Mercurial > repos > galaxyp > openms_proteinresolver
comparison ProteinResolver.xml @ 13:851f7c252d66 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author | galaxyp |
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date | Thu, 01 Dec 2022 18:57:06 +0000 |
parents | 95f90fab5ce8 |
children | c2612cb89529 |
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12:4242496df19e | 13:851f7c252d66 |
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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: [Quantitation]--> | 3 <!--Proposed Tool Section: [Quantitation]--> |
4 <tool id="ProteinResolver" name="ProteinResolver" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> | 4 <tool id="ProteinResolver" name="ProteinResolver" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> |
5 <description>protein inference</description> | 5 <description>protein inference</description> |
6 <macros> | 6 <macros> |
7 <token name="@EXECUTABLE@">ProteinResolver</token> | 7 <token name="@EXECUTABLE@">ProteinResolver</token> |
8 <import>macros.xml</import> | 8 <import>macros.xml</import> |
9 <import>macros_autotest.xml</import> | |
10 <import>macros_test.xml</import> | |
11 </macros> | 9 </macros> |
12 <expand macro="requirements"/> | 10 <expand macro="requirements"/> |
13 <expand macro="stdio"/> | 11 <expand macro="stdio"/> |
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ | 12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ |
15 @EXT_FOO@ | 13 @EXT_FOO@ |
16 #import re | 14 #import re |
17 | 15 |
18 ## Preprocessing | 16 ## Preprocessing |
19 mkdir fasta && | 17 mkdir fasta && |
20 ln -s '$fasta' 'fasta/${re.sub("[^\w\-_]", "_", $fasta.element_identifier)}.$gxy2omsext($fasta.ext)' && | 18 ln -s '$fasta' 'fasta/${re.sub("[^\w\-_]", "_", $fasta.element_identifier)}.$gxy2omsext($fasta.ext)' && |
21 #if $in: | 19 #if $in_cond.in: |
22 mkdir in && | 20 mkdir in_cond.in && |
23 ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) } | 21 #if $in_cond.in_select == "no" |
22 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && | |
23 ${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} | |
24 #else | |
25 ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && | |
26 #end if | |
24 #end if | 27 #end if |
25 #if $design: | 28 #if $design: |
26 mkdir design && | 29 mkdir design && |
27 ln -s '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' && | 30 ln -s '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' && |
28 #end if | 31 #end if |
45 @EXECUTABLE@ -write_ctd ./ && | 48 @EXECUTABLE@ -write_ctd ./ && |
46 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && | 49 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && |
47 @EXECUTABLE@ -ini @EXECUTABLE@.ctd | 50 @EXECUTABLE@ -ini @EXECUTABLE@.ctd |
48 -fasta | 51 -fasta |
49 'fasta/${re.sub("[^\w\-_]", "_", $fasta.element_identifier)}.$gxy2omsext($fasta.ext)' | 52 'fasta/${re.sub("[^\w\-_]", "_", $fasta.element_identifier)}.$gxy2omsext($fasta.ext)' |
50 #if $in: | 53 #if $in_cond.in: |
51 -in | 54 -in |
52 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} | 55 #if $in_cond.in_select == "no" |
56 ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} | |
57 #else | |
58 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' | |
59 #end if | |
53 #end if | 60 #end if |
54 #if $design: | 61 #if $design: |
55 -design | 62 -design |
56 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' | 63 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' |
57 #end if | 64 #end if |
94 <configfiles> | 101 <configfiles> |
95 <inputs name="args_json" data_style="paths"/> | 102 <inputs name="args_json" data_style="paths"/> |
96 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> | 103 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
97 </configfiles> | 104 </configfiles> |
98 <inputs> | 105 <inputs> |
99 <param name="fasta" argument="-fasta" type="data" format="fasta" optional="false" label="Input database file" help=" select fasta data sets(s)"/> | 106 <param argument="-fasta" type="data" format="fasta" optional="false" label="Input database file" help=" select fasta data sets(s)"/> |
100 <param name="in" argument="-in" type="data" format="consensusxml,idxml" multiple="true" optional="true" label="Input file(s) holding experimental data" help=" select consensusxml,idxml data sets(s)"/> | 107 <conditional name="in_cond"> |
