annotate SAINT_preprocessing.xml @ 19:9329d9ec60b0 draft

Deleted selected files
author bornea
date Thu, 14 Apr 2016 17:23:45 -0400
parents 3953103b56f9
children 0ac97a6298c2
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
3953103b56f9 Uploaded
bornea
parents:
diff changeset
1 <tool id="SAINT_preprocessing_v5" name="SAINT pre-processing">
3953103b56f9 Uploaded
bornea
parents:
diff changeset
2 <description></description>
3953103b56f9 Uploaded
bornea
parents:
diff changeset
3 <command interpreter="python">
3953103b56f9 Uploaded
bornea
parents:
diff changeset
4 #if (str($type) == 'Scaffold'):
3953103b56f9 Uploaded
bornea
parents:
diff changeset
5 SAINT_preprocessing.py $input $preybool $fasta_db $Inter_file $Prey_file
3953103b56f9 Uploaded
bornea
parents:
diff changeset
6 "
3953103b56f9 Uploaded
bornea
parents:
diff changeset
7 #for $ba in $bait
3953103b56f9 Uploaded
bornea
parents:
diff changeset
8 ${ba.bait1}
3953103b56f9 Uploaded
bornea
parents:
diff changeset
9 ${ba.assign}
3953103b56f9 Uploaded
bornea
parents:
diff changeset
10 ${ba.T_C}
3953103b56f9 Uploaded
bornea
parents:
diff changeset
11 #end for
3953103b56f9 Uploaded
bornea
parents:
diff changeset
12 "
3953103b56f9 Uploaded
bornea
parents:
diff changeset
13 $Bait_file \$INSTALL_RUN_PATH/ $bait_bool $bait_file_in
3953103b56f9 Uploaded
bornea
parents:
diff changeset
14 #elif (str($type) == 'MaxQuant'):
3953103b56f9 Uploaded
bornea
parents:
diff changeset
15 SAINT_preprocessing_mq_pep.py $input $preybool $fasta_db $Inter_file $Prey_file
3953103b56f9 Uploaded
bornea
parents:
diff changeset
16 "
3953103b56f9 Uploaded
bornea
parents:
diff changeset
17 #for $ba in $bait
3953103b56f9 Uploaded
bornea
parents:
diff changeset
18 ${ba.bait1}
3953103b56f9 Uploaded
bornea
parents:
diff changeset
19 ${ba.assign}
3953103b56f9 Uploaded
bornea
parents:
diff changeset
20 ${ba.T_C}
3953103b56f9 Uploaded
bornea
parents:
diff changeset
21 #end for
3953103b56f9 Uploaded
bornea
parents:
diff changeset
22 "
3953103b56f9 Uploaded
bornea
parents:
diff changeset
23 $Bait_file \$INSTALL_RUN_PATH/ $bait_bool $bait_file_in
3953103b56f9 Uploaded
bornea
parents:
diff changeset
24 #end if
3953103b56f9 Uploaded
bornea
parents:
diff changeset
25 </command>
3953103b56f9 Uploaded
bornea
parents:
diff changeset
26 <requirements>
3953103b56f9 Uploaded
bornea
parents:
diff changeset
27 <requirement type="set_environment">INSTALL_RUN_PATH</requirement>
3953103b56f9 Uploaded
bornea
parents:
diff changeset
28 <requirement type="package" version="3.2.1">package_r_3_2_1</requirement>
3953103b56f9 Uploaded
bornea
parents:
diff changeset
29 </requirements>
3953103b56f9 Uploaded
bornea
parents:
diff changeset
30 <inputs>
3953103b56f9 Uploaded
bornea
parents:
diff changeset
31 <param type="select" name="type" label="MaxQuant or Scaffold">
3953103b56f9 Uploaded
bornea
parents:
diff changeset
32 <option value="MaxQuant">MaxQuant</option>
3953103b56f9 Uploaded
bornea
parents:
diff changeset
33 <option value="Scaffold">Scaffold</option>
3953103b56f9 Uploaded
bornea
parents:
diff changeset
34 </param>
3953103b56f9 Uploaded
bornea
parents:
diff changeset
35 <param format="dat" name="input" type="data" label="Scaffold or MaxQuant proteinGroup Output"/>
3953103b56f9 Uploaded
bornea
parents:
diff changeset
36 <param type="boolean" name="preybool" checked="true" label="Create Prey File"/>
3953103b56f9 Uploaded
bornea
parents:
diff changeset
37 <param type="data" name="fasta_db" format="fasta" label="Provide Uniprot Fasta database" optional="true"/>
3953103b56f9 Uploaded
bornea
parents:
diff changeset
38 <param name="bait_bool" type="boolean" checked="true" label="Are You Providing Your Own bait file?"/>
3953103b56f9 Uploaded
bornea
parents:
diff changeset
39 <param type="data" format="dat" name="bait_file_in" label="Bait File" optional="true"/>
3953103b56f9 Uploaded
bornea
parents:
diff changeset
40 <repeat name="bait" title="Bait Create">
3953103b56f9 Uploaded
bornea
parents:
diff changeset
41 <param name="bait1" type="text" size="100" label="Bait"/>
3953103b56f9 Uploaded
bornea
parents:
diff changeset
42 <param name="assign" type="text" size="100" label="Group Assignment"/>
3953103b56f9 Uploaded
bornea
parents:
diff changeset
43 <param name="T_C" type="boolean" checked="true" label="Is this a Control?"/>
3953103b56f9 Uploaded
bornea
parents:
diff changeset
44 </repeat>
3953103b56f9 Uploaded
