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comparison trtr.xml @ 30:c92ea5a8dec6

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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/trtr commit 6f76316d57fa4ec6b16aeed61e197b2c117f006d-dirty
author lparsons
date Mon, 14 Mar 2016 16:18:55 -0400
parents 4e6b9640989f
children
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29:4e6b9640989f 30:c92ea5a8dec6
1 <tool id="trtr" name="TRTR"> 1 <tool id="trtr" name="TRTR" version="1.0galaxy1">
2 <requirements> 2 <description>Trim Reads of Tandem Repeat in a fastq file. </description>
3 <requirement type="package" version="1.0">trtr</requirement>
4 </requirements>
5 3
6 <description>Trim Reads of Tandem Repeat in a fastq file. </description> 4 <requirements>
7 5 <requirement type="package" version="1.0">trtr</requirement>
8 <command> 6 </requirements>
9 trtr $input $max_repeat $aggressive > $output
10 </command>
11
12 <inputs>
13 <param format="fastq" name="input" type="data" label="Source file"/>
14 <param name="max_repeat" type="integer" value="10" label="Maximum repeat length" />
15 <param name="aggressive" type="integer" value="1" label="Aggressive? See description."/>
16 </inputs>
17
18 <outputs>
19 <data format_source="input" name="output" />
20 </outputs>
21 7
22 <tests> 8 <command>
23 <test> 9 trtr $input $max_repeat $aggressive > $output
24 <param name="input" value="small.fastq"/> 10 </command>
25 <output name="output" file="smallTrimmed.fastq"/>
26 </test>
27 <test>
28 <param name="input" value="medium.fastq"/>
29 <output name="output" file="mediumTrimmed.fastq"/>
30 </test>
31 </tests>
32 11
33 <help> 12 <inputs>
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. 13 <param format="fastq" name="input" type="data" label="Source file"/>
14 <param name="max_repeat" type="integer" value="10" label="Maximum repeat length" />
15 <param name="aggressive" type="integer" value="1" label="Aggressive? See description."/>
16 </inputs>
35 17
36 The maximimum repeat length is adjustable (use 1 to trim only homopolymers). 18 <outputs>
19 <data format_source="input" name="output" />
20 </outputs>
37 21
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. 22 <tests>
23 <test>
24 <param name="input" value="small.fastq"/>
25 <output name="output" file="smallTrimmed.fastq"/>
26 </test>
27 <test>
28 <param name="input" value="medium.fastq"/>
29 <output name="output" file="mediumTrimmed.fastq"/>
30 </test>
31 </tests>
39 32
40 This could also be a useful first step before assembly. More testing needs to be done. 33 <help>
41 </help> 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.
35
36 The maximimum repeat length is adjustable (use 1 to trim only homopolymers).
37
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.
39
40 This could also be a useful first step before assembly. More testing needs to be done.
41 </help>
42 42
43 </tool> 43 </tool>