Mercurial > repos > galaxyp > openms_openswathfilesplitter
comparison OpenSwathFileSplitter.xml @ 10:2d856cba192b draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
author | galaxyp |
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date | Thu, 24 Sep 2020 12:17:48 +0000 |
parents | 0ab17cc5cf0c |
children | 40abe25cb21c |
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9:0ab17cc5cf0c | 10:2d856cba192b |
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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 ${on_string}: outputDirectory"> |
70 <discover_datasets directory="adv_opts_cond.outputDirectory" format="mzml" pattern="_?(?P<designation>.*)\.[^.]*"/> | 70 <discover_datasets directory="outputDirectory" format="mzml" pattern="_?(?P<designation>.*)\.[^.]*"/> |
71 </collection> | 71 </collection> |
72 <data name="out_qc" label="${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"> |