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comparison MultiplexResolver.xml @ 9:381448b2db6d 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 20:01:05 +0000
parents 8023d63040f6
children b3dcd2098472
comparison
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8:4e66c4e73909 9:381448b2db6d
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="MultiplexResolver" name="MultiplexResolver" version="2.3.0"> 4 <tool id="MultiplexResolver" name="MultiplexResolver" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Completes peptide multiplets and resolves conflicts within them.</description> 5 <description>Completes peptide multiplets and resolves conflicts within them.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">MultiplexResolver</token> 7 <token name="@EXECUTABLE@">MultiplexResolver</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[MultiplexResolver 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 $in_blacklist:
22 mkdir in_blacklist &&
23 ln -s '$in_blacklist' 'in_blacklist/${re.sub("[^\w\-_]", "_", $in_blacklist.element_identifier)}.$gxy2omsext($in_blacklist.ext)' &&
17 #end if 24 #end if
18 #if $param_out: 25 mkdir out &&
19 -out $param_out 26 #if "out_conflicts_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
27 mkdir out_conflicts &&
20 #end if 28 #end if
21 #if $param_out_conflicts: 29
22 -out_conflicts $param_out_conflicts 30 ## Main program call
31
32 set -o pipefail &&
33 @EXECUTABLE@ -write_ctd ./ &&
34 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
35 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
36 -in
37 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
38 #if $in_blacklist:
39 -in_blacklist
40 'in_blacklist/${re.sub("[^\w\-_]", "_", $in_blacklist.element_identifier)}.$gxy2omsext($in_blacklist.ext)'
23 #end if 41 #end if
24 #if $param_algorithm_labels: 42 -out
25 -algorithm:labels "$param_algorithm_labels" 43 'out/output.${gxy2omsext("consensusxml")}'
44 #if "out_conflicts_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
45 -out_conflicts
46 'out_conflicts/output.${gxy2omsext("consensusxml")}'
26 #end if 47 #end if
27 #if $param_algorithm_missed_cleavages: 48 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
28 -algorithm:missed_cleavages $param_algorithm_missed_cleavages 49 | tee '$stdout'
29 #end if 50 #end if
30 #if $adv_opts.adv_opts_selector=='advanced': 51
31 #if $adv_opts.param_force: 52 ## Postprocessing
32 -force 53 && mv 'out/output.${gxy2omsext("consensusxml")}' '$out'
54 #if "out_conflicts_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
55 && mv 'out_conflicts/output.${gxy2omsext("consensusxml")}' '$out_conflicts'
33 #end if 56 #end if
34 #if $adv_opts.param_algorithm_mass_tolerance: 57 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
35 -algorithm:mass_tolerance $adv_opts.param_algorithm_mass_tolerance 58 && mv '@EXECUTABLE@.ctd' '$ctd_out'
36 #end if 59 #end if]]></command>
37 #if $adv_opts.param_labels_Arg6: 60 <configfiles>
38 -labels:Arg6 $adv_opts.param_labels_Arg6 61 <inputs name="args_json" data_style="paths"/>
39 #end if 62 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
40 #if $adv_opts.param_labels_Arg10: 63 </configfiles>
41 -labels:Arg10 $adv_opts.param_labels_Arg10
42 #end if
43 #if $adv_opts.param_labels_Lys4:
44 -labels:Lys4 $adv_opts.param_labels_Lys4
45 #end if
46 #if $adv_opts.param_labels_Lys6:
47 -labels:Lys6 $adv_opts.param_labels_Lys6
48 #end if
49 #if $adv_opts.param_labels_Lys8:
50 -labels:Lys8 $adv_opts.param_labels_Lys8
51 #end if
52 #if $adv_opts.param_labels_Leu3:
53 -labels:Leu3 $adv_opts.param_labels_Leu3
54 #end if
