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comparison FileMerger.xml @ 15:b2fc8da99bcc draft

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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 19:10:42 +0000
parents 8b871a67ba56
children 0643576e7f51
comparison
equal deleted inserted replaced
14:92352a475eed 15:b2fc8da99bcc
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="FileMerger" name="FileMerger" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="FileMerger" name="FileMerger" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Merges several MS files into one file.</description> 5 <description>Merges several MS files into one file.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">FileMerger</token> 7 <token name="@EXECUTABLE@">FileMerger</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($in_cond.in.ext)' &&
23 #end if
21 mkdir out && 24 mkdir out &&
22 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 25 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
23 mkdir rt_concat_trafo_out && 26 mkdir rt_concat_trafo_out &&
27 mkdir ${' '.join(["'rt_concat_trafo_out/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} &&
24 #end if 28 #end if
25 29
26 ## Main program call 30 ## Main program call
27 31
28 set -o pipefail && 32 set -o pipefail &&
29 @EXECUTABLE@ -write_ctd ./ && 33 @EXECUTABLE@ -write_ctd ./ &&
30 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' &&
31 @EXECUTABLE@ -ini @EXECUTABLE@.ctd 35 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
32 -in 36 -in
33 ${' '.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($in_cond.in.ext)'
41 #end if
34 -out 42 -out
35 'out/output.${out_type}' 43 'out/output.${out_type}'
36 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 44 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
37 -rt_concat:trafo_out 45 -rt_concat:trafo_out
38 ${' '.join(["'rt_concat_trafo_out/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext("trafoxml")) for _ in $in if _])} 46 ${' '.join(["'rt_concat_trafo_out/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext("trafoxml")) for i, f in enumerate($in_cond.in) if f])}
39 #end if 47 #end if
40 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 48 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
41 | tee '$stdout' 49 | tee '$stdout'
42 #end if 50 #end if
43 51
44 ## Postprocessing 52 ## Postprocessing
45 && mv 'out/output.${out_type}' '$out' 53 && mv 'out/output.${out_type}' '$out'
46 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 54 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
47 ${' '.join(["&& mv -n 'in/%(id)s.%(gext)s' 'rt_concat_trafo_out/%(id)s'"%{"id": re.sub('[^\w\-_]', '_', _.element_identifier), "gext": $gxy2omsext("trafoxml")} for _ in $rt_concat_trafo_out if _])} 55 ${' '.join(["&& mv -n 'rt_concat_trafo_out/%(bn)s/%(id)s.%(gext)s' 'rt_concat_trafo_out/%(bn)s/%(id)s'"%{"bn": i, "id": re.sub('[^\w\-_]', '_', f.element_identifier), "gext": $gxy2omsext("trafoxml")} for i, f in enumerate($in_cond.in) if f])}
48 #end if 56 #end if
49 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS 57 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
50 && mv '@EXECUTABLE@.ctd' '$ctd_out' 58 && mv '@EXECUTABLE@.ctd' '$ctd_out'
51 #end if]]></command> 59 #end if]]></command>
52 <configfiles> 60 <configfiles>
53 <inputs name="args_json" data_style="paths"/> 61 <inputs name="args_json" data_style="paths"/>
54 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 62 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
55 </configfiles> 63 </configfiles>
56 <inputs> 64 <inputs>
57 <param name="in" argument="-in" type="data" format="consensusxml,dta,dta2d,fasta,featurexml,mgf,mzdata,mzml,mzxml,traml" multiple="true" optional="false" label="Input files separated by blank" help=" select consensusxml,dta,dta2d,fasta,featurexml,mgf,mzdata,mzml,mzxml,traml data sets(s)"/> 65 <conditional name="in_cond">
66 <param name="in_select" type="select" label="Run tool in batch mode for -in">
67 <option value="no">No: process all datasets jointly</option>
68 <option value="yes">Yes: process each dataset in an independent job</option>
