Mercurial > repos > bgruening > selectsequencesfrommsa

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f
author bgruening
date Sat, 11 Mar 2017 17:03:08 -0500
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d5bce745d0b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f
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1 <tool id="selectsequencesfrommsa" name="Select Sequences" version="1.0.2">
d5bce745d0b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f
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2 <description>
d5bce745d0b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f
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3 Tool to select representative sequences from a multiple sequence alignment.
d5bce745d0b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f
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4 </description>
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5 <requirements>
d5bce745d0b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f
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6 <requirement type="package" version="1.0.2">selectsequencesfrommsa</requirement>
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7 </requirements>
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8 <command detect_errors="aggressive"><![CDATA[
d5bce745d0b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f
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9 SelectSequencesFromMSA
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10 -c '$input_clustal'
d5bce745d0b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f
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11 $x
d5bce745d0b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f
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12 -o `pwd`
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13 -n $n
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14 -i $i
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15 -m $m
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16 > warnings
d5bce745d0b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f
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17 ]]>
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18 </command>
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19 <inputs>
d5bce745d0b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f
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20 <param name="input_clustal" type="data" format="clustal" label="Input clustal alignment"/>
d5bce745d0b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f
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21 <param argument="-n" type="integer" value="6" min="1" label="Number of sequences in the output alignment." help=""/>
d5bce745d0b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f
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22 <param argument="-i" type="float" value="80" min="0.1" label="Optimize for this percentage of mean pairwise identity" help=""/>
d5bce745d0b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f
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23 <param argument="-m" type="float" value="95" min="0.1" label="Sequences with a higher percentage of pairwise identity will be removed." help=""/>
d5bce745d0b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f
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24 <param argument="-x" truevalue="-x" falsevalue="" checked="True" type="boolean" label="The first sequence (=reference sequence) is always present in the output alignment." help=""/>
d5bce745d0b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f
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25 </inputs>
d5bce745d0b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f
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26 <outputs>
d5bce745d0b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f
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27 <data format="clustal" name="clustal" from_work_dir="result.selected" label="Clustal alignment of selected sequences"/>
d5bce745d0b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f
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28 </outputs>
d5bce745d0b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f
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29 <tests>
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30 <test>
d5bce745d0b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f
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31 <param name="input_clustal" value="result.clustal"/>
d5bce745d0b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f
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32 <output name="result.selected" file="result.selected"/>
d5bce745d0b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f
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33 </test>
d5bce745d0b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f
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34 </tests>
d5bce745d0b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f
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35 <help>
d5bce745d0b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f
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36
d5bce745d0b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f
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37 <![CDATA[
d5bce745d0b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f
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38
d5bce745d0b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f
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39 **What it does**
d5bce745d0b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f
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40
d5bce745d0b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f
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41 Tool to select representative sequences from a multiple sequence alignment in clustal format.
d5bce745d0b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f
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42 Useful before running RNAz, RNAcode, RNAalifold on alignments with many entries.
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43
d5bce745d0b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f
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44 **Input**
d5bce745d0b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f
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45 Multiple sequence alignment in clustal format
d5bce745d0b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f
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46
d5bce745d0b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f
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47 **Options**
d5bce745d0b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f
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48 -n Number of sequences in the output alignment. (Default: 6)
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49 -i Optimize for this percentage of mean pairwise identity (Default: 80)
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50 -m Sequences with a higher percentage of pairwise identity will be removed (Default: 95)
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51 -x The first sequence (=reference sequence) is always present in the output alignment per default. Default: True
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52
d5bce745d0b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f
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53 **Output**
d5bce745d0b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f
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54 Clustal alignment with selected sequences
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55
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56 ]]>
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57
d5bce745d0b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f
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58 </help>
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59 <citations>
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60 <citation type="doi">10.1093/nar/gkw558</citation>
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61 </citations>
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62 </tool>