Mercurial > repos > galaxyp > percolator
annotate nested_collection.xml @ 6:07107a686ce9 draft default tip
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit de8cdf895c3c6113f301a119788701b2465a1b1b"
author | galaxyp |
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date | Thu, 13 Aug 2020 03:53:33 -0400 |
parents | dce55ca21b98 |
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rev | line source |
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dce55ca21b98
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 4fd46e83045d78a4703c0ae7d0cfc396bdbc8e78
galaxyp
parents:
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1 <tool id="batched_set_list_creator" name="Create nested list" version="3.3"> |
1
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
diff
changeset
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2 <description>based on filenames and batch sizes</description> |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
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3 <stdio> |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
diff
changeset
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4 <exit_code range="1:" /> |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
diff
changeset
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5 </stdio> |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
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6 <command>python $__tool_directory__/nested_collection.py |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
diff
changeset
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7 #if $batchsize |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
diff
changeset
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8 --batchsize $batchsize |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
diff
changeset
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9 #end if |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
diff
changeset
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10 #if len($poolids) > 0 |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
diff
changeset
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11 --pool-ids |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
diff
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12 #for $pool in $poolids |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
diff
changeset
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13 '${pool.pool_identifier}' |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
diff
changeset
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14 #end for |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
diff
changeset
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15 #end if |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
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16 --real-names |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
diff
changeset
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17 #for $fname in $listtobatch.keys() |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
diff
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18 '$fname' |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
diff
changeset
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19 #end for |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
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20 --galaxy-files |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
diff
changeset
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21 #for $fname in $listtobatch.keys() |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
diff
changeset
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22 '$listtobatch[$fname]' |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
diff
changeset
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23 #end for |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
diff
changeset
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24 </command> |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
diff
changeset
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25 <inputs> |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
diff
changeset
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26 <param name="batchsize" type="integer" optional="true" value="" label="Maximal amount of fractions to batch." help="No value means no maximum" /> |
3
abed51712ed0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b3873302e7bb7917a43b455875208e6e9fcf8f66
galaxyp
parents:
2
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27 <param name="filetype" type="select" label="Which datatype to nest?"> |
abed51712ed0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b3873302e7bb7917a43b455875208e6e9fcf8f66
galaxyp
parents:
2
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28 <option value="mzid">mzIdentML</option> |
abed51712ed0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b3873302e7bb7917a43b455875208e6e9fcf8f66
galaxyp
parents:
2
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29 <option value="percout">Percolator out</option> |
abed51712ed0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b3873302e7bb7917a43b455875208e6e9fcf8f66
galaxyp
parents:
2
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30 <option value="tabular">Tabular</option> |
abed51712ed0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b3873302e7bb7917a43b455875208e6e9fcf8f66
galaxyp
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2
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31 </param> |
1
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
diff
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32 <repeat name="poolids" title="Batch pools" help="Pools containing batches (optional, not using this will result in one pool)"> |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
diff
changeset
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33 <param name="pool_identifier" type="text" label="Filename part identifying batchpool" |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
diff
changeset
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34 help="Specify part of the input filenames that are unique for each pool, e.g set_A. Do not use 3 consecutive underscores."/> |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
diff
changeset
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35 </repeat> |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
diff
changeset
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36 <param name="listtobatch" type="data_collection" collection_type="list" label="List of files to batch" /> |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
diff
changeset
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37 </inputs> |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
diff
changeset
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38 <outputs> |
3
abed51712ed0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b3873302e7bb7917a43b455875208e6e9fcf8f66
galaxyp
parents:
2
diff
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39 <collection name="batched_fractions_mzid" type="list:list" label="Pooled batched mzIdentML data"> |
abed51712ed0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b3873302e7bb7917a43b455875208e6e9fcf8f66
galaxyp
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40 <filter>filetype == "mzid"</filter> |
5
dce55ca21b98
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 4fd46e83045d78a4703c0ae7d0cfc396bdbc8e78
galaxyp
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41 <discover_datasets pattern="(?P<identifier_0>\w+[^_][^_][^_])___(?P<identifier_1>[\w.-]+)\.data" ext="mzid" visible="false" /> |
3
abed51712ed0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b3873302e7bb7917a43b455875208e6e9fcf8f66
galaxyp
parents:
2
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42 </collection> |
abed51712ed0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b3873302e7bb7917a43b455875208e6e9fcf8f66
