param>
125 </expand> 96 </expand>
97 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
98 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
99 </param>
126 </inputs> 100 </inputs>
127 <outputs> 101 <outputs>
128 <data name="param_out" format="traml"/> 102 <data name="out" label="${tool.name} on ${on_string}: out">
103 <change_format>
104 <when input="out_type" value="TraML" format="traml"/>
105 <when input="out_type" value="pqp" format="pqp"/>
106 <when input="out_type" value="tsv" format="tabular"/>
107 </change_format>
108 </data>
109 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
110 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
111 </data>
129 </outputs> 112 </outputs>
130 <help>Generates assays according to different models for a specific TraML 113 <tests>
114 <expand macro="autotest_OpenSwathAssayGenerator"/>
115 <expand macro="manutest_OpenSwathAssayGenerator"/>
116 </tests>
117 <help><![CDATA[Generates assays according to different models for a specific TraML
131 118
132 119
133 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_OpenSwathAssayGenerator.html</help> 120 For more information, visit http://www.openms.de/documentation/TOPP_OpenSwathAssayGenerator.html]]></help>
121 <expand macro="references"/>
134 </tool> 122 </tool>