101 <param name="in_path" argument="-in_path" type="text" optional="true" value="" label="Path to idXMLs or consensusXMLs files" help="Ignored if 'in' is given"> | 108 <param name="in_select" type="select" label="Run tool in batch mode for -in"> |
102 <expand macro="list_string_san"/> | 109 <option value="no">No: process all datasets jointly</option> |
110 <option value="yes">Yes: process each dataset in an independent job</option> | |
111 </param> | |
112 <when value="no"> | |
113 <param argument="-in" type="data" format="consensusxml,idxml" multiple="true" optional="true" label="Input file(s) holding experimental data" help=" select consensusxml,idxml data sets(s)"/> | |
114 </when> | |
115 <when value="yes"> | |
116 <param argument="-in" type="data" format="consensusxml,idxml" multiple="false" optional="true" label="Input file(s) holding experimental data" help=" select consensusxml,idxml data sets(s)"/> | |
117 </when> | |
118 </conditional> | |
119 <param argument="-in_path" type="text" optional="true" value="" label="Path to idXMLs or consensusXMLs files" help="Ignored if 'in' is given"> | |
120 <expand macro="list_string_san" name="in_path"/> | |
103 </param> | 121 </param> |
104 <param name="design" argument="-design" type="data" format="txt" optional="true" label="Text file containing the experimental design" help="See documentation for specific format requirements select txt data sets(s)"/> | 122 <param argument="-design" type="data" format="txt" optional="true" label="Text file containing the experimental design" help="See documentation for specific format requirements select txt data sets(s)"/> |
105 <section name="resolver" title="Additional options for algorithm" help="" expanded="false"> | 123 <section name="resolver" title="Additional options for algorithm" help="" expanded="false"> |
106 <param name="missed_cleavages" argument="-resolver:missed_cleavages" type="integer" optional="true" min="0" value="2" label="Number of allowed missed cleavages" help=""/> | 124 <param name="missed_cleavages" argument="-resolver:missed_cleavages" type="integer" optional="true" min="0" value="2" label="Number of allowed missed cleavages" help=""/> |
107 <param name="min_length" argument="-resolver:min_length" type="integer" optional="true" min="1" value="6" label="Minimum length of peptide" help=""/> | 125 <param name="min_length" argument="-resolver:min_length" type="integer" optional="true" min="1" value="6" label="Minimum length of peptide" help=""/> |
108 <param name="enzyme" argument="-resolver:enzyme" display="radio" type="select" optional="false" label="Digestion enzyme" help=""> | 126 <param name="enzyme" argument="-resolver:enzyme" type="select" optional="true" label="Digestion enzyme" help=""> |
109 <option value="Trypsin" selected="true">Trypsin</option> | 127 <option value="Trypsin" selected="true">Trypsin</option> |
110 <expand macro="list_string_san"/> | 128 <expand macro="list_string_san" name="enzyme"/> |
111 </param> | 129 </param> |
112 </section> | 130 </section> |
113 <section name="designer" title="Additional options for quantitative experimental design" help="" expanded="false"> | 131 <section name="designer" title="Additional options for quantitative experimental design" help="" expanded="false"> |
114 <param name="experiment" argument="-designer:experiment" type="text" optional="true" value="ExperimentalSetting" label="Identifier for the experimental design" help=""> | 132 <param name="experiment" argument="-designer:experiment" type="text" optional="true" value="ExperimentalSetting" label="Identifier for the experimental design" help=""> |
115 <expand macro="list_string_san"/> | 133 <expand macro="list_string_san" name="experiment"/> |
116 </param> | 134 </param> |
117 <param name="file" argument="-designer:file" type="text" optional="true" value="File" label="Identifier for the file name" help=""> | 135 <param name="file" argument="-designer:file" type="text" optional="true" value="File" label="Identifier for the file name" help=""> |
118 <expand macro="list_string_san"/> | 136 <expand macro="list_string_san" name="file"/> |