galaxyp
parents:
2
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43 <collection name="batched_fractions_perco" type="list:list" label="Pooled batched percolator data"> |
abed51712ed0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b3873302e7bb7917a43b455875208e6e9fcf8f66
galaxyp
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2
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44 <filter>filetype == "percout"</filter> |
5
dce55ca21b98
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 4fd46e83045d78a4703c0ae7d0cfc396bdbc8e78
galaxyp
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4
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45 <discover_datasets pattern="(?P<identifier_0>\w+[^_][^_][^_])___(?P<identifier_1>[\w.-]+)\.data" ext="percout" visible="false" /> |
3
abed51712ed0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b3873302e7bb7917a43b455875208e6e9fcf8f66
galaxyp
parents:
2
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46 </collection> |
abed51712ed0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b3873302e7bb7917a43b455875208e6e9fcf8f66
galaxyp
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2
diff
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47 <collection name="batched_fractions_tab" type="list:list" label="Pooled batched tabular data"> |
abed51712ed0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b3873302e7bb7917a43b455875208e6e9fcf8f66
galaxyp
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48 <filter>filetype == "tabular"</filter> |
5
dce55ca21b98
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 4fd46e83045d78a4703c0ae7d0cfc396bdbc8e78
galaxyp
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49 <discover_datasets pattern="(?P<identifier_0>\w+[^_][^_][^_])___(?P<identifier_1>[\w.-]+)\.data" ext="tabular" visible="false" /> |
1
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
diff
changeset
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50 </collection> |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
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diff
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51 </outputs> |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
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52 <tests> |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
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53 <test> |
4
154147805a33
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
galaxyp
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54 <param name="batchsize" value="6"/> |
3
abed51712ed0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b3873302e7bb7917a43b455875208e6e9fcf8f66
galaxyp
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2
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55 <param name="filetype" value="mzid" /> |
1
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
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diff
changeset
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56 <param name="listtobatch"> |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
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57 <collection type="list"> |
4
154147805a33
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
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58 <element name="fraction_one_spectra.mzML" value="empty_file1.mzid"/> |
1
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
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59 <element name="fraction_two_spectra" value="empty_file2.mzid"/> |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
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60 <element name="fraction_three_spectra" value="empty_file3.mzid"/> |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
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61 <element name="fraction_four_spectra" value="empty_file4.mzid"/> |
4
154147805a33
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
galaxyp
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62 <element name="fraction_five_spectra" value="empty_file5.mzid"/> |
154147805a33
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
galaxyp
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63 <element name="fraction_six_spectra" value="empty_file6.mzid"/> |
154147805a33
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
galaxyp
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64 <element name="fraction_seven_spectra" value="empty_file7.mzid"/> |
154147805a33
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
galaxyp
parents:
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65 <element name="fraction_eight_spectra" value="empty_file8.mzid"/> |
154147805a33
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
galaxyp
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66 <element name="fraction_nine_spectra" value="empty_file9.mzid"/> |
154147805a33
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
galaxyp
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67 <element name="fraction_ten_spectra" value="empty_file10.mzid"/> |
154147805a33
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
galaxyp
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68 <element name="fraction_eleven_spectra" value="empty_file11.mzid"/> |
1
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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69 </collection> |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
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70 </param> |
3
abed51712ed0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b3873302e7bb7917a43b455875208e6e9fcf8f66
galaxyp
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71 <output_collection name="batched_fractions_mzid" type="list:list"> |
2
7a0951d0e13e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 4ca7fcd1587c906db3314048a223d23b63b3f038
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72 <element name="pool0_batch0"> |
4
154147805a33
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
galaxyp
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73 <element name="inputfn00_fraction_one_spectra.mzML" ftype="mzid" file="empty_file1.mzid"/> |
154147805a33
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
galaxyp
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3
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74 <element name="inputfn01_fraction_two_spectra" ftype="mzid" file="empty_file2.mzid"/> |
154147805a33
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
galaxyp
parents:
3
diff
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75 <element name="inputfn02_fraction_three_spectra" ftype="mzid" file="empty_file3.mzid"/> |
154147805a33
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
galaxyp
parents:
3
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76 <element name="inputfn03_fraction_four_spectra" ftype="mzid" file="empty_file4.mzid"/> |
154147805a33
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
galaxyp
parents:
3
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77 <element name="inputfn04_fraction_five_spectra" ftype="mzid" file="empty_file5.mzid"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
galaxyp
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3
diff
changeset
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78 <element name="inputfn05_fraction_six_spectra" ftype="mzid" file="empty_file6.mzid"/> |
1
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
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diff
changeset
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79 </element> |
2
7a0951d0e13e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 4ca7fcd1587c906db3314048a223d23b63b3f038
galaxyp
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80 <element name="pool0_batch1"> |
4
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
galaxyp
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3
diff
