Mercurial > repos > galaxyp > probamconvert
annotate probamconvert.xml @ 1:37369e255465 draft default tip
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author | galaxyp |
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date | Wed, 15 Mar 2017 09:43:14 -0400 |
parents | 0a77e0c00146 |
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0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
galaxyp
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1 <tool id="probamconvert" name="proBAMconvert" version="0.1.0"> |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
galaxyp
parents:
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2 <description>peptide identifications to proBAM or proBED</description> |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
galaxyp
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3 <requirements> |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
galaxyp
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4 <requirement type="package" version="1.0.0">probamconvert</requirement> |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
galaxyp
parents:
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5 </requirements> |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
galaxyp
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6 <stdio> |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
galaxyp
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7 <exit_code range="1:" /> |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
galaxyp
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8 </stdio> |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
galaxyp
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9 <command><![CDATA[ |
1 | 10 #set $psm_file = 'input.'+str($input.datatype.file_ext) |
0
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
galaxyp
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11 ln -s "$input" $psm_file; |
1 | 12 proBAM.py --name="converted" --file=$psm_file --conversion_mode=$conversion_mode |
0
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
galaxyp
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13 --database=$refsrc.database |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
galaxyp
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14 #if str($refsrc.database) == 'ENSEMBL': |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
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15 --species=$refsrc.species |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
galaxyp
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16 #if $refsrc.version: |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
galaxyp
parents:
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17 --version=$refsrc.version |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
galaxyp
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18 #end if |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
galaxyp
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19 #end if |
1 | 20 #if str($optional.decoy_annotation) != '': |
0
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
galaxyp
parents:
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21 --decoy_annotation='$optional.decoy_annotation' |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
galaxyp
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22 #end if |
1 | 23 --pre_picked_annotation=$optional.pre_picked_annotation |
0
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
galaxyp
parents:
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24 --mismatches=$optional.mismatches |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
galaxyp
parents:
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25 $optional.rm_duplicates |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
galaxyp
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26 $optional.three_frame_translation |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
galaxyp
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27 $optional.include_unmapped |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
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28 ]]></command> |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
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29 <inputs> |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
galaxyp
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30 <param name="input" type="data" format="mzid,pepxml" label="Peptide Indentification (mzIdentML or pepXML)"/> |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
galaxyp
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31 <param name="conversion_mode" type="select" label="Convert to:"> |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
galaxyp
parents:
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32 <option value="proBAM_psm">proBAM_psm</option> |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
galaxyp
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33 <option value="proBAM_peptide">proBAM_peptide</option> |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
galaxyp
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34 <option value="proBAM_peptide_mod">proBAM_peptide_mod</option> |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
galaxyp
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35 <option value="proBED">proBED</option> |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
galaxyp
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36 </param> |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
galaxyp
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37 <conditional name="refsrc"> |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
galaxyp
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38 <param name="database" type="select" label="Genomics reference database"> |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
galaxyp
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39 <option value="ENSEMBL">ENSEMBL</option> |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
galaxyp
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40 </param> |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
galaxyp
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41 <when value="ENSEMBL"> |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
galaxyp
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42 <param name="species" type="select" label="species"> |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
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43 <option value="homo_sapiens">homo_sapiens</option> |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
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44 <option value="mus_musculus">mus_musculus</option> |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
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45 <option value="danio_rerio">danio_rerio</option> |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
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46 <option value="drosophila_melanogaster">drosophila_melanogaster</option> |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
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47 </param> |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
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48 <param name="version" type="select" optional="true" label="ensembl release version"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
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49 <option value="87">87</option> |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
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50 <option value="86">86</option> |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
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51 <option value="85">85</option> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
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52 <option value="84">84</option> |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
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53 <option value="83">83</option> |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
