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comparison SAINT_preprocessing_v5.xml @ 7:c88212194b4e draft

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author bornea
date Tue, 10 Nov 2015 13:15:11 -0500
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6:6cafc67e8cda 7:c88212194b4e
1 <tool id="SAINT_preprocessing_v5" name="SAINT pre-processing">
2 <description></description>
3 <command interpreter="python">
4 #if (str($type) == 'Scaffold'):
5 SAINT_preprocessing_v6.py $input $preybool $fasta_db $Inter_file $Prey_file
6 "
7 #for $ba in $bait
8 ${ba.bait1}
9 ${ba.assign}
10 ${ba.T_C}
11 #end for
12 "
13 $Bait_file \$INSTALL_RUN_PATH/
14 #elif (str($type) == 'MaxQuant'):
15 SAINT_preprocessing_v6_mq_pep.py $input $preybool $fasta_db $Inter_file $Prey_file
16 "
17 #for $ba in $bait
18 ${ba.bait1}
19 ${ba.assign}
20 ${ba.T_C}
21 #end for
22 "
23 $Bait_file \$INSTALL_RUN_PATH/
24 #end if
25 </command>
26 <requirements>
27 <requirement type="set_environment">INSTALL_RUN_PATH</requirement>
28 </requirments>
29 <inputs>
30 <param type="select" name="type" label="MaxQuant or Scaffold">
31 <option value="MaxQuant">MaxQuant</option>
32 <option value="Scaffold">Scaffold</option>
33 </param>
34 <param format="dat" name="input" type="data" label="Scaffold or MaxQuant proteinGroup Output"/>
35 <param type="boolean" name="preybool" checked="true" label="Create Prey File"/>
36 <param type="data" name="fasta_db" format="fasta" label="Provide Uniprot Fasta database" />
37 <repeat name="bait" title="Bait Create">
38 <param name="bait1" type="text" size="100"/>
39 <param name="assign" type="text" size="100"/>
40 <param name="T_C" type="boolean" checked="true" label="Is this a Control?"/>
41 </repeat>
42 </inputs>
43 <outputs>
44 <data format="txt" name="Inter_file" label="Inter File"/>
45 <data format="txt" name="Prey_file" label="Prey File" />
46 <data format="txt" name="Bait_file" label="Bait File" />
47 </outputs>
48 <stdio>
49 <regex match="error"
50 source="stdout"
51 level="fatal"
52 description="Unknown error"/>
53 <regex match="Error: bad bait"
54 source="stdout"
55 level="fatal"
56 description="Error: bad bait"/>
57 </stdio>
58
59 <tests>
60 <test>
61 <param name="input" value="fa_gc_content_input.fa"/>
62 <output name="out_file1" file="fa_gc_content_output.txt"/>
63 </test>
64 </tests>
65 <help>
66 Pre-processing:
67 APOSTL is able to recognize either a Scaffold "Samples Report" file (tab-delimited
68 txt file) or the "peptides.txt" file output in the maxquant "txt" output folder. No
69 modifications should be made to these files. Using the "Bait Create" tool, you can
70 create your "bait.txt" file. It is important that the individual bait names match the
71 bait names within your scaffold or maxquant output. APOSTL uses the bait file to find
72 the user's baits of interest. Additionally there is an option to make the prey file (Y/N).
73 When making a prey file, APOSTL queries uniprot in order to extract protein amino acid
74 lengths and gene names. This takes several minutes depending on your internet connection.
75 Some users may want to run SAINTexpress using the same data set while changing which baits
76 are considered test or control. It is useful to toggle "Make Prey" off in order to save
77 time by circumventing this step as the same prey file can be used for both SAINTexpress
78 runs.
79
80 INPUTS:
81
82 Scaffold file:
83
84 - Scaffold "Samples Report" output (tab-delimited txt file)
85
86
87 Maxquant file:
88
89 - maxquant "peptides.txt" file (tab-delimited txt file)
90 </help>
91 </tool>