55 #if $adv_opts.param_labels_Dimethyl0:
56 -labels:Dimethyl0 $adv_opts.param_labels_Dimethyl0
57 #end if
58 #if $adv_opts.param_labels_Dimethyl4:
59 -labels:Dimethyl4 $adv_opts.param_labels_Dimethyl4
60 #end if
61 #if $adv_opts.param_labels_Dimethyl6:
62 -labels:Dimethyl6 $adv_opts.param_labels_Dimethyl6
63 #end if
64 #if $adv_opts.param_labels_Dimethyl8:
65 -labels:Dimethyl8 $adv_opts.param_labels_Dimethyl8
66 #end if
67 #if $adv_opts.param_labels_ICPL0:
68 -labels:ICPL0 $adv_opts.param_labels_ICPL0
69 #end if
70 #if $adv_opts.param_labels_ICPL4:
71 -labels:ICPL4 $adv_opts.param_labels_ICPL4
72 #end if
73 #if $adv_opts.param_labels_ICPL6:
74 -labels:ICPL6 $adv_opts.param_labels_ICPL6
75 #end if
76 #if $adv_opts.param_labels_ICPL10:
77 -labels:ICPL10 $adv_opts.param_labels_ICPL10
78 #end if
79 #end if
80 ]]></command>
81 <inputs> 64 <inputs>
82 <param name="param_in" type="data" format="consensusxml" optional="False" label="Peptide multiplets with assigned sequence information" help="(-in) "/> 65 <param name="in" argument="-in" type="data" format="consensusxml" optional="false" label="Peptide multiplets with assigned sequence information" help=" select consensusxml data sets(s)"/>
83 <param name="param_algorithm_labels" type="text" size="30" value="[][Lys8,Arg10]" label="Labels used for labelling the samples" help="(-labels) [...] specifies the labels for a single sample. For example &lt;br&gt; &lt;br&gt;[][Lys8,Arg10] ... SILAC &lt;br&gt;[][Lys4,Arg6][Lys8,Arg10] ... triple-SILAC &lt;br&gt;[Dimethyl0][Dimethyl6] ... Dimethyl &lt;br&gt;[Dimethyl0][Dimethyl4][Dimethyl8] ... triple Dimethyl &lt;br&gt;[ICPL0][ICPL4][ICPL6][ICPL10] ... ICPL"> 66 <param name="in_blacklist" argument="-in_blacklist" type="data" format="mzml" optional="true" label="Optional input containing spectral peaks blacklisted during feature detection" help="Needed for generation of dummy features select mzml data sets(s)"/>
84 <sanitizer> 67 <section name="algorithm" title="Parameters for the algorithm" help="" expanded="false">
85 <valid initial="string.printable"> 68 <param name="labels" argument="-algorithm:labels" type="text" optional="true" value="[][Lys8,Arg10]" label="Labels used for labelling the samples" help="[...] specifies the labels for a single sample. For example. . [][Lys8,Arg10] ... SILAC. [][Lys4,Arg6][Lys8,Arg10] ... triple-SILAC. [Dimethyl0][Dimethyl6] ... Dimethyl. [Dimethyl0][Dimethyl4][Dimethyl8] ... triple Dimethyl. [ICPL0][ICPL4][ICPL6][ICPL10] ... ICPL">
86 <remove value="'"/> 69 <expand macro="list_string_san"/>
87 <remove value="&quot;"/> 70 </param>
88 </valid> 71 <param name="missed_cleavages" argument="-algorithm:missed_cleavages" type="integer" optional="true" min="0" value="0" label="Maximum number of missed cleavages due to incomplete digestion" help="(Only relevant if enzymatic cutting site coincides with labelling site. For example, Arg/Lys in the case of trypsin digestion and SILAC labelling.)"/>
89 </sanitizer> 72 <param name="mass_tolerance" argument="-algorithm:mass_tolerance" type="float" optional="true" value="0.1" label="Mass tolerance in Da for matching the mass shifts in the detected peptide multiplet to the theoretical mass shift pattern" help=""/>
73 <param name="mz_tolerance" argument="-algorithm:mz_tolerance" type="integer" optional="true" value="10" label="m/z tolerance in ppm for checking if dummy feature vicinity was blacklisted" help=""/>
74 <param name="rt_tolerance" argument="-algorithm:rt_tolerance" type="integer" optional="true" value="5" label="Retention time tolerance in seconds for checking if dummy feature vicinity was blacklisted" help=""/>