changeset
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81 <element name="inputfn06_fraction_seven_spectra" ftype="mzid" file="empty_file7.mzid"/> |
154147805a33
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
galaxyp
parents:
3
diff
changeset
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82 <element name="inputfn07_fraction_eight_spectra" ftype="mzid" file="empty_file8.mzid"/> |
154147805a33
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
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parents:
3
diff
changeset
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83 <element name="inputfn08_fraction_nine_spectra" ftype="mzid" file="empty_file9.mzid"/> |
154147805a33
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
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3
diff
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84 <element name="inputfn09_fraction_ten_spectra" ftype="mzid" file="empty_file10.mzid"/> |
6
07107a686ce9
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit de8cdf895c3c6113f301a119788701b2465a1b1b"
galaxyp
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diff
changeset
|
85 <element name="inputfn10_fraction_eleven_spectra" ftype="mzid" file="empty_file11.mzid"/> |
1
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
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86 </element> |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
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87 </output_collection> |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
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88 </test> |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
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changeset
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89 <test> |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
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diff
changeset
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90 <repeat name="poolids"> |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
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91 <param name="pool_identifier" value="set1"/> |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
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92 </repeat> |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
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diff
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93 <repeat name="poolids"> |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
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94 <param name="pool_identifier" value="set2"/> |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
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95 </repeat> |
3
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b3873302e7bb7917a43b455875208e6e9fcf8f66
galaxyp
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96 <param name="filetype" value="tabular" /> |
1
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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97 <param name="listtobatch"> |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
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98 <collection type="list"> |
5
dce55ca21b98
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 4fd46e83045d78a4703c0ae7d0cfc396bdbc8e78
galaxyp
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4
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99 <element name="fr_one_set1-spectra" value="empty_file1.mzid"/> |
1
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
diff
changeset
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100 <element name="fr_two_set1_spectra" value="empty_file2.mzid"/> |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
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diff
changeset
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101 <element name="fr_three_set1_spectra" value="empty_file3.mzid"/> |
4
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
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102 <element name="fr_four_set1_spectra" value="empty_file4.mzid"/> |
154147805a33
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
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103 <element name="fr_five_set1_spectra" value="empty_file5.mzid"/> |
154147805a33
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
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104 <element name="fr_six_set1_spectra" value="empty_file6.mzid"/> |
154147805a33
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
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105 <element name="fr_seven_set1_spectra" value="empty_file7.mzid"/> |
154147805a33
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
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106 <element name="fr_eight_set1_spectra" value="empty_file8.mzid"/> |
154147805a33
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
galaxyp
parents:
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107 <element name="fr_nine_set1_spectra" value="empty_file9.mzid"/> |
154147805a33
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
galaxyp
parents:
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108 <element name="fr_ten_set1_spectra" value="empty_file10.mzid"/> |
154147805a33
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
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parents:
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109 <element name="fr_eleven_set1_spectra" value="empty_file11.mzid"/> |
154147805a33
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
galaxyp
parents:
3
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110 <element name="fr_one_set2_spectra" value="empty_file12.mzid"/> |
154147805a33
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
galaxyp
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111 <element name="fr_two_set2_spectra" value="empty_file13.mzid"/> |
154147805a33
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
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3
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112 <element name="fr_three_set2_spectra" value="empty_file14.mzid"/> |
1
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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113 </collection> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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114 </param> |
3
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115 <output_collection name="batched_fractions_tab" type="list:list"> |
2
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 4ca7fcd1587c906db3314048a223d23b63b3f038
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116 <element name="set1_batch0"> |
5
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 4fd46e83045d78a4703c0ae7d0cfc396bdbc8e78
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117 <element name="inputfn00_fr_one_set1-spectra" ftype="tabular" file="empty_file1.mzid"/> |
4
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
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118 <element name="inputfn01_fr_two_set1_spectra" ftype="tabular" file="empty_file2.mzid"/> |
154147805a33
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
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3
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119 <element name="inputfn02_fr_three_set1_spectra" ftype="tabular" file="empty_file3.mzid"/> |
154147805a33
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
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120 <element name="inputfn03_fr_four_set1_spectra" ftype="tabular" file="empty_file4.mzid"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
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3
diff
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121 <element name="inputfn04_fr_five_set1_spectra" ftype="tabular" file="empty_file5.mzid"/> |
154147805a33
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
