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annotate pi_dbspec_align.xml @ 2:77ddaee887a8 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
author galaxyp
date Fri, 01 Sep 2017 03:14:54 -0400
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children 78afc81ab244
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77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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1 <tool id="pi_dbspec_align" name="Align DB fractions" version="0.3">
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2 <description>to resemble spectra fraction scheme</description>
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3 <requirements>
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4 <requirement type="package" version="3.6">python</requirement>
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5 <requirement type="package" version="1.62">biopython</requirement>
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6 </requirements>
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7 <command detect_errors="exit_code">
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8 <![CDATA[
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9 mkdir aligned_out &&
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10 python '$__tool_directory__/align_dbspec.py'
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11 --specnames $specnames
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12 --dbfiles
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13 #for $key in $databases.keys()
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14 '$databases[$key]'
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15 #end for
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16 --frspec '$frspec'
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17 --firstfr $firstfr
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18
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19 ]]>
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20 </command>
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21
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22 <inputs>
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23 <param name="specnames" type="data" format="text,tabular" label="Spectra files" />
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24 <param name="databases" type="data_collection" collection_type="list" format="fasta" label="Fractionated databases" />
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25 <param name="frspec" type="text" label="Regex to find fraction numbers in spectra file names" help="If spectra file is called myspectra_fr01b.mzML, use .*fr([0-9]+).*" >
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26 <sanitizer>
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27 <valid initial="string.printable">
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28 <remove value="&apos;"/>
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29 </valid>
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30 </sanitizer>
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31 </param>
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32 <param name="firstfr" type="integer" value="1" label="First fraction number in series" />
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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33 </inputs>
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34
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35 <outputs>
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36 <collection name="aligned_db" type="list" label="spectra-fraction-aligned DB">
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37 <discover_datasets pattern="__designation__" ext="fasta" directory="aligned_out" />
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38 </collection>
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39 </outputs>
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40 <tests>
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41 <test>
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42 <param name="specnames" value="specnames.txt" />
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43 <param name="databases">
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44 <collection type="list">
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45 <element name="fr1" value="target_splitdb_fr1.fasta" />
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46 <element name="fr2" value="target_splitdb_fr2.fasta" />
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47 <element name="fr3" value="target_splitdb_fr3.fasta" />
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48 <element name="fr4" value="decoy_splitdb_fr1.fasta" />
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49 <element name="fr5" value="decoy_splitdb_fr2.fasta" />
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50 <element name="fr6" value="decoy_splitdb_fr3.fasta" />
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51 <element name="fr7" value="decoy_splitdb_fr1.fasta" />
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52 <element name="fr8" value="decoy_splitdb_fr2.fasta" />
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53 <element name="fr9" value="decoy_splitdb_fr3.fasta" />
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54 </collection>
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55 </param>
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56 <param name="frspec" value=".*c_f([0-9]+).*" />
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57 <param name="firstfr" value="1" />
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58 <output_collection name="aligned_db" type="list">
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59 <element name="spec_f01.mzML" value="target_splitdb_fr1.fasta" />
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60 <element name="spec_f02.mzML" value="target_splitdb_fr2.fasta" />
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61 <element name="spec_f03.mzML" value="target_splitdb_fr3.fasta" />
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62 <element name="spec_f03b.mzML" value="target_splitdb_fr3.fasta" />
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63 <element name="spec_f09.mzML" value="merged_twice_decoy_fr1-3.fasta" compare="sim_size" />
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64 <element name="spec_f09b.mzML" value="merged_twice_decoy_fr1-3.fasta" compare="sim_size" />
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65 </output_collection>
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66 </test>
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67 </tests>
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68
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69 <help>
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70 Filters, pools and doubles fractionated databases with a set of identically fractionated spectra files which have been
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71 subjected to pooling and contain reruns.
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72 You may have fraction 1-10 in databases but spectra file fractions 4-7 have been pooled before loading to the MS,
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73 and spectra fraction 2 and 8 have been reran creating fractions 2 and 2a, and 8, 8a and 8b.
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74 This tool pools FASTA databases and duplicates them where needed to line up the databases to your spectra collections.
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75 </help>
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76
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77 </tool>