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comparison IDMerger.xml @ 15:34e7afee141d draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:18:45 +0000
parents 978de6b97ca8
children
comparison
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14:f817513840a9 15:34e7afee141d
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: [File Handling]--> 3 <!--Proposed Tool Section: [File Handling]-->
4 <tool id="IDMerger" name="IDMerger" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="IDMerger" name="IDMerger" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Merges several protein/peptide identification files into one file.</description> 5 <description>Merges several protein/peptide identification files into one file.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">IDMerger</token> 7 <token name="@EXECUTABLE@">IDMerger</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 in && 17 mkdir in_cond.in &&
20 ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) } 18 #if $in_cond.in_select == "no"
19 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} &&
20 ${' '.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])}
21 #else
22 ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
23 #end if
21 mkdir out && 24 mkdir out &&
22 #if $add_to: 25 #if $add_to:
23 mkdir add_to && 26 mkdir add_to &&
24 ln -s '$add_to' 'add_to/${re.sub("[^\w\-_]", "_", $add_to.element_identifier)}.$gxy2omsext($add_to.ext)' && 27 ln -s '$add_to' 'add_to/${re.sub("[^\w\-_]", "_", $add_to.element_identifier)}.$gxy2omsext($add_to.ext)' &&
25 #end if 28 #end if
29 set -o pipefail && 32 set -o pipefail &&
30 @EXECUTABLE@ -write_ctd ./ && 33 @EXECUTABLE@ -write_ctd ./ &&
31 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && 34 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
32 @EXECUTABLE@ -ini @EXECUTABLE@.ctd 35 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
33 -in 36 -in
34 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} 37 #if $in_cond.in_select == "no"
38 ${' '.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])}
39 #else
40 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)'
41 #end if
35 -out 42 -out
36 'out/output.${gxy2omsext("idxml")}' 43 'out/output.${out_type}'
37 #if $add_to: 44 #if $add_to:
38 -add_to 45 -add_to
39 'add_to/${re.sub("[^\w\-_]", "_", $add_to.element_identifier)}.$gxy2omsext($add_to.ext)' 46 'add_to/${re.sub("[^\w\-_]", "_", $add_to.element_identifier)}.$gxy2omsext($add_to.ext)'
40 #end if 47 #end if
41 48
42 ## Postprocessing 49 ## Postprocessing
43 && mv 'out/output.${gxy2omsext("idxml")}' '$out' 50 && mv 'out/output.${out_type}' '$out'
44 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS 51 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
45 && mv '@EXECUTABLE@.ctd' '$ctd_out' 52 && mv '@EXECUTABLE@.ctd' '$ctd_out'
46 #end if]]></command> 53 #end if]]></command>
47 <configfiles> 54 <configfiles>
48 <inputs name="args_json" data_style="paths"/> 55 <inputs name="args_json" data_style="paths"/>
49 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 56 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
50 </configfiles> 57 </configfiles>
51 <inputs> 58 <inputs>
52 <param name="in" argument="-in" type="data" format="idxml" multiple="true" optional="false" label="Input files separated by blanks" help=" select idxml data sets(s)"/> 59 <conditional name="in_cond">
53 <param name="add_to" argument="-add_to" type="data" format="idxml" optional="true" label="Optional input file" help="IDs from 'in' are added to this file, but only if the (modified) peptide sequences are not present yet (considering only best hits per spectrum) select idxml data sets(s)"/> 60 <param name="in_select" type="select" label="Run tool in batch mode for -in">
54 <param name="annotate_file_origin" argument="-annotate_file_origin" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Store the original filename in each protein/peptide identification (meta value: file_origin)" help=""/> 61 <option value="no">No: process all datasets jointly</option>
55 <param name="pepxml_protxml" argument="-pepxml_protxml" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Merge idXML files derived from a pepXML and corresponding protXML file" help="Exactly two input files are expected in this case. Not compatible with 'add_to'"/> 62 <option value="yes">Yes: process each dataset in an independent job</option>
56 <param name="merge_proteins_add_PSMs" argument="-merge_proteins_add_PSMs" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Merge all identified proteins by accession into one protein identification run but keep all the PSMs with updated links to potential new protein ID#s" help="Not compatible with 'add_to'"/> 63 </param>
