Mercurial > repos > galaxyp > openms_msstatsconverter
comparison PSMFeatureExtractor.patch @ 4:99c6cad61de6 draft default tip
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
| author | galaxyp |
|---|---|
| date | Sun, 13 Dec 2020 15:44:06 +0000 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| 3:64b10f17c9c0 | 4:99c6cad61de6 |
|---|---|
| 1 --- PSMFeatureExtractor.xml 2020-12-13 14:58:44.721454176 +0100 | |
| 2 +++ PSMFeatureExtractor.xml 2020-12-13 14:57:59.719941465 +0100 | |
| 3 @@ -17,7 +17,11 @@ | |
| 4 | |
| 5 ## Preprocessing | |
| 6 mkdir in && | |
| 7 +if $in | |
| 8 ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) } | |
| 9 +#else if $in_single | |
| 10 + ln -s '$in_single' 'in/${re.sub("[^\w\-_]", "_", $in_single.element_identifier)}.$gxy2omsext($in_single.ext)' && | |
| 11 +#end if | |
| 12 mkdir out && | |
| 13 | |
| 14 ## Main program call | |
| 15 @@ -27,7 +31,11 @@ | |
| 16 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && | |
| 17 @EXECUTABLE@ -ini @EXECUTABLE@.ctd | |
| 18 -in | |
| 19 +if $in | |
| 20 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} | |
| 21 +#else if $in_single | |
| 22 +'in/${re.sub("[^\w\-_]", "_", $in_single.element_identifier)}.$gxy2omsext($in_single.ext)' && | |
| 23 +#end if | |
| 24 -out | |
| 25 'out/output.${out_type}' | |
| 26 | |
| 27 @@ -41,7 +49,8 @@ | |
| 28 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> | |
| 29 </configfiles> | |
| 30 <inputs> | |
| 31 - <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)"/> | |
| 32 + <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)"/> | |
| 33 + <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)"/> | |
| 34 <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=""> | |
| 35 <option value="idXML">idxml</option> | |
| 36 <option value="mzid">mzid</option> |