Mercurial > repos > pieterlukasse > prims_proteomics
annotate napq.xml @ 28:6107b74eeb11 default tip
improved documentation
| author | pieter.lukasse@wur.nl |
|---|---|
| date | Fri, 30 Jan 2015 14:53:10 +0100 |
| parents | 34c4e7e0f23b |
| children |
| rev | line source |
|---|---|
|
17
40ec8770780d
* Added support for pepxml (and more specifically for
pieter.lukasse@wur.nl
parents:
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diff
changeset
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1 <tool name="NapQ" id="napq" version="0.0.3"> |
| 5 | 2 <description>'no alignment' (alignment-free) peptide quantification</description> |
| 0 | 3 <!-- |
| 4 For remote debugging start you listener on port 8000 and use the following as command interpreter: | |
| 5 java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000 | |
| 6 ////////////////////////// | |
| 7 --> | |
| 8 <command interpreter="java -jar "> | |
| 9 NapQ.jar | |
| 10 -identificationsConfigFile $identificationsConfigFile | |
| 6 | 11 -namingConventionCodesForSamples "$namingConventionCodesForSamples" |
| 0 | 12 #if $is2D_LC_MS.fractions == True |
| 6 | 13 -namingConventionCodesForFractions "$is2D_LC_MS.namingConventionCodesForFractions" |
| 0 | 14 #end if |
| 15 -outputApml $outputApml | |
| 16 -outputTsv $outputTsv | |
| 17 -outReport $htmlReportFile | |
| 18 -outReportPicturesPath $htmlReportFile.files_path | |
| 19 </command> | |
| 20 | |
| 21 <inputs> | |
| 22 | |
| 28 | 23 <repeat name="identificationFileList" title="(Filtered) Peptide identification files" help="Set of MS/MS peptide identification files that have some form of |
| 24 quantification data coupled to it (e.g. MSE identifications&intensity). This list of peptide identifications is | |
| 25 preferably pre-processed by a tool (e.g. MsFilt) that filters out as much as possible false-positive peptide identifications."> | |
| 26 <param name="identificationsFile" type="data" format="apml,prims.fileset.zip" label="Identifications file ([APML] or [MZIDENTML fileSet])" | |
| 27 help="When using MsFilt, select MsFilt's APML output file here."/> | |
| 0 | 28 </repeat> |
| 29 | |
| 30 <param name="namingConventionCodesForSamples" type="text" size="100" value="" | |
| 31 label="Part of run/file name that identifies the sample" | |
| 32 help="Add the CSV list of codes that occur in the file names | |
| 19 | 33 and that stand for a sample code. E.g. '_S1,_S2,_S3,etc.' "> <!-- could do regular expressions as well but this would be hard for biologists, e.g. _F\d\b --> |
| 34 <sanitizer> | |
| 35 <!-- adding more characters to the set of "valid" ones: --> | |
| 36 <valid> | |
| 23 | 37 <add preset="string.printable"/> |
| 19 | 38 <add value="#"/> |
| 39 <add value="@"/> | |
| 40 <add value="$"/> | |
| 41 <add value="%"/> | |
| 23 | 42 <add value="&"/> |
| 19 | 43 <add value="*"/> |
| 44 <add value="["/> | |
| 45 <add value="]"/> | |
| 46 <add value="|"/> | |
| 47 <add value="{"/> | |
| 48 <add value="}"/> | |
| 49 </valid> | |
| 50 </sanitizer> | |
| 51 </param> | |
| 0 | 52 |
| 53 <conditional name="is2D_LC_MS"> | |
| 54 <param name="fractions" type="boolean" truevalue="Yes" falsevalue="No" checked="false" | |
| 55 label="Data is from 2D LC-MS" | |
| 56 help="Data acquisition was done in multiple fractions."/> | |
| 57 <when value="Yes"> | |
| 58 <param name="namingConventionCodesForFractions" type="text" size="100" value="" | |
| 59 label="Part of run/file name that identifies the 2D LC-MS fraction" | |
| 60 help="Add the CSV list of codes that occur in the file names | |
| 61 and that stand for a fraction code. E.g. '_F1,_F2,_F3,etc.' Use this to avoid | |
| 19 | 62 that each (fraction) file is seen as a separate run."> <!-- could do regular expressions as well but this would be hard for biologists, e.g. _F\d\b --> |
| 63 <sanitizer> | |
| 64 <!-- adding more characters to the set of "valid" ones: --> | |
| 65 <valid> | |
| 66 <add preset="string.printable"/> | |
| 67 <add value="#"/> | |
| 68 <add value="@"/> | |
| 69 <add value="$"/> | |
| 70 <add value="%"/> | |
| 23 | 71 <add value="&"/> |
| 19 | 72 <add value="*"/> |
| 73 <add value="["/> | |
| 74 <add value="]"/> | |
| 75 <add value="|"/> | |
| 76 <add value="{"/> | |
| 77 <add value="}"/> | |
| 78 </valid> | |
| 79 </sanitizer> | |
| 80 </param> | |
| 81 | |
| 0 | 82 </when> |
| 6 | 83 <when value="No"> |
| 84 </when> | |
| 0 | 85 </conditional> |
| 86 | |
| 87 </inputs> | |
| 88 <configfiles> | |
| 89 <configfile name="identificationsConfigFile">## start comment | |
| 27 | 90 ## iterate over the selected files and store their names in the config file |
| 91 #for $i, $s in enumerate( $identificationFileList ) | |
| 92 ${s.identificationsFile} | |
| 93 ## also print out the datatype in the next line, based on previously configured datatype | |
| 94 #if isinstance( $s.identificationsFile.datatype, $__app__.datatypes_registry.get_datatype_by_extension('apml').__class__): | |
| 95 apml | |
| 96 #else: | |
| 97 mzid | |
| 98 #end if | |
| 99 #end for | |
| 0 | 100 ## end comment</configfile> |
| 101 </configfiles> | |
| 102 <outputs> | |
| 103 <data name="outputApml" format="apml" label="${tool.name} on ${on_string}: peptide quantifications (APML)"/> | |
| 104 <data name="outputTsv" format="tabular" label="${tool.name} on ${on_string}: peptide quantifications (TSV)"/> | |
| 105 <!-- in tsv we can have cols like: pep, avg_m/z, avg rt, m/z window, rt window, i_s1, i_s2, ...--> | |
| 106 <data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - HTML report"/> | |
| 107 <!-- here we show the samples extracted and the files used to 'build up' each sample --> | |
| 108 </outputs> | |
| 109 <tests> | |
| 110 </tests> | |
| 111 <help> | |
| 112 | |
| 113 .. class:: infomark | |
| 114 | |
| 115 This tool takes in multiple peptide identification result files that have peptide identifications | |
| 116 coupled to some quantification (e.g. precursor intensity information or for example data coming | |
| 117 from MS^E acquisition where peptide identification and quantification are done in the same run and reported together). | |
| 118 Then, based on the given experiment design parameters (i.e. how the result files related back to | |
| 119 replicate runs and samples), it produces a new file in which the peptides are reported with | |
| 120 their calculated quantifications at the sample level. | |
| 121 | |
| 122 The figure below explains this: | |
| 123 | |
| 124 .. image:: $PATH_TO_IMAGES/napq_overview.png | |
| 125 | |
| 4 | 126 . |
| 0 | 127 |
| 128 | |
| 129 | |
| 130 | |
| 131 </help> | |
| 132 </tool> |