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3
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122 <element name="inputfn05_fr_six_set1_spectra" ftype="tabular" file="empty_file6.mzid"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
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3
diff
changeset
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123 <element name="inputfn06_fr_seven_set1_spectra" ftype="tabular" file="empty_file7.mzid"/> |
154147805a33
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
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3
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124 <element name="inputfn07_fr_eight_set1_spectra" ftype="tabular" file="empty_file8.mzid"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
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125 <element name="inputfn08_fr_nine_set1_spectra" ftype="tabular" file="empty_file9.mzid"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
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126 <element name="inputfn09_fr_ten_set1_spectra" ftype="tabular" file="empty_file10.mzid"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
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127 <element name="inputfn10_fr_eleven_set1_spectra" ftype="tabular" file="empty_file11.mzid"/> |
1
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128 </element> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 4ca7fcd1587c906db3314048a223d23b63b3f038
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129 <element name="set2_batch1"> |
4
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130 <element name="inputfn0_fr_one_set2_spectra" ftype="tabular" file="empty_file12.mzid"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
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131 <element name="inputfn1_fr_two_set2_spectra" ftype="tabular" file="empty_file13.mzid"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
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132 <element name="inputfn2_fr_three_set2_spectra" ftype="tabular" file="empty_file14.mzid"/> |
1
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133 </element> |
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134 </output_collection> |
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135 </test> |
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136 <test> |
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137 <param name="batchsize" value="2"/> |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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138 <repeat name="poolids"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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139 <param name="pool_identifier" value="set1"/> |
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140 </repeat> |
86770eea5b09
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141 <repeat name="poolids"> |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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142 <param name="pool_identifier" value="set2"/> |
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143 </repeat> |
3
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144 <param name="filetype" value="percout" /> |
1
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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145 <param name="listtobatch"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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146 <collection type="list"> |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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147 <element name="fr_one_set1_spectra" value="empty_file1.mzid"/> |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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148 <element name="fr_two_set1_spectra" value="empty_file2.mzid"/> |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
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149 <element name="fr_three_set1_spectra" value="empty_file3.mzid"/> |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
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150 <element name="fr_one_set2_spectra" value="empty_file4.mzid"/> |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
diff
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151 <element name="fr_two_set2_spectra" value="empty_file5.mzid"/> |
86770eea5b09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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152 <element name="fr_three_set2_spectra" value="empty_file6.mzid"/> |
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153 </collection> |
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154 </param> |
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155 <output_collection name="batched_fractions_perco" type="list:list"> |
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156 <element name="set1_batch0"> |
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157 <element name="inputfn0_fr_one_set1_spectra" ftype="percout" file="empty_file1.mzid"/> |
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158 <element name="inputfn1_fr_two_set1_spectra" ftype="percout" file="empty_file2.mzid"/> |
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159 </element> |
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160 <element name="set1_batch1"> |
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161 <element name="inputfn2_fr_three_set1_spectra" ftype="percout" file="empty_file3.mzid"/> |
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162 </element> |
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163 <element name="set2_batch2"> |
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164 <element name="inputfn0_fr_one_set2_spectra" ftype="percout" file="empty_file4.mzid"/> |
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165 <element name="inputfn1_fr_two_set2_spectra" ftype="percout" file="empty_file5.mzid"/> |
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166 </element> |
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167 <element name="set2_batch3"> |
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168 <element name="inputfn2_fr_three_set2_spectra" ftype="percout" file="empty_file6.mzid"/> |
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169 </element> |
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170 </output_collection> |
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171 </test> |
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172 </tests> |
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173 <help> |
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174 Creates nested collection containing from a list containing datasets in batches of |
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175 a specific size. Useful when e.g. creating inputs to sqt2pin, msgfplus2pin or tandem2pin. |
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176 Use this feature when you want to batch a specific amount of datasets, or datasets with |
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177 a common file name pattern, or both. |
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178 The tool generates a collection containing batches which contain multiple batches |
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179 of input files. The pools are specified as a pattern in the input |
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180 files which makes sure the batching isn't continued through very different input sets |
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181 if that is a problem. Instead, for each filename-pattern it generates batches of the |
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182 specified size. |
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183 </help> |
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184 </tool> |