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comparison TextExporter.xml @ 11:1c596fdaf34a draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 20:09:21 +0000
parents 27aeff17fd2e
children 1b03536aa3c9
comparison
equal deleted inserted replaced
10:d063e2fe4ba4 11:1c596fdaf34a
16 #import re 16 #import re
17 17
18 ## Preprocessing 18 ## Preprocessing
19 mkdir in && 19 mkdir in &&
20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && 20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
21 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 21 mkdir out &&
22 mkdir out &&
23 #end if
24 #if "centroids_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 22 #if "centroids_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
25 mkdir consensus_centroids && 23 mkdir consensus_centroids &&
26 #end if 24 #end if
27 #if "elements_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 25 #if "elements_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
28 mkdir consensus_elements && 26 mkdir consensus_elements &&
37 @EXECUTABLE@ -write_ctd ./ && 35 @EXECUTABLE@ -write_ctd ./ &&
38 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && 36 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
39 @EXECUTABLE@ -ini @EXECUTABLE@.ctd 37 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
40 -in 38 -in
41 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' 39 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
42 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 40 -out
43 -out 41 'out/output.${gxy2omsext("tabular")}'
44 'out/output.${gxy2omsext("csv")}'
45 #end if
46 #if "centroids_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 42 #if "centroids_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
47 -consensus:centroids 43 -consensus:centroids
48 'consensus_centroids/output.${gxy2omsext("csv")}' 44 'consensus_centroids/output.${gxy2omsext("csv")}'
49 #end if 45 #end if
50 #if "elements_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 46 #if "elements_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
58 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 54 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
59 | tee '$stdout' 55 | tee '$stdout'
60 #end if 56 #end if
61 57
62 ## Postprocessing 58 ## Postprocessing
63 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 59 && mv 'out/output.${gxy2omsext("tabular")}' '$out'
64 && mv 'out/output.${gxy2omsext("csv")}' '$out'
65 #end if
66 #if "centroids_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 60 #if "centroids_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
67 && mv 'consensus_centroids/output.${gxy2omsext("csv")}' '$consensus_centroids' 61 && mv 'consensus_centroids/output.${gxy2omsext("csv")}' '$consensus_centroids'
68 #end if 62 #end if
69 #if "elements_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 63 #if "elements_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
70 && mv 'consensus_elements/output.${gxy2omsext("csv")}' '$consensus_elements' 64 && mv 'consensus_elements/output.${gxy2omsext("csv")}' '$consensus_elements'
120 </param> 114 </param>
121 <param name="sort_by_maps" argument="-consensus:sort_by_maps" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply a stable sort by the covered maps, lexicographically" help=""/> 115 <param name="sort_by_maps" argument="-consensus:sort_by_maps" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply a stable sort by the covered maps, lexicographically" help=""/>
122 <param name="sort_by_size" argument="-consensus:sort_by_size" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply a stable sort by decreasing size" help="(i.e., the number of elements)"/> 116 <param name="sort_by_size" argument="-consensus:sort_by_size" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply a stable sort by decreasing size" help="(i.e., the number of elements)"/>
123 </section> 117 </section>
124 <expand macro="adv_opts_macro"> 118 <expand macro="adv_opts_macro">
125 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> 119 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
126 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 120 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
127 <expand macro="list_string_san"/> 121 <expand macro="list_string_san"/>
128 </param> 122 </param>
129 </expand> 123 </expand>
130 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="false"> 124 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
131 <option value="out_FLAG">out (Apply a stable sort by decreasing size)</option> 125 <option value="centroids_FLAG">centroids (Output file for centroids of consensus features)</option>
132 <option value="centroids_FLAG">centroids (Apply a stable sort by decreasing size)</option> 126 <option value="elements_FLAG">elements (Output file for elements of consensus features)</option>
133 <option value="elements_FLAG">elements (Apply a stable sort by decreasing size)</option> 127 <option value="features_FLAG">features (Output file for consensus features and contained elements from all maps (writes 'nan's if elements are missing))</option>
134 <option value="features_FLAG">features (Apply a stable sort by decreasing size)</option>
135 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 128 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
136 </param> 129 </param>
137 </inputs> 130 </inputs>
138 <outputs> 131 <outputs>
139 <data name="out" label="${tool.name} on ${on_string}: out" format="csv"> 132 <data name="out" label="${tool.name} on ${on_string}: out" format="tabular"/>
140 <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
141 </data>
142 <data name="consensus_centroids" label="${tool.name} on ${on_string}: consensus:centroids" format="csv"> 133 <data name="consensus_centroids" label="${tool.name} on ${on_string}: consensus:centroids" format="csv">
143 <filter>OPTIONAL_OUTPUTS is not None and "centroids_FLAG" in OPTIONAL_OUTPUTS</filter> 134 <filter>OPTIONAL_OUTPUTS is not None and "centroids_FLAG" in OPTIONAL_OUTPUTS</filter>
144 </data> 135 </data>
145 <data name="consensus_elements" label="${tool.name} on ${on_string}: consensus:elements" format="csv"> 136 <data name="consensus_elements" label="${tool.name} on ${on_string}: consensus:elements" format="csv">
146 <filter>OPTIONAL_OUTPUTS is not None and "elements_FLAG" in OPTIONAL_OUTPUTS</filter> 137 <filter>OPTIONAL_OUTPUTS is not None and "elements_FLAG" in OPTIONAL_OUTPUTS</filter>
147 </data> 138 </data>
148 <data name="consensus_features" label="${tool.name} on ${on_string}: consensus:features" format="csv"> 139 <data name="consensus_features" label="${tool.name} on ${on_string}: consensus:features" format="csv">
149 <filter>OPTIONAL_OUTPUTS is not None and "features_FLAG" in OPTIONAL_OUTPUTS</filter> 140 <filter>OPTIONAL_OUTPUTS is not None and "features_FLAG" in OPTIONAL_OUTPUTS</filter>
150 </data>
151 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
152 <filter>OPTIONAL_OUTPUTS is None</filter>
153 </data> 141 </data>
154 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 142 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
155 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 143 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
156 </data> 144 </data>
157 </outputs> 145 </outputs>
160 <expand macro="manutest_TextExporter"/> 148 <expand macro="manutest_TextExporter"/>
161 </tests> 149 </tests>
162 <help><![CDATA[Exports various XML formats to a text file. 150 <help><![CDATA[Exports various XML formats to a text file.
163 151
164 152
165 For more information, visit http://www.openms.de/documentation/TOPP_TextExporter.html]]></help> 153 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_TextExporter.html]]></help>
166 <expand macro="references"/> 154 <expand macro="references"/>
167 </tool> 155 </tool>