69 </param>
70 <when value="no">
71 <param argument="-in" type="data" format="consensusxml,dta,dta2d,fasta,featurexml,mgf,mzdata,mzml,mzxml,traml" multiple="true" optional="false" label="Input files separated by blank" help=" select consensusxml,dta,dta2d,fasta,featurexml,mgf,mzdata,mzml,mzxml,traml data sets(s)"/>
72 </when>
73 <when value="yes">
74 <param argument="-in" type="data" format="consensusxml,dta,dta2d,fasta,featurexml,mgf,mzdata,mzml,mzxml,traml" multiple="false" optional="false" label="Input files separated by blank" help=" select consensusxml,dta,dta2d,fasta,featurexml,mgf,mzdata,mzml,mzxml,traml data sets(s)"/>
75 </when>
76 </conditional>
58 <param name="out_type" type="select" optional="false" label="File type of output out (Output file)"> 77 <param name="out_type" type="select" optional="false" label="File type of output out (Output file)">
59 <option value="mzML">mzml</option> 78 <option value="mzML">mzml</option>
60 <option value="featureXML">featurexml</option> 79 <option value="featureXML">featurexml</option>
61 <option value="consensusXML">consensusxml</option> 80 <option value="consensusXML">consensusxml</option>
62 <option value="traML">traml</option> 81 <option value="traML">traml</option>
63 <option value="fasta">fasta</option> 82 <option value="fasta">fasta</option>
64 </param> 83 </param>
65 <param name="annotate_file_origin" argument="-annotate_file_origin" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Store the original filename in each feature using meta value &quot;file_origin&quot; (for featureXML and consensusXML only)" help=""/> 84 <param argument="-annotate_file_origin" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Store the original filename in each feature using meta value &quot;file_origin&quot; (for featureXML and consensusXML only)" help=""/>
66 <param name="append_method" argument="-append_method" display="radio" type="select" optional="false" label="Append consensusMaps rowise or colwise" help="(Please use colwise for the MSstatsConverter)"> 85 <param argument="-append_method" type="select" optional="true" label="(ConsensusXML-only) Append quantitative information about features row-wise or column-wise" help="- 'append_rows' is usually used when the inputs come from the same MS run (e.g. caused by manual splitting or multiple algorithms on the same file). - 'append_cols' when you want to combine consensusXMLs from e.g. different fractions to be summarized in ProteinQuantifier or jointly exported with MzTabExporter">
67 <option value="append_rows" selected="true">append_rows</option> 86 <option value="append_rows" selected="true">append_rows</option>
68 <option value="append_cols">append_cols</option> 87 <option value="append_cols">append_cols</option>
69 <expand macro="list_string_san"/> 88 <expand macro="list_string_san" name="append_method"/>
70 </param> 89 </param>
71 <section name="rt_concat" title="Options for concatenating files in the retention time (RT) dimension" help="The RT ranges of inputs are adjusted so they don't overlap in the merged file (traML input not supported)" expanded="false"> 90 <section name="rt_concat" title="Options for concatenating files in the retention time (RT) dimension" help="The RT ranges of inputs are adjusted so they don't overlap in the merged file (traML input not supported)" expanded="false">
72 <param name="gap" argument="-rt_concat:gap" type="float" optional="true" value="0.0" label="The amount of gap (in seconds) to insert between the RT ranges of different input files" help="RT concatenation is enabled if a value &gt; 0 is set"/> 91 <param name="gap" argument="-rt_concat:gap" type="float" optional="true" value="0.0" label="The amount of gap (in seconds) to insert between the RT ranges of different input files" help="RT concatenation is enabled if a value &gt; 0 is set"/>
73 </section> 92 </section>
74 <section name="raw" title="Options for raw data input/output (primarily for DTA files)" help="" expanded="false"> 93 <section name="raw" title="Options for raw data input/output (primarily for DTA files)" help="" expanded="false">
