Mercurial > repos > pieterlukasse > prims_proteomics
annotate napq.xml @ 24:b35431dc4879
workaround
| author | pieter.lukasse@wur.nl |
|---|---|
| date | Mon, 26 Jan 2015 07:26:53 +0100 |
| parents | b1f68fcb7d99 |
| children | 17acaf080e76 |
| rev | line source |
|---|---|
|
17
40ec8770780d
* Added support for pepxml (and more specifically for
pieter.lukasse@wur.nl
parents:
16
diff
changeset
|
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 $htmlReportFile.files_path | |
| 19 </command> | |
| 20 | |
| 21 <inputs> | |
| 22 | |
| 16 | 23 <repeat name="identificationFileList" title="Peptide identification files" help="Set of MS/MS peptide identification files that have some form of quantification data coupled to it (e.g. MSE identifications&intensity)."> |
| 0 | 24 <param name="identificationsFile" type="data" format="apml,mzidentml,prims.fileset.zip" label="Identifications file (APML or MZIDENTML or MZIDENTML fileSet)" /> |
| 25 </repeat> | |
| 26 | |
| 27 <param name="namingConventionCodesForSamples" type="text" size="100" value="" | |
| 28 label="Part of run/file name that identifies the sample" | |
| 29 help="Add the CSV list of codes that occur in the file names | |
| 19 | 30 and that stand for a sample code. E.g. '_S1,_S2,_S3,etc.' "> <!-- could do regular expressions as well but this would be hard for biologists, e.g. _F\d\b --> |
| 31 <sanitizer> | |
| 32 <!-- adding more characters to the set of "valid" ones: --> | |
| 33 <valid> | |
| 23 | 34 <add preset="string.printable"/> |
| 19 | 35 <add value="#"/> |
| 36 <add value="@"/> | |
| 37 <add value="$"/> | |
| 38 <add value="%"/> | |
| 23 | 39 <add value="&"/> |
| 19 | 40 <add value="*"/> |
| 41 <add value="["/> | |
| 42 <add value="]"/> | |
| 43 <add value="|"/> | |
| 44 <add value="{"/> | |
| 45 <add value="}"/> | |
| 46 </valid> | |
| 47 </sanitizer> | |
| 48 </param> | |
| 0 | 49 |
| 50 <conditional name="is2D_LC_MS"> | |
| 51 <param name="fractions" type="boolean" truevalue="Yes" falsevalue="No" checked="false" | |
| 52 label="Data is from 2D LC-MS" | |
| 53 help="Data acquisition was done in multiple fractions."/> | |
| 54 <when value="Yes"> | |
| 55 <param name="namingConventionCodesForFractions" type="text" size="100" value="" | |
| 56 label="Part of run/file name that identifies the 2D LC-MS fraction" | |
| 57 help="Add the CSV list of codes that occur in the file names | |
| 58 and that stand for a fraction code. E.g. '_F1,_F2,_F3,etc.' Use this to avoid | |
| 19 | 59 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 --> |
| 60 <sanitizer> | |
| 61 <!-- adding more characters to the set of "valid" ones: --> | |
| 62 <valid> | |
| 63 <add preset="string.printable"/> | |
| 64 <add value="#"/> | |
| 65 <add value="@"/> | |
| 66 <add value="$"/> | |
| 67 <add value="%"/> | |
| 23 | 68 <add value="&"/> |
| 19 | 69 <add value="*"/> |
| 70 <add value="["/> | |
| 71 <add value="]"/> | |
| 72 <add value="|"/> | |
| 73 <add value="{"/> | |
| 74 <add value="}"/> | |
| 75 </valid> | |
| 76 </sanitizer> | |
| 77 </param> | |
| 78 | |
| 0 | 79 </when> |
| 6 | 80 <when value="No"> |
| 81 </when> | |
| 0 | 82 </conditional> |
| 83 | |
| 84 </inputs> | |
| 85 <configfiles> | |
| 86 <configfile name="identificationsConfigFile">## start comment | |
| 87 ## iterate over the selected files and store their names in the config file | |
| 88 #for $i, $s in enumerate( $identificationFileList ) | |
| 16 | 89 ${s.identificationsFile} |
| 0 | 90 ## also print out the datatype in the next line, based on previously configured datatype |
| 91 #if isinstance( $s.identificationsFile.datatype, $__app__.datatypes_registry.get_datatype_by_extension('apml').__class__): | |
| 92 apml | |
| 93 #else: | |
| 24 | 94 apml |
| 0 | 95 #end if |
| 96 #end for | |
| 97 ## end comment</configfile> | |
| 98 </configfiles> | |
| 99 <outputs> | |
| 100 <data name="outputApml" format="apml" label="${tool.name} on ${on_string}: peptide quantifications (APML)"/> | |
| 101 <data name="outputTsv" format="tabular" label="${tool.name} on ${on_string}: peptide quantifications (TSV)"/> | |
| 102 <!-- in tsv we can have cols like: pep, avg_m/z, avg rt, m/z window, rt window, i_s1, i_s2, ...--> | |
| 103 <data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - HTML report"/> | |
| 104 <!-- here we show the samples extracted and the files used to 'build up' each sample --> | |
| 105 </outputs> | |
| 106 <tests> | |
| 107 </tests> | |
| 108 <help> | |
| 109 | |
| 110 .. class:: infomark | |
| 111 | |
| 112 This tool takes in multiple peptide identification result files that have peptide identifications | |
| 113 coupled to some quantification (e.g. precursor intensity information or for example data coming | |
| 114 from MS^E acquisition where peptide identification and quantification are done in the same run and reported together). | |
| 115 Then, based on the given experiment design parameters (i.e. how the result files related back to | |
| 116 replicate runs and samples), it produces a new file in which the peptides are reported with | |
| 117 their calculated quantifications at the sample level. | |
| 118 | |
| 119 The figure below explains this: | |
| 120 | |
| 121 .. image:: $PATH_TO_IMAGES/napq_overview.png | |
| 122 | |
| 4 | 123 . |
| 0 | 124 |
| 125 | |
| 126 | |
| 127 | |
| 128 </help> | |
| 129 </tool> |