Mercurial > repos > jfb > commonality_finder
changeset 3:9610fd10d941 draft
Uploaded
| author | jfb |
|---|---|
| date | Wed, 23 May 2018 14:59:16 -0400 |
| parents | 6e3a0489af44 |
| children | 8931bea806a6 |
| files | C and D finder/CandD.xml |
| diffstat | 1 files changed, 10 insertions(+), 23 deletions(-) [+] |
line wrap: on
line diff
--- a/C and D finder/CandD.xml Tue May 22 18:49:28 2018 -0400 +++ b/C and D finder/CandD.xml Wed May 23 14:59:16 2018 -0400 @@ -1,5 +1,5 @@ <tool id="commonality_r" name="commonality_finder" version="1.0.0"> - <description>discover unphosphorylated substrates</description> + <description>finds commonality</description> <requirements> <requirement type="package">R</requirement> </requirements> @@ -11,17 +11,17 @@ <param format="csv" name="input2.csv" type="data" label="First Substrate Background Frequency"/> <param format="csv" name="input3.csv" type="data" label="Second Substrate Set"/> <param format="csv" name="input4.csv" type="data" label="Second Substrate Background Frequency"/> - <param format="csv" name="input5.csv" type="data" label="Substrate Background Frequency"/> - <param format="csv" name="input6.csv" type="data" label="Substrate Background Frequency"/> + <param format="csv" name="input5.csv" type="data" label="Third Substrate Set"/> + <param format="csv" name="input6.csv" type="data" label="Third Substrate Background Frequency"/> <param name="outGroup" type="text" value="kinase" label="Kinase Name"/> </inputs> <outputs> - <data format="csv" name="Negatives" from_work_dir="output1.csv" label="${outGroup}_Negative Motifs.csv"/> - <data format="csv" name="Negatives" from_work_dir="output1.csv" label="${outGroup}_Negative Motifs.csv"/> - <data format="csv" name="Negatives" from_work_dir="output1.csv" label="${outGroup}_Negative Motifs.csv"/> - <data format="csv" name="Negatives" from_work_dir="output1.csv" label="${outGroup}_Negative Motifs.csv"/> - <data format="csv" name="Negatives" from_work_dir="output1.csv" label="${outGroup}_Negative Motifs.csv"/> - <data format="csv" name="Negatives" from_work_dir="output1.csv" label="${outGroup}_Negative Motifs.csv"/> + <data format="csv" name="Negatives" from_work_dir="output1.csv" label="${outGroup}_First Unshared Substrates.csv"/> + <data format="csv" name="Negatives" from_work_dir="output1.csv" label="${outGroup}_First Unshared SBF.csv"/> + <data format="csv" name="Negatives" from_work_dir="output1.csv" label="${outGroup}_Second Unshared Substrates.csv"/> + <data format="csv" name="Negatives" from_work_dir="output1.csv" label="${outGroup}_Second Unshared SBF.csv"/> + <data format="csv" name="Negatives" from_work_dir="output1.csv" label="${outGroup}_Third Unshared Substrates.csv"/> + <data format="csv" name="Negatives" from_work_dir="output1.csv" label="${outGroup}_Third Unshared SBF.csv"/> </outputs> <tests> <test> @@ -32,20 +32,7 @@ </test> </tests> <help><![CDATA[ -Using the output from KinaMine, plus the Uniprot file that was used with KinaMine, this program finds all Y-centered motifs which *could* have been present as positive motifs but were not seen by the Mass Spec -This tool is intended to be used in conjunction with KinaMine 7-7 and Kinatest.R, the three together creating a GalaxyP version of the KINATEST-ID workbook. - - -Inputs - -**Substrate Background Frequency** -**Positive/Phosphorylated Substrate List** -These two come directly from the KinaMine output - -**Human Proteome Reference** -This should be a tabularized version of a FASTA taken from the Reviewed Human Uniprot database, consisting of all human proteins plus a list of common Mass Spectrometry contaminants. -This file should be created by using the same FASTA file used for KinaMine and running FASTA to Tabular on it using GalaxyP - + This tool uses the output from 3 Kinamine runs to determine what motifs are shared between the three runs ]]></help> <citations> <citation type="doi">10.1021/ja507164a</citation>