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annotate pout2mzid.xml @ 6:653d724a6b99 draft default tip

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit de8cdf895c3c6113f301a119788701b2465a1b1b"
author galaxyp
date Thu, 13 Aug 2020 07:53:09 +0000
parents 23141085ca9e
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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23141085ca9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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1 <tool id="pout2mzid" name="Pout2mzid" version="0.3.03">
23141085ca9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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2 <description>add Percolator scoring to mzIdentML</description>
23141085ca9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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3 <requirements>
23141085ca9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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4 <requirement type="package" version="0.3.03">pout2mzid</requirement>
23141085ca9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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5 </requirements>
23141085ca9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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6 <stdio>
23141085ca9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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7 <exit_code range="1:"/>
23141085ca9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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8 </stdio>
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9 <command><![CDATA[
23141085ca9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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10 #if $mzid.multifile == "true"
23141085ca9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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11 mkdir p2m_mzid_in &&
23141085ca9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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12 #set digits = "0" + str(len(str(len($mzid.mzids.keys()))))
23141085ca9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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13 #for $i, $fn in $enumerate($mzid.mzids.keys())
23141085ca9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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14 #set prefixnum = format($i, $digits)
23141085ca9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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15 ln -s '$mzid.mzids[$fn]' 'p2m_mzid_in/$fn' &&
23141085ca9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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16 #end for
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17 ls p2m_mzid_in > infiles.txt &&
23141085ca9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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18 pout2mzid -p '$percout' -i p2m_mzid_in -f infiles.txt -o p2m_result -c _perco
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19
23141085ca9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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20 #else
23141085ca9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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21 ln -s '$mzid.mzidsingle' '$mzid.mzidsingle.display_name' &&
23141085ca9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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22 pout2mzid -p '$percout' -m '$mzid.mzidsingle.display_name'
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23 #end if
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24
23141085ca9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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25 #if $targetdecoy == "decoy"
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26 -d
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27 #end if
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28 #if $schemaskip
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29 -v
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30 #end if
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31 #if $mzid.multifile == "false"
23141085ca9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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32 > '$output_single'
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33 #end if
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34 ]]></command>
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35 <inputs>
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36 <param name="percout" type="data" format="percout" label="Percolator output"/>
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37 <conditional name="mzid">
23141085ca9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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38 <param name="multifile" type="select" display="radio" label="Multiple mzIdentML files?">
23141085ca9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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39 <option value="true">Yes</option>
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40 <option value="false" selected="true">No</option>
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41 </param>
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42 <when value="true">
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43 <param name="mzids" type="data_collection" collection_type="list" format="mzid" label="mzIdentML from MSGF+" />
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44 </when>
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45 <when value="false">
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46 <param name="mzidsingle" type="data" format="mzid" label="mzIdentML from MSGF+" />
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47 </when>
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48 </conditional>
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49 <param name="targetdecoy" type="select" display="radio" label="Which features to add to mzIdentML">
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50 <option value="target" selected="true">Target</option>
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51 <option value="decoy">Decoy</option>
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52 </param>
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53 <param name="schemaskip" type="boolean" label="Skip percolator schema validation?" />
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54 </inputs>
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55 <outputs>
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56 <data name="output_single" format="mzid">
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57 <filter>mzid['multifile'] == "false"</filter>
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58 </data>
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59 <collection name="output_multi" type="list">
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60 <filter>mzid['multifile'] == "true"</filter>
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61 <discover_datasets pattern="__designation__" ext="mzid" directory="p2m_result" />
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62 </collection>
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63
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64 </outputs>
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65 <tests>
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66 <test>
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67 <param name="percout" value="percolatorOut.xml" />
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68 <param name="mzid|multifile" value="false" />
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69 <param name="mzid|mzidsingle" value="dataset_2.mzid" />
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70 <param name="targetdecoy" value="target" />
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71 <param name="schemaskip" value="true" />
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72 <output name="output_single" value="target_ds2_withperco.mzid" />
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73 </test>
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74 <test>
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75 <param name="percout" value="percolatorOut.xml" />
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76 <param name="mzid|multifile" value="true" />
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77 <param name="mzid|mzids">
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78 <collection type="list">
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79 <element name="dataset_2.mzid" value="dataset_2.mzid" />
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80 <element name="dataset_3.mzid" value="dataset_2.mzid" />
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81 </collection>
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82 </param>
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83 <param name="targetdecoy" value="target" />
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84 <param name="schemaskip" value="true" />
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85 <output_collection name="output_multi" type="list">
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86 <element name="dataset_2_perco.mzid" value="target_ds2_withperco.mzid" />
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87 <element name="dataset_3_perco.mzid" value="target_ds3_withperco.mzid" />
23141085ca9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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88 </output_collection>
23141085ca9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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89 </test>
23141085ca9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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90 </tests>
23141085ca9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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91 <help>Pout2Mzid extracts statistics from a percolator input file, and writes them to the mzIdentML file(s) that have been used
23141085ca9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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92 to generate the percolator data. You may either pass multiple mzIdentML files in a list and one percolator file, or a single one.
23141085ca9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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93 </help>
23141085ca9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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94 </tool>