Mercurial > repos > galaxyp > openms_openswathfilesplitter

comparison OpenSwathFileSplitter.xml @ 15:3b7a5393b033 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f5fcdd54599554099fb00b1973cc91a766ad246a"
author galaxyp
date Wed, 23 Sep 2020 14:11:22 +0000
parents b45a21325d16
children a86191c455d9
comparison
equal deleted inserted replaced
14:b45a21325d16 15:3b7a5393b033
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($in.ext)' &&
21 mkdir adv_opts_cond.outputDirectory && 21 mkdir outputDirectory &&
22 #if "out_qc_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 22 #if "out_qc_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
23 mkdir out_qc && 23 mkdir out_qc &&
24 #end if 24 #end if
25 25
26 ## Main program call 26 ## Main program call
30 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && 30 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
31 @EXECUTABLE@ -ini @EXECUTABLE@.ctd 31 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
32 -in 32 -in
33 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' 33 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
34 -outputDirectory 34 -outputDirectory
35 adv_opts_cond.outputDirectory/ 35 outputDirectory/
36 #if "out_qc_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 36 #if "out_qc_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
37 -out_qc 37 -out_qc
38 'out_qc/output.${gxy2omsext("json")}' 38 'out_qc/output.${gxy2omsext("json")}'
39 #end if 39 #end if
40 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 40 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
64 <option value="out_qc_FLAG">out_qc (Enables the test mode (needed for internal use only))</option> 64 <option value="out_qc_FLAG">out_qc (Enables the test mode (needed for internal use only))</option>
65 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 65 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
66 </param> 66 </param>
67 </inputs> 67 </inputs>
68 <outputs> 68 <outputs>
69 <collection type="list" name="adv_opts_cond.outputDirectory" label="${tool.name} on ${on_string}: outputDirectory"> 69 <collection type="list" name="outputDirectory" label="${tool.name} on ${on_string}: outputDirectory">
70 <discover_datasets directory="adv_opts_cond.outputDirectory" format="mzml" pattern="_?(?P&lt;designation&gt;.*)\.[^.]*"/> 70 <discover_datasets directory="outputDirectory" format="mzml" pattern="_?(?P&lt;designation&gt;.*)\.[^.]*"/>
71 </collection> 71 </collection>
72 <data name="out_qc" label="${tool.name} on ${on_string}: out_qc" format="json"> 72 <data name="out_qc" label="${tool.name} on ${on_string}: out_qc" format="json">
73 <filter>OPTIONAL_OUTPUTS is not None and "out_qc_FLAG" in OPTIONAL_OUTPUTS</filter> 73 <filter>OPTIONAL_OUTPUTS is not None and "out_qc_FLAG" in OPTIONAL_OUTPUTS</filter>
74 </data> 74 </data>
75 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 75 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">