64 <when value="no">
65 <param argument="-in" type="data" format="idxml,sqlite" multiple="true" optional="false" label="Input files separated by blanks (all must have the same type)" help=" select idxml,sqlite data sets(s)"/>
66 </when>
67 <when value="yes">
68 <param argument="-in" type="data" format="idxml,sqlite" multiple="false" optional="false" label="Input files separated by blanks (all must have the same type)" help=" select idxml,sqlite data sets(s)"/>
69 </when>
70 </conditional>
71 <param argument="-out_type" display="radio" type="select" optional="false" label="Output file type (default: determined from file extension)" help="">
72 <option value="idXML">idxml</option>
73 <option value="oms">sqlite (oms)</option>
74 <expand macro="list_string_san" name="out_type"/>
75 </param>
76 <param argument="-add_to" type="data" format="idxml" optional="true" label="Optional input file" help="IDs from 'in' are added to this file, but only if the (modified) peptide sequences are not present yet (considering only best hits per spectrum) select idxml data sets(s)"/>
77 <param argument="-annotate_file_origin" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Store the original filename in each protein/peptide identification (meta value: 'file_origin') - idXML input/output only" help=""/>
78 <param argument="-pepxml_protxml" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Merge idXML files derived from a pepXML and corresponding protXML file" help="Exactly two input files are expected in this case. Not compatible with 'add_to'"/>
79 <param argument="-merge_proteins_add_PSMs" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Merge all identified proteins by accession into one protein identification run but keep all the PSMs with updated links to potential new protein ID#s" help="Not compatible with 'add_to'"/>
57 <expand macro="adv_opts_macro"> 80 <expand macro="adv_opts_macro">
58 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 81 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
59 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 82 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
60 <expand macro="list_string_san"/> 83 <expand macro="list_string_san" name="test"/>
61 </param> 84 </param>
62 </expand> 85 </expand>
63 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 86 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
64 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 87 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
65 </param> 88 </param>
66 </inputs> 89 </inputs>
67 <outputs> 90 <outputs>
68 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/> 91 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml">
92 <change_format>
93 <when input="out_type" value="oms" format="sqlite"/>
94 </change_format>
95 </data>
69 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 96 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
70 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 97 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
71 </data> 98 </data>
72 </outputs> 99 </outputs>
73 <tests> 100 <tests><!-- TOPP_IDMerger_1 -->
74 <expand macro="autotest_IDMerger"/> 101 <test expect_num_outputs="2">
75 <expand macro="manutest_IDMerger"/> 102 <section name="adv_opts">
103 <param name="force" value="false"/>
104 <param name="test" value="true"/>
105 </section>
106 <conditional name="in_cond">
107 <param name="in" value="IDMerger_1_input1.idXML,IDMerger_1_input2.idXML"/>
108 </conditional>
109 <output name="out" file="IDMerger_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
110 <param name="out_type" value="idXML"/>
111 <param name="annotate_file_origin" value="true"/>
112 <param name="pepxml_protxml" value="false"/>
113 <param name="merge_proteins_add_PSMs" value="false"/>
114 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
115 <output name="ctd_out" ftype="xml">
116 <assert_contents>
117 <is_valid_xml/>
118 </assert_contents>
119 </output>
120 </test>
121 <!-- TOPP_IDMerger_2 -->
122 <test expect_num_outputs="2">
123 <section name="adv_opts">
124 <param name="force" value="false"/>
125 <param name="test" value="true"/>
126 </section>
127 <conditional name="in_cond">
128 <param name="in" value="IDMerger_2_input1.idXML,IDMerger_2_input2.idXML"/>
129 </conditional>
130 <output name="out" file="IDMerger_2_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
131 <param name="out_type" value="idXML"/>
132 <param name="annotate_file_origin" value="false"/>
133 <param name="pepxml_protxml" value="true"/>
134 <param name="merge_proteins_add_PSMs" value="false"/>
135 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
