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comparison ProteinQuantifier.xml @ 9:f874f2998576 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author galaxyp
date Thu, 27 Aug 2020 19:36:58 -0400
parents 9d9660679916
children bb1e75938909
comparison
equal deleted inserted replaced
8:e992ed59d3e5 9:f874f2998576
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: [Quantitation]--> 3 <!--Proposed Tool Section: [Quantitation]-->
4 <tool id="ProteinQuantifier" name="ProteinQuantifier" version="2.3.0"> 4 <tool id="ProteinQuantifier" name="ProteinQuantifier" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Compute peptide and protein abundances</description> 5 <description>Compute peptide and protein abundances</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">ProteinQuantifier</token> 7 <token name="@EXECUTABLE@">ProteinQuantifier</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[ProteinQuantifier 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 $protein_groups:
22 mkdir protein_groups &&
23 ln -s '$protein_groups' 'protein_groups/${re.sub("[^\w\-_]", "_", $protein_groups.element_identifier)}.$gxy2omsext($protein_groups.ext)' &&
17 #end if 24 #end if
18 #if $param_protein_groups: 25 #if $design:
19 -protein_groups $param_protein_groups 26 mkdir design &&
27 ln -s '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' &&
20 #end if 28 #end if
21 #if $param_out: 29 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
22 -out $param_out 30 mkdir out &&
23 #end if 31 #end if
24 #if $param_peptide_out: 32 #if "peptide_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
25 -peptide_out $param_peptide_out 33 mkdir peptide_out &&
26 #end if 34 #end if
27 #if str($param_top): 35 #if "mztab_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
28 -top $param_top 36 mkdir mztab &&
29 #end if 37 #end if
30 #if $param_average: 38
31 -average 39 ## Main program call
32 #if " " in str($param_average): 40
33 "$param_average" 41 set -o pipefail &&
34 #else 42 @EXECUTABLE@ -write_ctd ./ &&
35 $param_average 43 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
36 #end if 44 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
45 -in
46 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
47 #if $protein_groups:
48 -protein_groups
49 'protein_groups/${re.sub("[^\w\-_]", "_", $protein_groups.element_identifier)}.$gxy2omsext($protein_groups.ext)'
37 #end if 50 #end if
38 #if $param_include_all: 51 #if $design:
39 -include_all 52 -design
53 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)'
40 #end if 54 #end if
41 #if $param_filter_charge: 55 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
42 -filter_charge 56 -out
57 'out/output.${gxy2omsext("csv")}'
43 #end if 58 #end if
44 #if $param_ratios: 59 #if "peptide_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
45 -ratios 60 -peptide_out
61 'peptide_out/output.${gxy2omsext("csv")}'
46 #end if 62 #end if
47 #if $param_ratiosSILAC: 63 #if "mztab_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
48 -ratiosSILAC 64 -mztab
65 'mztab/output.${gxy2omsext("mztab")}'
49 #end if 66 #end if
50 #if $param_consensus_normalize: 67 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
51 -consensus:normalize 68 | tee '$stdout'
52 #end if 69 #end if
53 #if $param_consensus_fix_peptides: 70
54 -consensus:fix_peptides 71 ## Postprocessing
72 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
73 && mv 'out/output.${gxy2omsext("csv")}' '$out'
55 #end if 74 #end if
56 #if $param_format_separator: 75 #if "peptide_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
57 -format:separator "$param_format_separator" 76 && mv 'peptide_out/output.${gxy2omsext("csv")}' '$peptide_out'
58 #end if 77 #end if
59 #if $param_format_quoting: 78 #if "mztab_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
60 -format:quoting 79 && mv 'mztab/output.${gxy2omsext("mztab")}' '$mztab'
61 #if " " in str($param_format_quoting):
62 "$param_format_quoting"
63 #else
64 $param_format_quoting
65 #end if
66 #end if 80 #end if
67 #if $param_format_replacement: 81 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
68 -format:replacement "$param_format_replacement" 82 && mv '@EXECUTABLE@.ctd' '$ctd_out'
69 #end if 83 #end if]]></command>
70 #if $adv_opts.adv_opts_selector=='advanced': 84 <configfiles>
71 #if $adv_opts.param_force: 85 <inputs name="args_json" data_style="paths"/>
72 -force 86 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
73 #end if 87 </configfiles>
74 #end if
75 ]]></command>
76 <inputs> 88 <inputs>
77 <param name="param_in" type="data" format="featurexml,consensusxml,idxml" optional="False" label="Input file" help="(-in) "/> 89 <param name="in" argument="-in" type="data" format="consensusxml,featurexml,idxml" optional="false" label="Input file" help=" select consensusxml,featurexml,idxml data sets(s)"/>
78 <param name="param_protein_groups" type="data" format="idxml" optional="True" label="Protein inference results for the identification runs that were used to annotate the input (" help="(-protein_groups) e.g. from ProteinProphet via IDFileConverter or Fido via FidoAdapter). &lt;br&gt;Information about indistinguishable proteins will be used for protein quantification"/> 90 <param name="protein_groups" argument="-protein_groups" type="data" format="idxml" optional="true" label="Protein inference results for the identification runs that were used to annotate the input" help="(e.g. from ProteinProphet via IDFileConverter or Fido via FidoAdapter).. Information about indistinguishable proteins will be used for protein quantification select idxml data sets(s)"/>
