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