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annotate BlibFilter.xml @ 0:5a4801b7d106 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
author galaxyp
date Tue, 08 May 2018 14:16:45 -0400
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5a4801b7d106 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
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1 <tool id="BlibFilter" name="BlibFilter" version="@VERSION@.0">
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2 <description>remove redundant spectra from a library</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 BlibFilter
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9 --min-peaks $min_peaks
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10 --min-score $min_score
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11 --best-scoring $best_scoring
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12 '$redundant_blib' '$filtered_blib'
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13 #if $convert_to_ms2:
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14 && BlibToMs2 -f '$ms2' '$filtered_blib'
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15 #end if
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16 ]]></command>
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17 <inputs>
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18 <param name="redundant_blib" type="data" format="sqlite" label="Redundant Blib"/>
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19 <param name="min_peaks" type="integer" value="1" min="1"
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20 label="Only include spectra with at least this peaks"
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21 help="--min-peaks"/>
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22 <param name="min_score" type="float" value="0" min="0"
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23 label="Best spectrum must have at least this average score to be included."
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24 help="--min-score"/>
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25 <param name="best_scoring" type="boolean" truevalue="1" falsevalue="0" checked="false"
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26 label="Use best scoring"/>
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27 <param name="convert_to_ms2" type="boolean" truevalue="yes" falsevalue="no" label="Output a MS2"/>
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28 </inputs>
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29 <outputs>
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30 <data name="filtered_blib" format="sqlite" label="Filtered Blib"/>
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31 <data name="ms2" format="ms2" label="MS2 from ${on_string}" from_work_dir="spectra.ms2" >
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32 <filter>convert_to_ms2 == True</filter>
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33 </data>
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34 </outputs>
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35 <tests>
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36 <test>
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37 <param name="redundant_blib" ftype="sqlite" value="msgf.blib"/>
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38 <param name="convert_to_ms2" value="True"/>
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39 <output name="ms2">
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40 <assert_contents>
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41 <has_text_matching expression="D\tseq\tFKWNGTDTNSAAEK" />
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42 <has_text_matching expression="D\tmodified seq\tFKWNGTDTNSAAEK" />
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43 </assert_contents>
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44 </output>
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45 </test>
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46 </tests>
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47 <help><![CDATA[
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48 BiblioSpec_ is a suite of software tools for creating and searching MS/MS peptide spectrum libraries.
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49
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50 BlibFilter_ creates a library of peptide MS/MS spectra from a variety of different database search results.
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51
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52 ::
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53
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54 Usage: BlibFilter [options] <redundant-library> <filtered-library>
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55
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56 Options:
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57 -m [ --memory-cache ] arg (=250) SQLite memory cache size in Megs. Default
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58 250M.
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59 -n [ --min-peaks ] arg (=1) Only include spectra with at least this
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60 many peaks. Default 1.
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61 -s [ --min-score ] arg (=0) Best spectrum must have at least this
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62 average score to be included. Default 0.
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63 -b [ --best-scoring ] arg (=0) Description of option. Default false.
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64 -p [ --parameter-file ] arg File containing search parameters. Command
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65 line values override file values.
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66 -v [ --verbosity ] arg (=status) Control the level of output to stderr.
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67 (silent, error, status, warn, debug,
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68 detail, all) Default status.
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69 -h [ --help ] Print help message.
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70
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71
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72 .. _BlibFilter: https://skyline.ms/wiki/home/software/BiblioSpec/page.view?name=BlibFilter
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73 .. _BiblioSpec: https://skyline.ms/project/home/software/BiblioSpec/begin.view?
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74 ]]></help>
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75 <expand macro="citations" />
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76 </tool>