79 <param name="param_top" type="integer" min="0" optional="True" value="3" label="Calculate protein abundance from this number of proteotypic peptides (most abundant first; '0' for all)" help="(-top) "/> 91 <param name="design" argument="-design" type="data" format="tabular" optional="true" label="input file containing the experimental design" help=" select tabular data sets(s)"/>
80 <param name="param_average" display="radio" type="select" optional="False" value="median" label="Averaging method used to compute protein abundances from peptide abundances" help="(-average) "> 92 <param name="top" argument="-top" type="integer" optional="true" min="0" value="3" label="Calculate protein abundance from this number of proteotypic peptides (most abundant first; '0' for all)" help=""/>
93 <param name="average" argument="-average" display="radio" type="select" optional="false" label="Averaging method used to compute protein abundances from peptide abundances" help="">
81 <option value="median" selected="true">median</option> 94 <option value="median" selected="true">median</option>
82 <option value="mean">mean</option> 95 <option value="mean">mean</option>
83 <option value="weighted_mean">weighted_mean</option> 96 <option value="weighted_mean">weighted_mean</option>
84 <option value="sum">sum</option> 97 <option value="sum">sum</option>
98 <expand macro="list_string_san"/>
85 </param> 99 </param>
86 <param name="param_include_all" display="radio" type="boolean" truevalue="-include_all" falsevalue="" checked="false" optional="True" label="Include results for proteins with fewer proteotypic peptides than indicated by 'top' (no effect if 'top' is 0 or 1)" help="(-include_all) "/> 100 <param name="include_all" argument="-include_all" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Include results for proteins with fewer proteotypic peptides than indicated by 'top' (no effect if 'top' is 0 or 1)" help=""/>
87 <param name="param_filter_charge" display="radio" type="boolean" truevalue="-filter_charge" falsevalue="" checked="false" optional="True" label="Distinguish between charge states of a peptide" help="(-filter_charge) For peptides, abundances will be reported separately for each charge; &lt;br&gt;for proteins, abundances will be computed based only on the most prevalent charge of each peptide. &lt;br&gt;By default, abundances are summed over all charge states"/> 101 <param name="best_charge_and_fraction" argument="-best_charge_and_fraction" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Distinguish between fraction and charge states of a peptide" help="For peptides, abundances will be reported separately for each fraction and charge;. for proteins, abundances will be computed based only on the most prevalent charge observed of each peptide (over all fractions).. By default, abundances are summed over all charge states"/>
88 <param name="param_ratios" display="radio" type="boolean" truevalue="-ratios" falsevalue="" checked="false" optional="True" label="Add the log2 ratios of the abundance values to the output" help="(-ratios) Format: log_2(x_0/x_0) &lt;sep&gt; log_2(x_1/x_0) &lt;sep&gt; log_2(x_2/x_0) "/> 102 <param name="greedy_group_resolution" argument="-greedy_group_resolution" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Pre-process identifications with greedy resolution of shared peptides based on the protein group probabilities" help="(Only works with an idXML file given as protein_groups parameter)"/>
89 <param name="param_ratiosSILAC" display="radio" type="boolean" truevalue="-ratiosSILAC" falsevalue="" checked="false" optional="True" label="Add the log2 ratios for a triple SILAC experiment to the output" help="(-ratiosSILAC) Only applicable to consensus maps of exactly three sub-maps. Format: log_2(heavy/light) &lt;sep&gt; log_2(heavy/middle) &lt;sep&gt; log_2(middle/light)"/> 103 <param name="ratios" argument="-ratios" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add the log2 ratios of the abundance values to the output" help="Format: log_2(x_0/x_0) &lt;sep&gt; log_2(x_1/x_0) &lt;sep&gt; log_2(x_2/x_0) "/>
90 <param name="param_consensus_normalize" display="radio" type="boolean" truevalue="-consensus:normalize" falsevalue="" checked="false" optional="True" label="Scale peptide abundances so that medians of all samples are equal" help="(-normalize) "/> 104 <param name="ratiosSILAC" argument="-ratiosSILAC" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add the log2 ratios for a triple SILAC experiment to the output" help="Only applicable to consensus maps of exactly three sub-maps. Format: log_2(heavy/light) &lt;sep&gt; log_2(heavy/middle) &lt;sep&gt; log_2(middle/light)"/>
91 <param name="param_consensus_fix_peptides" display="radio" type="boolean" truevalue="-consensus:fix_peptides" falsevalue="" checked="false" optional="True" label="Use the same peptides for protein quantification across all samples" help="(-fix_peptides) &lt;br&gt;With 'top 0', all peptides that occur in every sample are considered. &lt;br&gt;Otherwise ('top N'), the N peptides that occur in the most samples (independently of each other) are selected, &lt;br&gt;breaking ties by total abundance (there is no guarantee that the best co-ocurring peptides are chosen!)"/> 105 <section name="consensus" title="Additional options for consensus maps (and identification results comprising multiple runs)" help="" expanded="false">