75 <param name="rt_auto" argument="-raw:rt_auto" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Assign retention times automatically (integers starting at 1)" help=""/> 94 <param name="rt_auto" argument="-raw:rt_auto" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Assign retention times automatically (integers starting at 1)" help=""/>
76 <param name="rt_custom" argument="-raw:rt_custom" type="text" optional="true" value="" label="List of custom retention times that are assigned to the files" help="The number of given retention times must be equal to the number of input files (space separated list, in order to allow for spaces in list items surround them by single quotes)"> 95 <param name="rt_custom" argument="-raw:rt_custom" type="text" optional="true" value="" label="List of custom retention times that are assigned to the files" help="The number of given retention times must be equal to the number of input files (space separated list, in order to allow for spaces in list items surround them by single quotes)">
77 <expand macro="list_float_valsan"/> 96 <expand macro="list_float_valsan" name="rt_custom"/>
78 </param> 97 </param>
79 <param name="rt_filename" argument="-raw:rt_filename" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Try to guess the retention time of a file based on the filename" help="This option is useful for merging DTA files, where filenames should contain the string 'rt' directly followed by a floating point number, e.g. 'my_spectrum_rt2795.15.dta'"/> 98 <param name="rt_filename" argument="-raw:rt_filename" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Try to guess the retention time of a file based on the filename" help="This option is useful for merging DTA files, where filenames should contain the string 'rt' directly followed by a floating point number, e.g. 'my_spectrum_rt2795.15.dta'"/>
80 <param name="ms_level" argument="-raw:ms_level" type="integer" optional="true" value="0" label="If 1 or higher, this number is assigned to spectra as the MS level" help="This option is useful for DTA files which do not contain MS level information"/> 99 <param name="ms_level" argument="-raw:ms_level" type="integer" optional="true" value="0" label="If 1 or higher, this number is assigned to spectra as the MS level" help="This option is useful for DTA files which do not contain MS level information"/>
81 </section> 100 </section>
82 <expand macro="adv_opts_macro"> 101 <expand macro="adv_opts_macro">
83 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 102 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
84 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 103 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
85 <expand macro="list_string_san"/> 104 <expand macro="list_string_san" name="test"/>
86 </param> 105 </param>
87 </expand> 106 </expand>
88 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 107 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
89 <option value="trafo_out_FLAG">trafo_out (Output of retention time transformations that were applied to the input files to produce non-overlapping RT ranges)</option> 108 <option value="trafo_out_FLAG">trafo_out (Output of retention time transformations that were applied to the input files to produce non-overlapping RT ranges)</option>
90 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 109 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
91 </param> 110 </param>
92 </inputs> 111 </inputs>
93 <outputs> 112 <outputs>
94 <data name="out" label="${tool.name} on ${on_string}: out"> 113 <data name="out" label="${tool.name} on ${on_string}: out" format="consensusxml">
95 <change_format> 114 <change_format>
96 <when input="out_type" value="consensusXML" format="consensusxml"/>
97 <when input="out_type" value="fasta" format="fasta"/> 115 <when input="out_type" value="fasta" format="fasta"/>
98 <when input="out_type" value="featureXML" format="featurexml"/> 116 <when input="out_type" value="featureXML" format="featurexml"/>
99 <when input="out_type" value="mzML" format="mzml"/> 117 <when input="out_type" value="mzML" format="mzml"/>
