Mercurial > repos > jjohnson > spectrast

annotate spectrast_create.xml @ 3:7f02fc51bddf draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
author jjohnson
date Wed, 25 Jul 2018 10:58:17 -0400
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7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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1 <tool id="specrast_create" name="SpectraST Create" version="@VERSION@.0">
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2 <description>Spectral Library from Search Results</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 ## Need to symlink to data using name with extension that spectrast recognizes
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9 #import re
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10 ## pepxml datasets
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11 #set $input_files = []
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12 #for $px in $pepxml_files:
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13 #set $input_name = $re.sub('[.]?pep[.]?xml$','',$re.sub('[ ]','_',$input.display_name.split('/')[-1])) + '.pep.xml'
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14 #silent $input_files.append($input_name)
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15 ln -s -f '${px}' '${input_name}' &&
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16 #end for
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17 #set $input_names = ' '.join($input_files)
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18 python $__tool_directory__/link_scan_datasets.py
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19 #for spectrum_file in spectrum_files:
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20 -n '$spectrum_file.display_name' -f '$spectrum_file'
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21 #end for
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22 $input_names &&
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23 python $__tool_directory__/spectrast_params.py
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24 --mode=create
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25 #if $spectrastParams:
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26 '$spectrastParams'
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27 #end if
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28 '$spectrast_params' -o spectrast_create.params &&
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29 mkdir -p libdir &&
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30 spectrast -cFspectrast_create.params -cN'libdir/library' $input_names &&
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31 mkdir -p '$output.files_path' &&
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32 for i in library.splib library.sptxt library.spidx library.pepidx; do if [ -e outdir/${i} ]; then cp -p outdir/${i} '$output.files_path'; fi; done
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33 ]]></command>
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34 <configfiles>
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35 <configfile name="spectrast_params"><![CDATA[#slurp
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36 ]]>
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37 @LIBRARY_CREATE_OPTIONS@
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38 @LIBRARY_IMPORT_OPTIONS@
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39 </configfile>
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40 </configfiles>
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41 <inputs>
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42 <param name="pepxml_files" multiple="true" type="data" format="pepxml,peptideprophet_pepxml,interprophet_pepxml" label="PepXML Files to use in library generation" help=""/>
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43 <param name="spectrum_files" multiple="true" type="data" format="mzxml" label="Data files containing spectra referred to in pepxml files" help=""/>
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44 <param name="spectrastParams" type="data" format="txt" optional="true" label="SpectraST param file" help=""/>
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45 <expand macro="library_create_options"/>
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46 <expand macro="library_import_options"/>
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47 </inputs>
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48 <outputs>
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49 <data name="log" format="txt" label="spectrast.log" from_work_dir="spectrast.log"/>
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50 <data name="params" format="txt" label="spectrast_create.params" from_work_dir="spectrast_create.params"/>
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51 <expand macro="library_create_outputs"/>
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52 <data name="output" format="splib" label="libary.splib" />
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53 </outputs>
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54 <tests>
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55 <test>
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56 </test>
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57 </tests>
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58 <help><![CDATA[
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59 **Create Libraries from Sequence Search Results**
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60
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61 Note: As per TPP convention, the spectrum query must be named:
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62 <mzXML file name>.<start scan>.<end scan>.<charge>
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63 in the .pepXML file, so that SpectraST knows where to find the corresponding experimental spectrum. (If the .pepXML file is created with TPP tools, this should not be an issue.)
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64
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65 SpectraST can create a spectral library from a .pepXML file, which contains peptide identifications from a previous shotgun proteomics experiment. For this purpose, it is preferable that the .pepXML has been processed with PeptideProphet and/or iProphet, such that all the search hits have probabilities assigned. (iProphet probabilities are used over PeptideProphet ones if both are present.)
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66
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67 When importing from a .pepXML file, SpectraST scans through the .pepXML file for confident identifications, and attempts to extract the corresponding experimental spectra from .mzXML files.
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68 ]]></help>
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69 <expand macro="citations" />
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70 </tool>