annotate SMART/galaxy/trimSequences.xml @ 42:2abc37c27164

Deleted selected files
author m-zytnicki
date Wed, 18 Sep 2013 07:45:59 -0400
parents 2c0c0a89fad7
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
38
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
1 <tool id="trimSequences" name="trim sequences">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
2 <description>Remove the 5' and/or 3' adapters of a list of reads.</description>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
3 <requirements>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
4 <requirement type="set_environment">PYTHONPATH</requirement>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
5 </requirements>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
6 <command interpreter="python"> ../Java/Python/trimSequences.py -i $inputFile -f fastq
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
7 #if $OptionFPADP.FPADP == "Yes":
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
8 -5 $OptionFPADP.fivePAdaptor
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
9 #end if
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
10 #if $OptionTPADP.TPADP == "Yes":
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
11 -3 $OptionTPADP.threePAdaptor
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
12 #end if
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
13 -e $errors
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
14 $indels
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
15 $noAdaptor5p $noAdaptorFile5p
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
16 $noAdaptor3p $noAdaptorFile3p
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
17 -o $outputFile
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
18
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
19 </command>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
20
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
21
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
22 <inputs>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
23 <param name="inputFile" type="data" label="Input fastq File" format="fastq"/>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
24
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
25 <conditional name="OptionFPADP">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
26 <param name="FPADP" type="select" label="5' adapter">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
27 <option value="Yes">Yes</option>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
28 <option value="No" selected="true">No</option>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
29 </param>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
30 <when value="Yes">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
31 <param name="fivePAdaptor" type="text" value="None" />
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
32 </when>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
33 <when value="No">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
34 </when>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
35 </conditional>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
36
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
37 <conditional name="OptionTPADP">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
38 <param name="TPADP" type="select" label="3' adapter">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
39 <option value="Yes">Yes</option>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
40 <option value="No" selected="true">No</option>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
41 </param>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
42 <when value="Yes">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
43 <param name="threePAdaptor" type="text" value="None" />
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
44 </when>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
45 <when value="No">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
46 </when>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
47 </conditional>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
48
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
49 <param name="errors" type="integer" label="number of errors in percent" value="0" />
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
50 <param name="indels" type="boolean" truevalue="-d" falsevalue="" checked="false" label="indels option" help="also accept indels"/>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
51 <param name="noAdaptor5p" type="boolean" truevalue="-n" falsevalue="" checked="false" label="noAdaptor 5' option" help="file name where to print sequences with no 5' adapter "/>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
52 <param name="noAdaptor3p" type="boolean" truevalue="-m" falsevalue="" checked="false" label="noAdaptor 3' option" help="file name where to print sequences with no 3' adapter "/>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
53
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
54 </inputs>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
55
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
56 <outputs>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
57 <data format="fastq" name="outputFile" label="[trim sequences] output file"/>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
58 <data name="noAdaptorFile5p" format="fastq" label="[trim sequences] noAdapter5p file">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
59 <filter>noAdaptor5p</filter>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
60 </data>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
61 <data name="noAdaptorFile3p" format="fastq" label="[trim sequences] noAdapter3p file">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
62 <filter>noAdaptor3p</filter>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
63 </data>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
64 </outputs>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
65
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
66 <help>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
67 This function removes the adaptor from the 5' or 3' end of your reads. It can even recognize the adaptators which are partially present. You can specify whether you are ready to accept indels or not.
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
68 </help>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
69 <tests>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
70 <test>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
71 <param name="inputFile" value="short_fastq.fastq" />
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
72 <param name="FPADP" value="Yes"/>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
73 <param name="fivePAdaptor" value="AAAA" />
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
74 <param name="TPADP" value="No"/>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
75 <param name="errors" value="1"/>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
76 <param name="indels" value="False"/>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
77 <param name="noAdaptor5p" value="False"/>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
78 <param name= "noAdaptor3p" value="False"/>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
79 <output name="outputFile" file="exp_trimsequences_short_fastq.fastq" />
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
80 </test>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
81 </tests>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
82 </tool>