Mercurial > repos > galaxyp > flashlfq

comparison flashlfq.xml @ 2:e70198847b2a draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 38eecdb36b6b505afcdd99de7351eed9c3729843
author galaxyp
date Thu, 25 Jan 2018 20:37:09 -0500
parents 1e2fc34b1f20
children ff1148892ce3
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1:1e2fc34b1f20 2:e70198847b2a
29 --pau false 29 --pau false
30 && cat *_FlashLFQ_Log.txt | sed 's/\(Analysis summary for:\).*working./\1 /' > '$log' 30 && cat *_FlashLFQ_Log.txt | sed 's/\(Analysis summary for:\).*working./\1 /' > '$log'
31 && cp *_FlashLFQ_QuantifiedBaseSequences.tsv '$quantifiedBaseSequences' 31 && cp *_FlashLFQ_QuantifiedBaseSequences.tsv '$quantifiedBaseSequences'
32 && cp *_FlashLFQ_QuantifiedModifiedSequences.tsv '$quantifiedModifiedSequences' 32 && cp *_FlashLFQ_QuantifiedModifiedSequences.tsv '$quantifiedModifiedSequences'
33 && cp *_FlashLFQ_QuantifiedPeaks.tsv '$quantifiedPeaks' 33 && cp *_FlashLFQ_QuantifiedPeaks.tsv '$quantifiedPeaks'
34 && cp *_FlashLFQ_QuantifiedProteins.tsv '$quantifiedProteins' 34 ## create issue for FlashLFQ to name column headers correctly
35 && grep -v '^test$' *_FlashLFQ_QuantifiedProteins.tsv > '$quantifiedProteins'
35 ]]></command> 36 ]]></command>
36 <inputs> 37 <inputs>
37 <param name="idt" type="data" format="tabular" label="identification file" 38 <param name="idt" type="data" format="tabular" label="identification file"
38 help="MetaMorpheus,Morpheus"/> 39 help="MetaMorpheus,Morpheus"/>
39 <param name="peak_lists" type="data" format="mzml" multiple="true" label="spectrum files"/> 40 <param name="peak_lists" type="data" format="mzml" multiple="true" label="spectrum files"/>
74 </actions> 75 </actions>
75 </data> 76 </data>
76 <data name="quantifiedProteins" format="tabular" label="${tool.name} on ${on_string}: QuantifiedProteins.tsv"> 77 <data name="quantifiedProteins" format="tabular" label="${tool.name} on ${on_string}: QuantifiedProteins.tsv">
77 <actions> 78 <actions>
78 <action name="column_names" type="metadata" 79 <action name="column_names" type="metadata"
79 default="Protein"/> 80 default="Protein,${','.join([i.name for i in $peak_lists])}"/>
80 </actions> 81 </actions>
81 </data> 82 </data>
82 </outputs> 83 </outputs>
83 <tests> 84 <tests>
84 <test> 85 <test>