100 <when input="out_type" value="traML" format="traml"/> 118 <when input="out_type" value="traML" format="traml"/>
101 </change_format> 119 </change_format>
102 </data> 120 </data>
103 <collection type="list" name="rt_concat_trafo_out" label="${tool.name} on ${on_string}: rt_concat:trafo_out"> 121 <collection type="list" name="rt_concat_trafo_out" label="${tool.name} on ${on_string}: rt_concat:trafo_out">
104 <discover_datasets directory="rt_concat.trafo_out" format="trafoxml" pattern="__name__"/> 122 <discover_datasets directory="rt_concat_trafo_out" recurse="true" format="trafoxml" pattern="__name__"/>
105 <filter>OPTIONAL_OUTPUTS is not None and "trafo_out_FLAG" in OPTIONAL_OUTPUTS</filter> 123 <filter>OPTIONAL_OUTPUTS is not None and "trafo_out_FLAG" in OPTIONAL_OUTPUTS</filter>
106 </collection> 124 </collection>
107 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 125 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
108 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 126 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
109 </data> 127 </data>
110 </outputs> 128 </outputs>
111 <tests> 129 <tests><!-- TOPP_FileMerger_2 -->
112 <expand macro="autotest_FileMerger"/> 130 <test expect_num_outputs="2">
113 <expand macro="manutest_FileMerger"/> 131 <section name="adv_opts">
132 <param name="force" value="false"/>
133 <param name="test" value="true"/>
134 </section>
135 <conditional name="in_cond">
136 <param name="in" value="FileMerger_2_input1.dta,FileMerger_2_input2.dta" ftype="dta"/>
137 </conditional>
138 <param name="out_type" value="mzML"/>
139 <output name="out" file="FileMerger_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
140 <param name="annotate_file_origin" value="false"/>
141 <param name="append_method" value="append_rows"/>
142 <section name="rt_concat">
143 <param name="gap" value="0.0"/>
144 </section>
145 <section name="raw">
146 <param name="rt_auto" value="false"/>
147 <param name="rt_custom" value="5.0 10.0"/>
148 <param name="rt_filename" value="false"/>
149 <param name="ms_level" value="0"/>
150 </section>
151 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
152 <output name="ctd_out" ftype="xml">
153 <assert_contents>
154 <is_valid_xml/>
155 </assert_contents>
156 </output>
157 </test>
158 <!-- TOPP_FileMerger_3 -->
159 <test expect_num_outputs="2">
160 <section name="adv_opts">
161 <param name="force" value="false"/>
162 <param name="test" value="true"/>
163 </section>
164 <conditional name="in_cond">
165 <param name="in" value="FileMerger_3_input1.dta,FileMerger_3_input2.dta" ftype="dta"/>
166 </conditional>
167 <param name="out_type" value="mzML"/>
168 <output name="out" file="FileMerger_3_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
169 <param name="annotate_file_origin" value="false"/>
170 <param name="append_method" value="append_rows"/>
171 <section name="rt_concat">
172 <param name="gap" value="0.0"/>
173 </section>
174 <section name="raw">
175 <param name="rt_auto" value="true"/>
176 <param name="rt_custom" value=""/>
177 <param name="rt_filename" value="false"/>
178 <param name="ms_level" value="0"/>
179 </section>
180 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
181 <output name="ctd_out" ftype="xml">
182 <assert_contents>
183 <is_valid_xml/>
184 </assert_contents>
185 </output>
186 </test>
187 <!-- TOPP_FileMerger_4 -->
188 <test expect_num_outputs="2">
189 <section name="adv_opts">
190 <param name="force" value="false"/>
191 <param name="test" value="true"/>
192 </section>
193 <conditional name="in_cond">
194 <param name="in" value="FileMerger_4_input1.dta2d,FileMerger_4_input2.dta2d" ftype="dta2d"/>
195 </conditional>
196 <param name="out_type" value="mzML"/>
197 <output name="out" file="FileMerger_4_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
198 <param name="annotate_file_origin" value="false"/>
199 <param name="append_method" value="append_rows"/>
200 <section name="rt_concat">
201 <param name="gap" value="0.0"/>
202 </section>
203 <section name="raw">
204 <param name="rt_auto" value="false"/>
205 <param name="rt_custom" value=""/>
