Mercurial > repos > galaxyp > openms_metaboliteadductdecharger

comparison MetaboliteAdductDecharger.xml @ 6:ebc51eae71cd 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 20:39:58 +0000
parents 68e3317532cb
children 7e7e6a5b9c01
comparison
equal deleted inserted replaced
5:51203b9c8ef5 6:ebc51eae71cd
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($in.ext)' &&
21 mkdir out_cm && 21 #if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
22 mkdir out_cm &&
23 #end if
22 #if "out_fm_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 24 #if "out_fm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
23 mkdir out_fm && 25 mkdir out_fm &&
24 #end if 26 #end if
25 #if "outpairs_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 27 #if "outpairs_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
26 mkdir outpairs && 28 mkdir outpairs &&
32 @EXECUTABLE@ -write_ctd ./ && 34 @EXECUTABLE@ -write_ctd ./ &&
33 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && 35 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
34 @EXECUTABLE@ -ini @EXECUTABLE@.ctd 36 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
35 -in 37 -in
36 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' 38 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
37 -out_cm 39 #if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
38 'out_cm/output.${gxy2omsext("consensusxml")}' 40 -out_cm
41 'out_cm/output.${gxy2omsext("consensusxml")}'
42 #end if
39 #if "out_fm_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 43 #if "out_fm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
40 -out_fm 44 -out_fm
41 'out_fm/output.${gxy2omsext("featurexml")}' 45 'out_fm/output.${gxy2omsext("featurexml")}'
42 #end if 46 #end if
43 #if "outpairs_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 47 #if "outpairs_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
47 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 51 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
48 | tee '$stdout' 52 | tee '$stdout'
49 #end if 53 #end if
50 54
51 ## Postprocessing 55 ## Postprocessing
52 && mv 'out_cm/output.${gxy2omsext("consensusxml")}' '$out_cm' 56 #if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
57 && mv 'out_cm/output.${gxy2omsext("consensusxml")}' '$out_cm'
58 #end if
53 #if "out_fm_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 59 #if "out_fm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
54 && mv 'out_fm/output.${gxy2omsext("featurexml")}' '$out_fm' 60 && mv 'out_fm/output.${gxy2omsext("featurexml")}' '$out_fm'
55 #end if 61 #end if
56 #if "outpairs_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 62 #if "outpairs_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
57 && mv 'outpairs/output.${gxy2omsext("consensusxml")}' '$outpairs' 63 && mv 'outpairs/output.${gxy2omsext("consensusxml")}' '$outpairs'
103 </param> 109 </param>
104 <param name="verbose_level" argument="-algorithm:MetaboliteFeatureDeconvolution:verbose_level" type="integer" optional="true" min="0" max="3" value="0" label="Amount of debug information given during processing" help=""/> 110 <param name="verbose_level" argument="-algorithm:MetaboliteFeatureDeconvolution:verbose_level" type="integer" optional="true" min="0" max="3" value="0" label="Amount of debug information given during processing" help=""/>
105 </section> 111 </section>
106 </section> 112 </section>
107 <expand macro="adv_opts_macro"> 113 <expand macro="adv_opts_macro">
108 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> 114 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
109 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 115 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
110 <expand macro="list_string_san"/> 116 <expand macro="list_string_san"/>
111 </param> 117 </param>
112 </expand> 118 </expand>
113 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> 119 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
114 <option value="out_fm_FLAG">out_fm (Amount of debug information given during processing)</option> 120 <option value="out_cm_FLAG">out_cm (output consensus map)</option>
115 <option value="outpairs_FLAG">outpairs (Amount of debug information given during processing)</option> 121 <option value="out_fm_FLAG">out_fm (output feature map)</option>
122 <option value="outpairs_FLAG">outpairs (output file)</option>
116 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 123 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
117 </param> 124 </param>
118 </inputs> 125 </inputs>
119 <outputs> 126 <outputs>
120 <data name="out_cm" label="${tool.name} on ${on_string}: out_cm" format="consensusxml"/> 127 <data name="out_cm" label="${tool.name} on ${on_string}: out_cm" format="consensusxml">
128 <filter>OPTIONAL_OUTPUTS is not None and "out_cm_FLAG" in OPTIONAL_OUTPUTS</filter>
129 </data>
121 <data name="out_fm" label="${tool.name} on ${on_string}: out_fm" format="featurexml"> 130 <data name="out_fm" label="${tool.name} on ${on_string}: out_fm" format="featurexml">
122 <filter>OPTIONAL_OUTPUTS is not None and "out_fm_FLAG" in OPTIONAL_OUTPUTS</filter> 131 <filter>OPTIONAL_OUTPUTS is not None and "out_fm_FLAG" in OPTIONAL_OUTPUTS</filter>
123 </data> 132 </data>
124 <data name="outpairs" label="${tool.name} on ${on_string}: outpairs" format="consensusxml"> 133 <data name="outpairs" label="${tool.name} on ${on_string}: outpairs" format="consensusxml">
125 <filter>OPTIONAL_OUTPUTS is not None and "outpairs_FLAG" in OPTIONAL_OUTPUTS</filter> 134 <filter>OPTIONAL_OUTPUTS is not None and "outpairs_FLAG" in OPTIONAL_OUTPUTS</filter>
135 </data>
136 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
137 <filter>OPTIONAL_OUTPUTS is None</filter>
126 </data> 138 </data>
127 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 139 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
128 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 140 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
129 </data> 141 </data>
130 </outputs> 142 </outputs>
133 <expand macro="manutest_MetaboliteAdductDecharger"/> 145 <expand macro="manutest_MetaboliteAdductDecharger"/>
134 </tests> 146 </tests>
135 <help><![CDATA[Decharges and merges different feature charge variants of the same metabolite. 147 <help><![CDATA[Decharges and merges different feature charge variants of the same metabolite.
136 148
137 149
138 For more information, visit http://www.openms.de/documentation/UTILS_MetaboliteAdductDecharger.html]]></help> 150 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_MetaboliteAdductDecharger.html]]></help>
139 <expand macro="references"/> 151 <expand macro="references"/>
140 </tool> 152 </tool>