Mercurial > repos > galaxyp > openms_idposteriorerrorprobability
diff PSMFeatureExtractor.patch @ 21:cd7195c581e3 draft default tip
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 457cbb4095391627fa8a16e4cba146e69ed4e936-dirty"
| author | galaxyp |
|---|---|
| date | Sun, 13 Dec 2020 17:18:29 +0000 |
| parents | 592cce24581e |
| children |
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--- a/PSMFeatureExtractor.patch Sun Dec 13 15:20:20 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,36 +0,0 @@ ---- PSMFeatureExtractor.xml 2020-12-13 14:58:44.721454176 +0100 -+++ PSMFeatureExtractor.xml 2020-12-13 14:57:59.719941465 +0100 -@@ -17,7 +17,11 @@ - - ## Preprocessing - mkdir in && -+if $in - ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) } -+#else if $in_single -+ ln -s '$in_single' 'in/${re.sub("[^\w\-_]", "_", $in_single.element_identifier)}.$gxy2omsext($in_single.ext)' && -+#end if - mkdir out && - - ## Main program call -@@ -27,7 +31,11 @@ - python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && - @EXECUTABLE@ -ini @EXECUTABLE@.ctd - -in -+if $in - ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} -+#else if $in_single -+'in/${re.sub("[^\w\-_]", "_", $in_single.element_identifier)}.$gxy2omsext($in_single.ext)' && -+#end if - -out - 'out/output.${out_type}' - -@@ -41,7 +49,8 @@ - <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> - </configfiles> - <inputs> -- <param name="in" argument="-in" type="data" format="idxml,mzid" multiple="true" optional="false" label="Input file(s)" help=" select idxml,mzid data sets(s)"/> -+ <param name="in_single" argument="-in" type="data" format="idxml,mzid" multiple="false" optional="true" label="Input file for batch processing" help="(exactly one of -in or -in_list is required)"/> -+ <param name="in" argument="-in" type="data" format="idxml,mzid" multiple="true" optional="true" label="Input file(s) for joint processing" help="(exactly one of -in or -in_list is required)"/> - <param name="out_type" argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help=""> - <option value="idXML">idxml</option> - <option value="mzid">mzid</option>