119 </param> | 137 </param> |
120 <param name="separator" argument="-designer:separator" display="radio" type="select" optional="false" label="Separator, which should be used to split a row into columns" help=""> | 138 <param name="separator" argument="-designer:separator" type="select" optional="true" label="Separator, which should be used to split a row into columns" help=""> |
121 <option value="tab" selected="true">tab</option> | 139 <option value="tab" selected="true">tab</option> |
122 <option value="semi-colon">semi-colon</option> | 140 <option value="semi-colon">semi-colon</option> |
123 <option value="comma">comma</option> | 141 <option value="comma">comma</option> |
124 <option value="whitespace">whitespace</option> | 142 <option value="whitespace">whitespace</option> |
125 <expand macro="list_string_san"/> | 143 <expand macro="list_string_san" name="separator"/> |
126 </param> | 144 </param> |
127 </section> | 145 </section> |
128 <expand macro="adv_opts_macro"> | 146 <expand macro="adv_opts_macro"> |
129 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> | 147 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> |
130 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> | 148 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> |
131 <expand macro="list_string_san"/> | 149 <expand macro="list_string_san" name="test"/> |
132 </param> | 150 </param> |
133 </expand> | 151 </expand> |
134 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> | 152 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> |
135 <option value="protein_groups_FLAG">protein_groups (output file. Contains all protein groups)</option> | 153 <option value="protein_groups_FLAG">protein_groups (output file. Contains all protein groups)</option> |
136 <option value="peptide_table_FLAG">peptide_table (output file)</option> | 154 <option value="peptide_table_FLAG">peptide_table (output file)</option> |
157 </data> | 175 </data> |
158 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | 176 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> |
159 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | 177 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> |
160 </data> | 178 </data> |
161 </outputs> | 179 </outputs> |
162 <tests> | 180 <tests><!-- TOPP_ProteinResolver_1 --> |
163 <expand macro="autotest_ProteinResolver"/> | 181 <test expect_num_outputs="4"> |
164 <expand macro="manutest_ProteinResolver"/> | 182 <section name="adv_opts"> |
183 <param name="force" value="false"/> | |
184 <param name="test" value="true"/> | |
185 </section> | |
186 <param name="fasta" value="ProteinResolver_1_input.fasta"/> | |
187 <conditional name="in_cond"> | |
188 <param name="in" value="ProteinResolver_1_input.consensusXML"/> | |
189 </conditional> | |
190 <param name="in_path" value=""/> | |
191 <output name="protein_groups" file="ProteinResolver_1_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> | |
192 <output name="peptide_table" file="ProteinResolver_1_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> | |
193 <output name="protein_table" file="ProteinResolver_1_output3.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> | |
194 <section name="resolver"> | |
195 <param name="missed_cleavages" value="2"/> | |
196 <param name="min_length" value="6"/> | |
197 <param name="enzyme" value="Trypsin"/> | |
198 </section> | |
199 <section name="designer"> | |
200 <param name="experiment" value="ExperimentalSetting"/> | |
201 <param name="file" value="File"/> | |
202 <param name="separator" value="tab"/> | |
203 </section> | |
204 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,protein_groups_FLAG,peptide_table_FLAG,protein_table_FLAG"/> | |
205 <output name="ctd_out" ftype="xml"> | |
206 <assert_contents> | |
207 <is_valid_xml/> | |
208 </assert_contents> | |
209 </output> | |
210 </test> | |
165 </tests> | 211 </tests> |
166 <help><![CDATA[protein inference | 212 <help><![CDATA[protein inference |
167 | 213 |
168 | 214 |
169 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_ProteinResolver.html]]></help> | 215 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_ProteinResolver.html]]></help> |
170 <expand macro="references"/> | 216 <expand macro="references"/> |
171 </tool> | 217 </tool> |