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"planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
author genouest
date Fri, 10 Dec 2021 10:25:44 +0000
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1 <tool id="PepMatch" name="PepMatch" version="2.0">
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2 <description>align PSTs on sequence and cluster hits</description>
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3 <requirements>
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4 <container type="docker">dockerprotim/peptimapper</container>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 LXRunPepMatch -D $D -t $t -T $T -d $d '$fastafile' '$tagsfile' &&
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8 mv '${tagsfile}'.\$(basename '${fastafile}').trans.${D}.hit ${hitsfile} &&
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9 mv '${tagsfile}'.\$(basename '${fastafile}').trans.${D}.hit.${t}.${T}.${d}.clust '${clustersfile}'
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10 ]]></command>
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11 <inputs>
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12 <param name="tagsfile" type="data" format="txt" label="PSTs file (Text)" help="Peptide sequence tags file generated by PepnovoTag" />
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13 <param name="fastafile" type="data" format="fasta" label="Chromosome file (Fasta)" help="Chromosome file" />
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14
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15 <param name="D" type="select" label="Mass tolerance" help="uma">
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16 <option value="0.5" selected="selected">0.5</option>
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17 <option value="0.25">0.25</option>
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18 <option value="0.025">0.025</option>
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19 <option value="0.0025">0.0025</option>
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20 <option value="0">0</option>
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21 </param>
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22
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23 <param name="t" type="select" label="Min. hits" help="Minimal hits number per cluster">
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24 <option value="2" selected="selected">2</option>
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25 <option value="3">3</option>
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26 <option value="4">4</option>
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27 </param>
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28
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29 <param name="T" type="select" label="Min. peptides" help="Minimal peptides number per cluster">
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30 <option value="2" selected="selected">2</option>
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31 <option value="3">3</option>
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32 <option value="4">4</option>
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33 </param>
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34
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35 <param name="d" type="select" label="Distance" help="Maximum distance between two hits to be clustered">
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36 <option value="500">500</option>
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37 <option value="1000">1000</option>
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38 <option value="2000">2000</option>
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39 <option value="5000" selected="selected">5000</option>
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40 <option value="10000">10000</option>
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41 <option value="15000">15000</option>
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42 <option value="20000">20000</option>
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43 <option value="50000">50000</option>
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44 <option value="80000">80000</option>
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45 <option value="100000">100000</option>
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46 <option value="120000">120000</option>
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47 </param>
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48 </inputs>
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49
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50 <outputs>
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51 <data format="txt" name="hitsfile" label="${tagsfile.element_identifier}.${fastafile.element_identifier}.${D}.hit"/>
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52 <data format="txt" name="clustersfile" label="${tagsfile.element_identifier}.${fastafile.element_identifier}.${D}.hit.${t}.${T}.${d}.clust"/>
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53 </outputs>
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54 <tests>
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55 <test>
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56 <param name="tagsfile" value="pepnovotag/sample_02.mgf.3.5.tag"/>
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57 <param name="fastafile" value="pepmatch/Nuc_genome_small.fasta"/>
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58 <param name="D" value="0.5"/>
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59 <param name="t" value="2"/>
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60 <param name="T" value="2"/>
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61 <param name="d" value="5000"/>
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62 <output name="hitsfile" file="pepmatch/sample_02.mgf.3.5.tag.Nuc_genome_small.fasta.0.5.hit"/>
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63 <output name="clustersfile" file="pepmatch/sample_02.mgf.3.5.tag.Nuc_genome_small.fasta.0.5.hit.2.2.5000.clust"/>
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64 </test>
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65 </tests>
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66 <help><![CDATA[
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67 **Description**
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68
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69 PepMatch : run LXRunPepMatch from peptimapper docker. It translates chromosome sequence into six-frame translations, aligns PSTs and clusters hits. PepMatch outputs are a hits (or PST locations) file on the genome and a clusters (hits list per cluster) file. PepMatch clusters results are compatible with ClustQualify and ClustToGff to be annotated and analysed into a genome viewer.
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70
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71 It is based on the PepLine software developed by Ferro and collaborators
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72 Ferro, M., Tardif, M., Reguer, E., Cahuzac, R., Bruley, C., Vermat, T., Nugues, E., Vigouroux, M., Vandenbrouck, Y., Garin, J. & Viari, A. 2008. PepLine: a software pipeline for high-throughput direct mapping of tandem mass spectrometry data on genomic sequences. J Proteome Res 7:1873-83.
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73
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74 **Integrated by**
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75
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76 Laetitia Guillot Cloarec
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77 PROTIM Biogenouest proteomics Core Facility, Rennes
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78 May,2016
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79 ]]></help>
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80 <citations>
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81 <citation type="bibtex">
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82 @misc{renameTODO,
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83 author = {Protim Core facility},
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84 year = {2016},
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85 title = {PepMatch},
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86 url = {protim.eu},
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87 }
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88 </citation>
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89 </citations>
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90 </tool>