136 <output name="ctd_out" ftype="xml">
137 <assert_contents>
138 <is_valid_xml/>
139 </assert_contents>
140 </output>
141 </test>
142 <!-- TOPP_IDMerger_3 -->
143 <test expect_num_outputs="2">
144 <section name="adv_opts">
145 <param name="force" value="false"/>
146 <param name="test" value="true"/>
147 </section>
148 <conditional name="in_cond">
149 <param name="in" value="IDMerger_1_input1.idXML,IDMerger_1_input1_2.idXML"/>
150 </conditional>
151 <output name="out" file="IDMerger_3_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
152 <param name="out_type" value="idXML"/>
153 <param name="annotate_file_origin" value="false"/>
154 <param name="pepxml_protxml" value="false"/>
155 <param name="merge_proteins_add_PSMs" value="false"/>
156 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
157 <output name="ctd_out" ftype="xml">
158 <assert_contents>
159 <is_valid_xml/>
160 </assert_contents>
161 </output>
162 </test>
163 <!-- TOPP_IDMerger_4 -->
164 <test expect_num_outputs="2">
165 <section name="adv_opts">
166 <param name="force" value="false"/>
167 <param name="test" value="true"/>
168 </section>
169 <conditional name="in_cond">
170 <param name="in" value="degenerated_empty.idXML,degenerated_empty_2.idXML"/>
171 </conditional>
172 <output name="out" file="IDMerger_4_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
173 <param name="out_type" value="idXML"/>
174 <param name="annotate_file_origin" value="false"/>
175 <param name="pepxml_protxml" value="false"/>
176 <param name="merge_proteins_add_PSMs" value="false"/>
177 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
178 <output name="ctd_out" ftype="xml">
179 <assert_contents>
180 <is_valid_xml/>
181 </assert_contents>
182 </output>
183 </test>
184 <!-- TOPP_IDMerger_5 -->
185 <test expect_num_outputs="2">
186 <section name="adv_opts">
187 <param name="force" value="false"/>
188 <param name="test" value="true"/>
189 </section>
190 <conditional name="in_cond">
191 <param name="in" value="IDMerger_2_input1.idXML"/>
192 </conditional>
193 <output name="out" file="IDMerger_5_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
194 <param name="out_type" value="idXML"/>
195 <param name="add_to" value="IDMerger_5_input1.idXML"/>
196 <param name="annotate_file_origin" value="false"/>
197 <param name="pepxml_protxml" value="false"/>
198 <param name="merge_proteins_add_PSMs" value="false"/>
199 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
200 <output name="ctd_out" ftype="xml">
201 <assert_contents>
202 <is_valid_xml/>
203 </assert_contents>
204 </output>
205 </test>
206 <!-- TOPP_IDMerger_6 -->
207 <test expect_num_outputs="2">
208 <section name="adv_opts">
209 <param name="force" value="false"/>
210 <param name="test" value="true"/>
211 </section>
212 <conditional name="in_cond">
213 <param name="in" value="IDMerger_6_input1.oms,IDMerger_6_input2.oms"/>
214 </conditional>
215 <output name="out" file="IDMerger_6_output1.oms" compare="sim_size" delta_frac="0.7" ftype="sqlite"/>
216 <param name="out_type" value="oms"/>
217 <param name="annotate_file_origin" value="true"/>
218 <param name="pepxml_protxml" value="false"/>
219 <param name="merge_proteins_add_PSMs" value="false"/>
220 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
221 <output name="ctd_out" ftype="xml">
222 <assert_contents>
223 <is_valid_xml/>
224 </assert_contents>
225 </output>
226 </test>
227 <!-- TOPP_IDRipper_3_prep -->
228 <test expect_num_outputs="2">
229 <section name="adv_opts">
230 <param name="force" value="false"/>
231 <param name="test" value="true"/>
232 </section>
233 <conditional name="in_cond">
234 <param name="in" value="IDRipper_3_input1.idXML,IDRipper_3_input2.idXML"/>
235 </conditional>
236 <output name="out" file="IDRipper_3_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
237 <param name="out_type" value="idXML"/>
238 <param name="annotate_file_origin" value="true"/>
239 <param name="pepxml_protxml" value="false"/>
240 <param name="merge_proteins_add_PSMs" value="false"/>
241 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
242 <output name="ctd_out" ftype="xml">
243 <assert_contents>
244 <is_valid_xml/>
245 </assert_contents>
246 </output>
247 </test>
76 </tests> 248 </tests>
77 <help><![CDATA[Merges several protein/peptide identification files into one file. 249 <help><![CDATA[Merges several protein/peptide identification files into one file.
78 250
79 251
80 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_IDMerger.html]]></help> 252 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_IDMerger.html]]></help>
81 <expand macro="references"/> 253 <expand macro="references"/>
82 </tool> 254 </tool>