75 </section>
76 <section name="labels" title="Isotopic labels that can be specified in section 'algorithm:labels'" help="" expanded="false">
77 <param name="Arg6" argument="-labels:Arg6" type="float" optional="true" min="0.0" value="6.0201290268" label="Label:13C(6) | C(-6) 13C(6) | unimod #188" help=""/>
78 <param name="Arg10" argument="-labels:Arg10" type="float" optional="true" min="0.0" value="10.0082686" label="Label:13C(6)15N(4) | C(-6) 13C(6) N(-4) 15N(4) | unimod #267" help=""/>
79 <param name="Lys4" argument="-labels:Lys4" type="float" optional="true" min="0.0" value="4.0251069836" label="Label:2H(4) | H(-4) 2H(4) | unimod #481" help=""/>
80 <param name="Lys6" argument="-labels:Lys6" type="float" optional="true" min="0.0" value="6.0201290268" label="Label:13C(6) | C(-6) 13C(6) | unimod #188" help=""/>
81 <param name="Lys8" argument="-labels:Lys8" type="float" optional="true" min="0.0" value="8.0141988132" label="Label:13C(6)15N(2) | C(-6) 13C(6) N(-2) 15N(2) | unimod #259" help=""/>
82 <param name="Leu3" argument="-labels:Leu3" type="float" optional="true" min="0.0" value="3.01883" label="Label:2H(3) | H(-3) 2H(3) | unimod #262" help=""/>
83 <param name="Dimethyl0" argument="-labels:Dimethyl0" type="float" optional="true" min="0.0" value="28.0313" label="Dimethyl | H(4) C(2) | unimod #36" help=""/>
84 <param name="Dimethyl4" argument="-labels:Dimethyl4" type="float" optional="true" min="0.0" value="32.056407" label="Dimethyl:2H(4) | 2H(4) C(2) | unimod #199" help=""/>
85 <param name="Dimethyl6" argument="-labels:Dimethyl6" type="float" optional="true" min="0.0" value="34.063117" label="Dimethyl:2H(4)13C(2) | 2H(4) 13C(2) | unimod #510" help=""/>
86 <param name="Dimethyl8" argument="-labels:Dimethyl8" type="float" optional="true" min="0.0" value="36.07567" label="Dimethyl:2H(6)13C(2) | H(-2) 2H(6) 13C(2) | unimod #330" help=""/>
87 <param name="ICPL0" argument="-labels:ICPL0" type="float" optional="true" min="0.0" value="105.021464" label="ICPL | H(3) C(6) N O | unimod #365" help=""/>
88 <param name="ICPL4" argument="-labels:ICPL4" type="float" optional="true" min="0.0" value="109.046571" label="ICPL:2H(4) | H(-1) 2H(4) C(6) N O | unimod #687" help=""/>
89 <param name="ICPL6" argument="-labels:ICPL6" type="float" optional="true" min="0.0" value="111.041593" label="ICPL:13C(6) | H(3) 13C(6) N O | unimod #364" help=""/>
90 <param name="ICPL10" argument="-labels:ICPL10" type="float" optional="true" min="0.0" value="115.0667" label="ICPL:13C(6)2H(4) | H(-1) 2H(4) 13C(6) N O | unimod #866" help=""/>
91 </section>
92 <expand macro="adv_opts_macro">
93 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
94 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
95 <expand macro="list_string_san"/>
96 </param>
97 </expand>
98 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
99 <option value="out_conflicts_FLAG">out_conflicts (ICPL:13C(6)2H(4) | H(-1) 2H(4) 13C(6) N O | unimod #866)</option>
100 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
90 </param> 101 </param>
91 <param name="param_algorithm_missed_cleavages" type="integer" min="0" optional="True" value="0" label="Maximum number of missed cleavages due to incomplete digestion" help="(-missed_cleavages) (Only relevant if enzymatic cutting site coincides with labelling site. For example, Arg/Lys in the case of trypsin digestion and SILAC labelling.)"/>
92 <expand macro="advanced_options">
93 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
94 <param name="param_algorithm_mass_tolerance" type="float" value="0.1" label="Mass tolerance in Da for matching the detected to the theoretical mass shifts" help="(-mass_tolerance) "/>
