Mercurial > repos > iuc > mothur_chimera_ccode

annotate chimera.ccode.xml @ 0:d6b58ab6093a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 17:32:53 -0400
parents
children ca67593968a3
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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1 <tool profile="16.07" id="mothur_chimera_ccode" name="Chimera.ccode" version="@WRAPPER_VERSION@.0">
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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2 <description>Find putative chimeras using ccode</description>
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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3 <macros>
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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4 <import>macros.xml</import>
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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5 </macros>
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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6 <expand macro="requirements"/>
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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7 <expand macro="version_command"/>
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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8 <command detect_errors="aggressive"><![CDATA[
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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9 ## create symlinks to input datasets
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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10 ln -s "$fasta" fasta.dat &&
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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11 ln -s "$alignment.template" alignment.template.dat &&
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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12 #if $mask.source2 == "history":
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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13 ln -s "$mask.input" mask.input.dat &&
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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14 #end if
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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15
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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16 echo 'chimera.ccode(
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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17 fasta=fasta.dat,
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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18 reference=alignment.template.dat,
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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19 filter=$filter,
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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20 #if $mask.source2 == "default":
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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21 mask=default,
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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22 #elif $mask.source2 == "history":
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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23 mask=mask.input.dat,
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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24 #end if
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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25 #if int($window) > 0:
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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26 window=$window,
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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27 #end if
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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28 #if int($numwanted) > 0:
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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29 numwanted=$numwanted,
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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30 #end if
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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31 processors='\${GALAXY_SLOTS:-8}'
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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32 )'
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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33 | sed 's/ //g' ## mothur trips over whitespace
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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34 | mothur
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35 ]]></command>
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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36 <inputs>
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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37 <param name="fasta" type="data" format="mothur.align" label="fasta - Candiate Aligned Sequences"/>
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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38 <conditional name="alignment">
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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39 <param name="source" type="select" label="Select Reference Template from" help="">
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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40 <option value="hist">History</option>
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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41 <option value="ref">Cached Reference</option>
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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42 </param>
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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43 <when value="ref">
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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44 <param name="template" type="select" label="reference - Select an alignment database" help="">
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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45 <options from_data_table="mothur_aligndb">
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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46 </options>
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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47 </param>
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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48 </when>
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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49 <when value="hist">
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50 <param name="template" type="data" format="fasta" label="reference - Reference to align with" help=""/>
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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51 </when>
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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52 </conditional>
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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53 <param name="filter" type="boolean" falsevalue="False" truevalue="True" checked="false" label="filter - Apply a 50% soft vertical filter"/>
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54 <conditional name="mask">
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55 <param name="source2" type="select" label="Mask option">
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56 <option value="">None</option>
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57 <option value="default">default ecoli mask</option>
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58 <option value="history">From Your History</option>
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59 </param>
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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60 <when value="history">
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61 <param name="input" type="data" format="mothur.filter" label="Mask for the reference file" help=""/>
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62 </when>
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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63 <when value=""/>
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64 <when value="default"/>
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65 </conditional>
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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66 <param name="window" type="integer" value="0" label="window - Length of sequence you want in each window analyzed (default if &lt; 1)" help="Recommended window size is between 5 and 20% of your trimmed sequence length. Default is 10% of the sequence length."/>
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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67 <param name="numwanted" type="integer" value="20" label="numwanted - Number of sequences compared with each query (uses default if set to 0)"/>
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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68 </inputs>
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69 <outputs>
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70 <expand macro="logfile-output"/>
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71 <data name="out_file" format="txt" from_work_dir="fasta.*ccode.chimeras" label="${tool.name} on ${on_string}: ccode.chimeras"/>
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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72 <data name="out_accnos" format="mothur.accnos" from_work_dir="fasta.*ccode.accnos" label="${tool.name} on ${on_string}: ccode.accnos"/>
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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73 <data name="mapinfo" format="tabular" from_work_dir="*.mapinfo" label="${tool.name} on ${on_string}: mapinfo"/>
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74 </outputs>
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75 <tests>
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76 <test>
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77 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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78 <param name="source" value="hist"/>
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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79 <param name="template" value="HMP_MOCK.v35.align"/>
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80 <output name="out_file" ftype="txt">
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81 <assert_contents>
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82 <has_line_matching expression="^Window\tAvgQ\t\(sdQ\)\tAvgR\t\(sdR\)\tRatio\tAnova$"/>
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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83 </assert_contents>
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84 </output>
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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85 <output name="out_accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.good.ccode.accnos" ftype="mothur.accnos"/>
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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86 <output name="mapinfo" md5="ef3353b1467fe95a24153513917e6444" ftype="tabular"/>
d6b58ab6093a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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87 <expand macro="logfile-test"/>
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88 </test>
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89 <test> <!-- test with default ecoli mask -->
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90 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
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91 <param name="source" value="hist"/>
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92 <param name="template" value="HMP_MOCK.v35.align"/>
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93 <param name="source2" value="default"/>
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94 <param name="window" value="100"/>
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95 <output name="out_file" ftype="txt">
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96 <assert_contents>
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97 <has_line_matching expression="^Window\tAvgQ\t\(sdQ\)\tAvgR\t\(sdR\)\tRatio\tAnova$"/>
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98 </assert_contents>
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99 </output>
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100 <output name="out_accnos" md5="47ddf86ec36aafd495aa902b3e06ffca" ftype="mothur.accnos"/>
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101 <output name="mapinfo" md5="25221b1e109d9c0a939efb319e7a9896" ftype="tabular"/>
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102 <expand macro="logfile-test"/>
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103 </test>
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104 </tests>
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105 <help>
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106 <![CDATA[
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107
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108 @MOTHUR_OVERVIEW@
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109
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110 **Command Documenation**
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111
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112 The chimera.ccode_ command identifies putative chimeras using the ccode approach (Chimera and Cross-Over Detection and Evaluation). Ccode_ compares differences in distances, for each word, between query sequence and reference sequences, and reference sequences and themselves.
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113
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114 This method was written using the algorithms described in the paper_ "Evaluating putative chimeric sequences from PCR-amplified products" by Juan M. Gonzalez, Johannes Zimmerman and Cesareo Saiz-Jimenez.
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115
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116 The program can analyze sequences for any required word length. Generally, values of 5-20% of sequence length appear to deliver accurate results, for example, working on 16S rDNA sequences with a full-length of #1500 nt. It should be noted that the use of fragments either too long or too short might result in a reduction of sensitivity.
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117
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118 .. _Ccode: http://www.microextreme.net/downloads.html
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119 .. _paper: http://bioinformatics.oxfordjournals.org/content/21/3/333.full.pdf
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120 .. _chimera.ccode: http://www.mothur.org/wiki/Chimera.ccode
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121
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122 ]]>
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123 </help>
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124 <expand macro="citations"/>
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125 </tool>