annotate trtr.xml @ 15:cffb3efb1726

Uploaded
author mrvollger
date Fri, 12 Dec 2014 17:55:05 -0500
parents 5c3ec718c26f
children 4e6b9640989f
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
11
5c3ec718c26f Uploaded
mrvollger
parents:
diff changeset
1 <tool id="trtr" name="TRTR">
5c3ec718c26f Uploaded
mrvollger
parents:
diff changeset
2 <requirements>
5c3ec718c26f Uploaded
mrvollger
parents:
diff changeset
3 <requirement type="package" version="1.0">trtr</requirement>
5c3ec718c26f Uploaded
mrvollger
parents:
diff changeset
4 </requirements>
5c3ec718c26f Uploaded
mrvollger
parents:
diff changeset
5
5c3ec718c26f Uploaded
mrvollger
parents:
diff changeset
6 <description>Trim Reads of Tandem Repeat in a fastq file. </description>
5c3ec718c26f Uploaded
mrvollger
parents:
diff changeset
7
5c3ec718c26f Uploaded
mrvollger
parents:
diff changeset
8 <command>
5c3ec718c26f Uploaded
mrvollger
parents:
diff changeset
9 trtr $input $max_repeat $aggressive > $output
5c3ec718c26f Uploaded
mrvollger
parents:
diff changeset
10 </command>
5c3ec718c26f Uploaded
mrvollger
parents:
diff changeset
11
5c3ec718c26f Uploaded
mrvollger
parents:
diff changeset
12 <inputs>
5c3ec718c26f Uploaded
mrvollger
parents:
diff changeset
13 <param format="fastq" name="input" type="data" label="Source file"/>
5c3ec718c26f Uploaded
mrvollger
parents:
diff changeset
14 <param name="max_repeat" type="integer" value="10" label="Maximum repeat length" />
5c3ec718c26f Uploaded
mrvollger
parents:
diff changeset
15 <param name="aggressive" type="integer" value="1" label="Aggressive? See description."/>
5c3ec718c26f Uploaded
mrvollger
parents:
diff changeset
16 </inputs>
5c3ec718c26f Uploaded
mrvollger
parents:
diff changeset
17
5c3ec718c26f Uploaded
mrvollger
parents:
diff changeset
18 <outputs>
5c3ec718c26f Uploaded
mrvollger
parents:
diff changeset
19 <data format="fastq" name="output" />
5c3ec718c26f Uploaded
mrvollger
parents:
diff changeset
20 </outputs>
5c3ec718c26f Uploaded
mrvollger
parents:
diff changeset
21
5c3ec718c26f Uploaded
mrvollger
parents:
diff changeset
22 <tests>
5c3ec718c26f Uploaded
mrvollger
parents:
diff changeset
23 <test>
5c3ec718c26f Uploaded
mrvollger
parents:
diff changeset
24 <param name="input" value="small.fastq"/>
5c3ec718c26f Uploaded
mrvollger
parents:
diff changeset
25 <output name="output" file="smallTrimmed.fastq"/>
5c3ec718c26f Uploaded
mrvollger
parents:
diff changeset
26 </test>
5c3ec718c26f Uploaded
mrvollger
parents:
diff changeset
27 <test>
5c3ec718c26f Uploaded
mrvollger
parents:
diff changeset
28 <param name="input" value="medium.fastq"/>
5c3ec718c26f Uploaded
mrvollger
parents:
diff changeset
29 <output name="output" file="mediumTrimmed.fastq"/>
5c3ec718c26f Uploaded
mrvollger
parents:
diff changeset
30 </test>
5c3ec718c26f Uploaded
mrvollger
parents:
diff changeset
31 </tests>
5c3ec718c26f Uploaded
mrvollger
parents:
diff changeset
32
5c3ec718c26f Uploaded
mrvollger
parents:
diff changeset
33 <help>
5c3ec718c26f Uploaded
mrvollger
parents:
diff changeset
34 This tool removes tandem repeats from ends of unaligned sequencing reads (leaving one copy). This prevents reads that don't span the repeated region from overlapping and leading to innaccurate SNPs calls.
5c3ec718c26f Uploaded
mrvollger
parents:
diff changeset
35
5c3ec718c26f Uploaded
mrvollger
parents:
diff changeset
36 The maximimum repeat length is adjustable (use 1 to trim only homopolymers).
5c3ec718c26f Uploaded
mrvollger
parents:
diff changeset
37
5c3ec718c26f Uploaded
mrvollger
parents:
diff changeset
38 The "aggressive" option should not be touched in general. Setting to 0 will prevent the program from trimming to exactly 1 copy of the repeat, instead leaving between 1 and 2 copies.
5c3ec718c26f Uploaded
mrvollger
parents:
diff changeset
39
5c3ec718c26f Uploaded
mrvollger
parents:
diff changeset
40 This could also be a useful first step before assembly. More testing needs to be done.
5c3ec718c26f Uploaded
mrvollger
parents:
diff changeset
41 </help>
5c3ec718c26f Uploaded
mrvollger
parents:
diff changeset
42
5c3ec718c26f Uploaded
mrvollger
parents:
diff changeset
43 </tool>