Mercurial > repos > jfb > commonality_finder
view C and D finder/CandD.xml @ 2:6e3a0489af44 draft
Uploaded
author | jfb |
---|---|
date | Tue, 22 May 2018 18:49:28 -0400 |
parents | ac16c0cefedb |
children | 9610fd10d941 |
line wrap: on
line source
<tool id="commonality_r" name="commonality_finder" version="1.0.0"> <description>discover unphosphorylated substrates</description> <requirements> <requirement type="package">R</requirement> </requirements> <command><![CDATA[ Rscript '$__tool_directory__/CandD.R' NO NO YES ]]></command> <inputs> <param format="csv" name="input1.csv" type="data" label="First Substrate Set"/> <param format="csv" name="input2.csv" type="data" label="First Substrate Background Frequency"/> <param format="csv" name="input3.csv" type="data" label="Second Substrate Set"/> <param format="csv" name="input4.csv" type="data" label="Second Substrate Background Frequency"/> <param format="csv" name="input5.csv" type="data" label="Substrate Background Frequency"/> <param format="csv" name="input6.csv" type="data" label="Substrate Background Frequency"/> <param name="outGroup" type="text" value="kinase" label="Kinase Name"/> </inputs> <outputs> <data format="csv" name="Negatives" from_work_dir="output1.csv" label="${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"/> </outputs> <tests> <test> <param name="input1.csv" ftype="csv" value="input1.csv"/> <param name="positives" ftype="csv" value="substrates.csv"/> <param name="SBF" ftype="csv" value="SBF.csv"/> <output name="Negatives" file="negatives.csv"/> </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 ]]></help> <citations> <citation type="doi">10.1021/ja507164a</citation> </citations> </tool>