92 <param name="param_format_separator" type="text" size="30" label="Character(s) used to separate fields; by default, the 'tab' character is used" help="(-separator) "> 106 <param name="normalize" argument="-consensus:normalize" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Scale peptide abundances so that medians of all samples are equal" help=""/>
93 <sanitizer> 107 <param name="fix_peptides" argument="-consensus:fix_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the same peptides for protein quantification across all samples" help="With 'top 0', all peptides that occur in every sample are considered.. Otherwise ('top N'), the N peptides that occur in the most samples (independently of each other) are selected,. breaking ties by total abundance (there is no guarantee that the best co-ocurring peptides are chosen!)"/>
94 <valid initial="string.printable"> 108 </section>
95 <remove value="'"/> 109 <section name="format" title="Output formatting options" help="" expanded="false">
96 <remove value="&quot;"/> 110 <param name="separator" argument="-format:separator" type="text" optional="true" value="" label="Character(s) used to separate fields; by default, the 'tab' character is used" help="">
97 </valid> 111 <expand macro="list_string_san"/>
98 </sanitizer> 112 </param>
113 <param name="quoting" argument="-format: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">
114 <option value="none">none</option>
115 <option value="double" selected="true">double</option>
116 <option value="escape">escape</option>
117 <expand macro="list_string_san"/>
118 </param>
119 <param name="replacement" argument="-format:replacement" type="text" optional="true" value="_" label="If 'quoting' is 'none', used to replace occurrences of the separator in strings before writing" help="">
120 <expand macro="list_string_san"/>
121 </param>
122 </section>
123 <expand macro="adv_opts_macro">
124 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
125 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
126 <expand macro="list_string_san"/>
127 </param>
128 </expand>
129 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="false">
130 <option value="out_FLAG">out (If 'quoting' is 'none', used to replace occurrences of the separator in strings before writing)</option>
131 <option value="peptide_out_FLAG">peptide_out (If 'quoting' is 'none', used to replace occurrences of the separator in strings before writing)</option>
132 <option value="mztab_FLAG">mztab (If 'quoting' is 'none', used to replace occurrences of the separator in strings before writing)</option>
133 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
99 </param> 134 </param>
100 <param name="param_format_quoting" display="radio" type="select" optional="False" value="double" label="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes, &lt;br&gt;'escape' for quoting with backslash-escaping of embedded quotes" help="(-quoting) ">
101 <option value="none">none</option>
102 <option value="double" selected="true">double</option>
103 <option value="escape">escape</option>
104 </param>
105 <param name="param_format_replacement" type="text" size="30" value="_" label="If 'quoting' is 'none', used to replace occurrences of the separator in strings before writing" help="(-replacement) ">
106 <sanitizer>
107 <valid initial="string.printable">
108 <remove value="'"/>
109 <remove value="&quot;"/>
110 </valid>
111 </sanitizer>
112 </param>
113 <expand macro="advanced_options">
114 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
115 </expand>
116 </inputs> 135 </inputs>
117 <outputs> 136 <outputs>
118 <data name="param_out" format="tabular"/> 137 <data name="out" label="${tool.name} on ${on_string}: out" format="csv">
119 <data name="param_peptide_out" format="tabular"/> 138 <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
139 </data>
140 <data name="peptide_out" label="${tool.name} on ${on_string}: peptide_out" format="csv">
141 <filter>OPTIONAL_OUTPUTS is not None and "peptide_out_FLAG" in OPTIONAL_OUTPUTS</filter>
142 </data>
143 <data name="mztab" label="${tool.name} on ${on_string}: mztab" format="mztab">
144 <filter>OPTIONAL_OUTPUTS is not None and "mztab_FLAG" in OPTIONAL_OUTPUTS</filter>
145 </data>
146 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
147 <filter>OPTIONAL_OUTPUTS is None</filter>
148 </data>
149 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
150 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
151 </data>
120 </outputs> 152 </outputs>
121 <help>Compute peptide and protein abundances 153 <tests>
154 <expand macro="autotest_ProteinQuantifier"/>
155 <expand macro="manutest_ProteinQuantifier"/>
156 </tests>
157 <help><![CDATA[Compute peptide and protein abundances
122 158
123 159
124 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_ProteinQuantifier.html</help> 160 For more information, visit http://www.openms.de/documentation/TOPP_ProteinQuantifier.html]]></help>
161 <expand macro="references"/>
125 </tool> 162 </tool>