Mercurial > repos > jjohnson > pecan
comparison pecan2blib.xml @ 0:69274b068a48 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pecan commit 21855dec2949420d3bccfd6c9912578e9aacecf0
| author | jjohnson |
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| date | Fri, 25 Aug 2017 14:25:21 -0400 |
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| -1:000000000000 | 0:69274b068a48 |
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| 1 <tool id="pecan2blib" name="pecan2blib" version="0.1.0"> | |
| 2 <description>Convert PECAN results after percolator (.peptides) into spectral library (.blib)</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="0.9.9.3">pecan</requirement> | |
| 5 </requirements> | |
| 6 <stdio> | |
| 7 <exit_code range="1:" /> | |
| 8 </stdio> | |
| 9 <command><![CDATA[ | |
| 10 pecan2blib -o pecan_spectral_lib --ionTypes=$ionTypes -q $qValue $toMinutes | |
| 11 #if $extension and str($extension): | |
| 12 -e $extension | |
| 13 #end if | |
| 14 -l $percolator_results | |
| 15 && cat "pecan_spectral_lib"*.blib > '$spectral_lib' | |
| 16 ]]></command> | |
| 17 <inputs> | |
| 18 <param name="percolator_results" type="data" format="percout" multiple="true" label="percolator results"/> | |
| 19 <param name="ionTypes" type="select" label="Fragment ion types" help="suggested HCD: y, reCID: by"> | |
| 20 <option value="by">by</option> | |
| 21 <option value="y">y</option> | |
| 22 <option value="b">b</option> | |
| 23 </param> | |
| 24 <param name="qValue" type="float" value="0.01" label="q-value threshold"/> | |
| 25 <param name="toMinutes" type="boolean" truevalue="--toMinutes" falsevalue="" checked="false" | |
| 26 label="Convert retention time from seconds to minutes" | |
| 27 help="Only needed when mzML files recorded retention time in seconds"/> | |
| 28 <param name="extension" type="text" value="" optional="true" label="raw file extension for skyline" | |
| 29 help="original file extension (e.g. raw/wiff) for proper Skyline views"/> | |
| 30 | |
| 31 </inputs> | |
| 32 <outputs> | |
| 33 <data name="spectral_lib" format="sqlite" /> | |
| 34 </outputs> | |
| 35 <help><![CDATA[ | |
| 36 TODO: Fill in help. | |
| 37 ]]></help> | |
| 38 </tool> |