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54 <option value="82">82</option> |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
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55 <option value="81">81</option> |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
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56 <option value="80">80</option> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
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57 <option value="79">79</option> |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
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58 <option value="78">78</option> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
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59 <option value="77">77</option> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
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60 <option value="76">76</option> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
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61 <option value="75">75</option> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
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62 <option value="74">74</option> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
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63 </param> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
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64 </when> |
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65 </conditional> |
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66 <section name="optional" expanded="false" title="Optional settings"> |
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67 <param name="decoy_annotation" type="text" value="" optional="true" label="decoy_annotation list" |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
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68 help="default is: REV_,DECOY_,_REVERSED,REVERSED_,_DECOY"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
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69 </param> |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
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70 <param name="mismatches" type="integer" value="0" min="0" max="5" label="allowed mismatches"/> |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
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71 <param name="rm_duplicates" type="boolean" truevalue="--rm_duplicates=Y" falsevalue="--rm_duplicates=N" checked="false" |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
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72 label="remove duplicates"/> |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
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73 <param name="three_frame_translation" type="boolean" truevalue="--three_frame_translation=Y" falsevalue="--three_frame_translation=N" checked="false" |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
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74 label="translate transcript sequences in 3 frames"/> |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
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75 <param name="include_unmapped" type="boolean" truevalue="--include_unmapped=Y" falsevalue="--include_unmapped=N" checked="false" |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
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76 label="unmapped psm should be included in the output"/> |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
galaxyp
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77 <param name="pre_picked_annotation" type="select" label="pre_picked_annotation"> |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
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78 <option value="all" selected="true">all</option> |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
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79 <option value="UniProt_ACC">UniProt_ACC</option> |
0a77e0c00146
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probamconvert commit 4ca7fcd1587c906db3314048a223d23b63b3f038-dirty
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80 <option value="UniProt_Entry">UniProt_Entry</option> |
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81 <option value="Ensembl_tr">Ensembl_tr</option> |
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82 <option value="Ensembl_pr">Ensembl_pr</option> |
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83 <option value="RefSeq">RefSeq</option> |
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84 <option value="First">First</option> |
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85 </param> |
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86 </section> |
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87 </inputs> |
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88 <outputs> |
1 | 89 <data name="output_bam" format="bam" label="${conversion_mode} ${input.display_name}.pro.bam" from_work_dir="converted.sorted.bam"> |
0
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90 <filter>conversion_mode != 'proBED'</filter> |
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91 </data> |
1 | 92 <data name="output_bed" format="bed" label="${conversion_mode} ${input.display_name}.pro.bed" from_work_dir="converted.pro.bed"> |
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93 <filter>conversion_mode == 'proBED'</filter> |
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94 </data> |
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95 </outputs> |
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96 <tests> |
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97 <test> |
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98 <param name="input" ftype="mzid" value="test.mzid"/> |
1 | 99 <param name="conversion_mode" value="proBED"/> |
0
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100 <param name="database" value="ENSEMBL"/> |
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101 <param name="species" value="homo_sapiens"/> |
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102 <param name="version" value="87"/> |
1 | 103 <output name="output_bed"> |
0
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104 <assert_contents> |
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105 <has_text text="Q7Z6Z7_0" /> |
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106 </assert_contents> |
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107 </output> |
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108 </test> |
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109 </tests> |
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110 <help><![CDATA[ |
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111 |
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112 proBAMconvert reads common peptide identification files and attempt to extract all relevant attributes from the files, including comments and enzyme information, and converts these attributes to comply with proBAM/proBED. Next, protein identifiers are extracted from the peptide identification files for every PSM. Different software tend to have their own rules to encode protein identifiers, proBAMconvert is designed to be compliant with a wide range of encodings. A crucial prerequisite of proBAMconvert is that the protein identifiers are among the identifiers that proBAM can recognize (see chapter 4). Once the protein identifiers have been retrieved, genomic information is extracted from Ensembl (transcript sequence, exon information, genomic coordinates,...). Next, using this genomic information the peptides are mapped onto the corresponding sequence reconstructed from Ensembl. Combining the genomic information from Ensembl and PSM information from the peptide identification file, the proBAM/proBED file is generated. proBAMconvert has various options, allowing to adopt proBAM/proBED output for a specific research question. |
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113 |
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114 ]]></help> |
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115 </tool> |