bornea
parents:
diff changeset
45
3953103b56f9 Uploaded
bornea
parents:
diff changeset
46 </inputs>
3953103b56f9 Uploaded
bornea
parents:
diff changeset
47 <outputs>
3953103b56f9 Uploaded
bornea
parents:
diff changeset
48 <data format="txt" name="Inter_file" label="Inter File"/>
3953103b56f9 Uploaded
bornea
parents:
diff changeset
49 <data format="txt" name="Prey_file" label="Prey File" />
3953103b56f9 Uploaded
bornea
parents:
diff changeset
50 <data format="txt" name="Bait_file" label="Bait File" />
3953103b56f9 Uploaded
bornea
parents:
diff changeset
51 </outputs>
3953103b56f9 Uploaded
bornea
parents:
diff changeset
52 <stdio>
3953103b56f9 Uploaded
bornea
parents:
diff changeset
53 <regex match="Error|error"
3953103b56f9 Uploaded
bornea
parents:
diff changeset
54 source="stdout"
3953103b56f9 Uploaded
bornea
parents:
diff changeset
55 level="fatal"
3953103b56f9 Uploaded
bornea
parents:
diff changeset
56 description="Unknown error"/>
3953103b56f9 Uploaded
bornea
parents:
diff changeset
57 <regex match="Error|error"
3953103b56f9 Uploaded
bornea
parents:
diff changeset
58 source="stderr"
3953103b56f9 Uploaded
bornea
parents:
diff changeset
59 level="fatal"
3953103b56f9 Uploaded
bornea
parents:
diff changeset
60 description="Unknown error"/>
3953103b56f9 Uploaded
bornea
parents:
diff changeset
61 <regex match="Error: bad bait"
3953103b56f9 Uploaded
bornea
parents:
diff changeset
62 source="stdout"
3953103b56f9 Uploaded
bornea
parents:
diff changeset
63 level="fatal"
3953103b56f9 Uploaded
bornea
parents:
diff changeset
64 description="Error: bad bait"/>
3953103b56f9 Uploaded
bornea
parents:
diff changeset
65 </stdio>
3953103b56f9 Uploaded
bornea
parents:
diff changeset
66
3953103b56f9 Uploaded
bornea
parents:
diff changeset
67 <tests>
3953103b56f9 Uploaded
bornea
parents:
diff changeset
68 <test>
3953103b56f9 Uploaded
bornea
parents:
diff changeset
69 <param name="input" value="fa_gc_content_input.fa"/>
3953103b56f9 Uploaded
bornea
parents:
diff changeset
70 <output name="out_file1" file="fa_gc_content_output.txt"/>
3953103b56f9 Uploaded
bornea
parents:
diff changeset
71 </test>
3953103b56f9 Uploaded
bornea
parents:
diff changeset
72 </tests>
3953103b56f9 Uploaded
bornea
parents:
diff changeset
73 <help>
3953103b56f9 Uploaded
bornea
parents:
diff changeset
74
3953103b56f9 Uploaded
bornea
parents:
diff changeset
75 Pre-processing:
3953103b56f9 Uploaded
bornea
parents:
diff changeset
76
3953103b56f9 Uploaded
bornea
parents:
diff changeset
77 APOSTL is able to recognize either a Scaffold "Samples Report" file (tab-delimited txt file) or the "peptides.txt" file output in the MaxQuant "txt" output folder. No modifications should be made to these files. Using the "Bait Create" tool, you can create your "bait.txt" file. It is important that the individual bait names match the bait names within your scaffold or MaxQuant output. APOSTL uses the bait file to findthe user's baits of interest. Additionally there is an option to make the prey file (Y/N). When making a prey file, APOSTL queries Uniprot ( http://www.uniprot.org ) in order to extract protein amino acidlengths and gene names. This takes several minutes depending on your internet connection. Some users may want to run SAINTexpress using the same data set while changing which baits are considered test or control It is useful to toggle "Make Prey" off in order to save time by circumventing this step as the same prey file can be used for both SAINTexpress runs.
3953103b56f9 Uploaded
bornea
parents:
diff changeset
78
3953103b56f9 Uploaded
bornea
parents:
diff changeset
79 INPUTS:
3953103b56f9 Uploaded
bornea
parents:
diff changeset
80
3953103b56f9 Uploaded
bornea
parents:
diff changeset
81 Scaffold file:
3953103b56f9 Uploaded
bornea
parents:
diff changeset
82
3953103b56f9 Uploaded
bornea
parents:
diff changeset
83 - Scaffold "Samples Report" output (tab-delimited txt file)
3953103b56f9 Uploaded
bornea
parents:
diff changeset
84
3953103b56f9 Uploaded
bornea
parents:
diff changeset
85
3953103b56f9 Uploaded
bornea
parents:
diff changeset
86 MaxQuant file:
3953103b56f9 Uploaded
bornea
parents:
diff changeset
87
3953103b56f9 Uploaded
bornea
parents:
diff changeset
88 - MaxQuant "peptides.txt" file (tab-delimited txt file)
3953103b56f9 Uploaded
bornea
parents:
diff changeset
89 </help>
3953103b56f9 Uploaded
bornea
parents:
diff changeset
90 </tool>