95 <param name="param_labels_Arg6" type="float" min="0.0" optional="True" value="6.0201290268" label="Label:13C(6) | C(-6) 13C(6) | unimod #188" help="(-Arg6) "/>
96 <param name="param_labels_Arg10" type="float" min="0.0" optional="True" value="10.0082686" label="Label:13C(6)15N(4) | C(-6) 13C(6) N(-4) 15N(4) | unimod #267" help="(-Arg10) "/>
97 <param name="param_labels_Lys4" type="float" min="0.0" optional="True" value="4.0251069836" label="Label:2H(4) | H(-4) 2H(4) | unimod #481" help="(-Lys4) "/>
98 <param name="param_labels_Lys6" type="float" min="0.0" optional="True" value="6.0201290268" label="Label:13C(6) | C(-6) 13C(6) | unimod #188" help="(-Lys6) "/>
99 <param name="param_labels_Lys8" type="float" min="0.0" optional="True" value="8.0141988132" label="Label:13C(6)15N(2) | C(-6) 13C(6) N(-2) 15N(2) | unimod #259" help="(-Lys8) "/>
100 <param name="param_labels_Leu3" type="float" min="0.0" optional="True" value="3.01883" label="Label:2H(3) | H(-3) 2H(3) | unimod #262" help="(-Leu3) "/>
101 <param name="param_labels_Dimethyl0" type="float" min="0.0" optional="True" value="28.0313" label="Dimethyl | H(4) C(2) | unimod #36" help="(-Dimethyl0) "/>
102 <param name="param_labels_Dimethyl4" type="float" min="0.0" optional="True" value="32.056407" label="Dimethyl:2H(4) | 2H(4) C(2) | unimod #199" help="(-Dimethyl4) "/>
103 <param name="param_labels_Dimethyl6" type="float" min="0.0" optional="True" value="34.063117" label="Dimethyl:2H(4)13C(2) | 2H(4) 13C(2) | unimod #510" help="(-Dimethyl6) "/>
104 <param name="param_labels_Dimethyl8" type="float" min="0.0" optional="True" value="36.07567" label="Dimethyl:2H(6)13C(2) | H(-2) 2H(6) 13C(2) | unimod #330" help="(-Dimethyl8) "/>
105 <param name="param_labels_ICPL0" type="float" min="0.0" optional="True" value="105.021464" label="ICPL | H(3) C(6) N O | unimod #365" help="(-ICPL0) "/>
106 <param name="param_labels_ICPL4" type="float" min="0.0" optional="True" value="109.046571" label="ICPL:2H(4) | H(-1) 2H(4) C(6) N O | unimod #687" help="(-ICPL4) "/>
107 <param name="param_labels_ICPL6" type="float" min="0.0" optional="True" value="111.041593" label="ICPL:13C(6) | H(3) 13C(6) N O | unimod #364" help="(-ICPL6) "/>
108 <param name="param_labels_ICPL10" type="float" min="0.0" optional="True" value="115.0667" label="ICPL:13C(6)2H(4) | H(-1) 2H(4) 13C(6) N O | unimod #866" help="(-ICPL10) "/>
109 </expand>
110 </inputs> 102 </inputs>
111 <outputs> 103 <outputs>
112 <data name="param_out" format="consensusxml"/> 104 <data name="out" label="${tool.name} on ${on_string}: out" format="consensusxml"/>
113 <data name="param_out_conflicts" format="consensusxml"/> 105 <data name="out_conflicts" label="${tool.name} on ${on_string}: out_conflicts" format="consensusxml">
106 <filter>OPTIONAL_OUTPUTS is not None and "out_conflicts_FLAG" in OPTIONAL_OUTPUTS</filter>
107 </data>
108 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
109 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
110 </data>
114 </outputs> 111 </outputs>
115 <help>Completes peptide multiplets and resolves conflicts within them. 112 <tests>
113 <expand macro="autotest_MultiplexResolver"/>
114 <expand macro="manutest_MultiplexResolver"/>
115 </tests>
116 <help><![CDATA[Completes peptide multiplets and resolves conflicts within them.
116 117
117 118
118 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_MultiplexResolver.html</help> 119 For more information, visit http://www.openms.de/documentation/UTILS_MultiplexResolver.html]]></help>
120 <expand macro="references"/>
119 </tool> 121 </tool>