206 <param name="rt_filename" value="false"/>
207 <param name="ms_level" value="0"/>
208 </section>
209 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
210 <output name="ctd_out" ftype="xml">
211 <assert_contents>
212 <is_valid_xml/>
213 </assert_contents>
214 </output>
215 </test>
216 <!-- TOPP_FileMerger_5 -->
217 <test expect_num_outputs="2">
218 <section name="adv_opts">
219 <param name="force" value="false"/>
220 <param name="test" value="true"/>
221 </section>
222 <conditional name="in_cond">
223 <param name="in" value="FileMerger_5_input_rt1023.331.dta,FileMerger_5_input_rt2044.334.dta,FileMerger_5_input_rt889.32.dta" ftype="dta"/>
224 </conditional>
225 <param name="out_type" value="mzML"/>
226 <output name="out" file="FileMerger_5_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
227 <param name="annotate_file_origin" value="false"/>
228 <param name="append_method" value="append_rows"/>
229 <section name="rt_concat">
230 <param name="gap" value="0.0"/>
231 </section>
232 <section name="raw">
233 <param name="rt_auto" value="false"/>
234 <param name="rt_custom" value=""/>
235 <param name="rt_filename" value="true"/>
236 <param name="ms_level" value="2"/>
237 </section>
238 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
239 <output name="ctd_out" ftype="xml">
240 <assert_contents>
241 <is_valid_xml/>
242 </assert_contents>
243 </output>
244 </test>
245 <!-- TOPP_FileMerger_6 -->
246 <test expect_num_outputs="2">
247 <section name="adv_opts">
248 <param name="force" value="false"/>
249 <param name="test" value="true"/>
250 </section>
251 <conditional name="in_cond">
252 <param name="in" value="FileMerger_6_input1.mzML,FileMerger_6_input2.mzML"/>
253 </conditional>
254 <param name="out_type" value="mzML"/>
255 <output name="out" file="FileMerger_6_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
256 <param name="annotate_file_origin" value="false"/>
257 <param name="append_method" value="append_rows"/>
258 <section name="rt_concat">
259 <param name="gap" value="0.0"/>
260 </section>
261 <section name="raw">
262 <param name="rt_auto" value="false"/>
263 <param name="rt_custom" value=""/>
264 <param name="rt_filename" value="false"/>
265 <param name="ms_level" value="0"/>
266 </section>
267 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
268 <output name="ctd_out" ftype="xml">
269 <assert_contents>
270 <is_valid_xml/>
271 </assert_contents>
272 </output>
273 </test>
274 <!-- TOPP_FileMerger_7 -->
275 <test expect_num_outputs="2">
276 <section name="adv_opts">
277 <param name="force" value="false"/>
278 <param name="test" value="true"/>
279 </section>
280 <conditional name="in_cond">
281 <param name="in" value="FileMerger_7_input1.featureXML,FileMerger_7_input2.featureXML"/>
282 </conditional>
283 <param name="out_type" value="featureXML"/>
284 <output name="out" file="FileMerger_7_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
285 <param name="annotate_file_origin" value="false"/>
286 <param name="append_method" value="append_rows"/>
287 <section name="rt_concat">
288 <param name="gap" value="0.0"/>
289 </section>
290 <section name="raw">
291 <param name="rt_auto" value="false"/>
292 <param name="rt_custom" value=""/>
293 <param name="rt_filename" value="false"/>
294 <param name="ms_level" value="0"/>
295 </section>
296 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
297 <output name="ctd_out" ftype="xml">
298 <assert_contents>
299 <is_valid_xml/>
300 </assert_contents>
301 </output>
302 </test>
303 <!-- TOPP_FileMerger_8 -->
304 <test expect_num_outputs="2">
305 <section name="adv_opts">
306 <param name="force" value="false"/>
307 <param name="test" value="true"/>
308 </section>
309 <conditional name="in_cond">
310 <param name="in" value="FileMerger_8_input1.consensusXML,FileMerger_8_input2.consensusXML"/>
311 </conditional>
312 <param name="out_type" value="consensusXML"/>
313 <output name="out" file="FileMerger_8_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
314 <param name="annotate_file_origin" value="false"/>
315 <param name="append_method" value="append_rows"/>
316 <section name="rt_concat">
