Mercurial > repos > jfb > negative_motif_finder_7_7

comparison NMF/NMF.xml @ 2:83c34194a973 draft

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author jfb
date Wed, 28 Feb 2018 14:11:55 -0500
parents a098e1274f63
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1:a098e1274f63 2:83c34194a973
11 ]]></command> 11 ]]></command>
12 <inputs> 12 <inputs>
13 <param format="csv" name="SBF" type="data" label="Substrate Background Frequency"/> 13 <param format="csv" name="SBF" type="data" label="Substrate Background Frequency"/>
14 <param format="tabular" name="FASTA" type="data" label="Human Proteome Reference"/> 14 <param format="tabular" name="FASTA" type="data" label="Human Proteome Reference"/>
15 <param format="csv" name="positives" type="data" label="Positive/Phosphorylated Substrate List"/> 15 <param format="csv" name="positives" type="data" label="Positive/Phosphorylated Substrate List"/>
16 <param name="outGroup" type="text" value"kinase" label="Kinase Name"/> 16 <param name="outGroup" type="text" value="kinase" label="Kinase Name"/>
17 </inputs> 17 </inputs>
18 <outputs> 18 <outputs>
19 <data format="csv" name="Negatives" from_work_dir="output1.csv" label="${outGroup}_Negative Motifs.csv"/> 19 <data format="csv" name="Negatives" from_work_dir="output1.csv" label="${outGroup}_Negative Motifs.csv"/>
20 </outputs> 20 </outputs>
21 <tests> 21 <tests>
27 </test> 27 </test>
28 </tests> 28 </tests>
29 <help><![CDATA[ 29 <help><![CDATA[
30 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 30 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
31 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. 31 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.
32 =========== 32
33
33 Inputs 34 Inputs
34 =========== 35
35 **Substrate Background Frequency** 36 **Substrate Background Frequency**
36 **Positive/Phosphorylated Substrate List** 37 **Positive/Phosphorylated Substrate List**
37 These two come directly from the KinaMine output 38 These two come directly from the KinaMine output
38 39
39 **Human Proteome Reference** 40 **Human Proteome Reference**