317 <param name="gap" value="0.0"/>
318 </section>
319 <section name="raw">
320 <param name="rt_auto" value="false"/>
321 <param name="rt_custom" value=""/>
322 <param name="rt_filename" value="false"/>
323 <param name="ms_level" value="0"/>
324 </section>
325 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
326 <output name="ctd_out" ftype="xml">
327 <assert_contents>
328 <is_valid_xml/>
329 </assert_contents>
330 </output>
331 </test>
332 <!-- TOPP_FileMerger_9 -->
333 <test expect_num_outputs="2">
334 <section name="adv_opts">
335 <param name="force" value="false"/>
336 <param name="test" value="true"/>
337 </section>
338 <conditional name="in_cond">
339 <param name="in" value="FileMerger_9_input1.traML,FileMerger_9_input2.traML"/>
340 </conditional>
341 <param name="out_type" value="traML"/>
342 <output name="out" file="FileMerger_9_output.traML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
343 <param name="annotate_file_origin" value="false"/>
344 <param name="append_method" value="append_rows"/>
345 <section name="rt_concat">
346 <param name="gap" value="0.0"/>
347 </section>
348 <section name="raw">
349 <param name="rt_auto" value="false"/>
350 <param name="rt_custom" value=""/>
351 <param name="rt_filename" value="false"/>
352 <param name="ms_level" value="0"/>
353 </section>
354 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
355 <output name="ctd_out" ftype="xml">
356 <assert_contents>
357 <is_valid_xml/>
358 </assert_contents>
359 </output>
360 </test>
361 <!-- TOPP_FileMerger_10 -->
362 <test expect_num_outputs="3">
363 <section name="adv_opts">
364 <param name="force" value="false"/>
365 <param name="test" value="true"/>
366 </section>
367 <conditional name="in_cond">
368 <param name="in" value="FileMerger_6_input2.mzML,FileMerger_6_input2_2.mzML"/>
369 </conditional>
370 <param name="out_type" value="mzML"/>
371 <output name="out" file="FileMerger_10_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
372 <param name="annotate_file_origin" value="false"/>
373 <param name="append_method" value="append_rows"/>
374 <section name="rt_concat">
375 <param name="gap" value="10.0"/>
376 </section>
377 <output_collection name="rt_concat_trafo_out" count="2"/>
378 <section name="raw">
379 <param name="rt_auto" value="false"/>
380 <param name="rt_custom" value=""/>
381 <param name="rt_filename" value="false"/>
382 <param name="ms_level" value="0"/>
383 </section>
384 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/>
385 <output name="ctd_out" ftype="xml">
386 <assert_contents>
387 <is_valid_xml/>
388 </assert_contents>
389 </output>
390 </test>
391 <!-- TOPP_FileMerger_11 -->
392 <test expect_num_outputs="2">
393 <section name="adv_opts">
394 <param name="force" value="false"/>
395 <param name="test" value="true"/>
396 </section>
397 <conditional name="in_cond">
398 <param name="in" value="FileMerger_8_input1.consensusXML,FileMerger_8_input2.consensusXML"/>
399 </conditional>
400 <param name="out_type" value="consensusXML"/>
401 <output name="out" file="FileMerger_11_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
402 <param name="annotate_file_origin" value="false"/>
403 <param name="append_method" value="append_cols"/>
404 <section name="rt_concat">
405 <param name="gap" value="0.0"/>
406 </section>
407 <section name="raw">
408 <param name="rt_auto" value="false"/>
409 <param name="rt_custom" value=""/>
410 <param name="rt_filename" value="false"/>
411 <param name="ms_level" value="0"/>
412 </section>
413 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
414 <output name="ctd_out" ftype="xml">
415 <assert_contents>
416 <is_valid_xml/>
417 </assert_contents>
418 </output>
419 </test>
114 </tests> 420 </tests>
115 <help><![CDATA[Merges several MS files into one file. 421 <help><![CDATA[Merges several MS files into one file.
116 422
117 423
118 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_FileMerger.html]]></help> 424 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FileMerger.html]]></help>
119 <expand macro="references"/> 425 <expand macro="references"/>
120 </tool> 426 </tool>