Mercurial > repos > iuc > mothur_chimera_check

annotate chimera.check.xml @ 2:37bd32018025 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 22:20:22 -0400
parents 8e874c18a298
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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8e874c18a298 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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1 <tool profile="16.07" id="mothur_chimera_check" name="Chimera.check" version="@WRAPPER_VERSION@.0">
8e874c18a298 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 <description>Find putative chimeras using chimeraCheck</description>
8e874c18a298 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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3 <macros>
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iuc
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4 <import>macros.xml</import>
8e874c18a298 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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5 </macros>
8e874c18a298 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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6 <expand macro="requirements"/>
8e874c18a298 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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7 <expand macro="stdio"/>
8e874c18a298 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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8 <expand macro="version_command"/>
8e874c18a298 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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9 <command><![CDATA[
2
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10 @SHELL_OPTIONS@
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11
2
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12 ## create symlinks to input datasets
37bd32018025 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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13 ln -s '$fasta' fasta.dat &&
37bd32018025 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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14 ln -s '$alignment.reference' alignment.reference.dat &&
37bd32018025 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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15 #if $svg_cond.svg == "yes":
37bd32018025 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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16 ln -s '$svg_cond.name' svg.name.dat &&
37bd32018025 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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17 #end if
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18
2
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19 echo 'chimera.check(
37bd32018025 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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20 fasta=fasta.dat,
37bd32018025 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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21 reference=alignment.reference.dat,
37bd32018025 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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22 #if $svg_cond.svg == "yes":
37bd32018025 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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23 svg=yes,
37bd32018025 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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24 name=svg.name.dat,
37bd32018025 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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25 #end if
37bd32018025 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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26 increment=$increment,
37bd32018025 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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27 ksize=$ksize,
37bd32018025 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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28 processors='\${GALAXY_SLOTS:-8}'
37bd32018025 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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29 )'
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iuc
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30 | sed 's/ //g' ## mothur trips over whitespace
37bd32018025 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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31 | mothur
37bd32018025 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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32 | tee mothur.out.log
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8e874c18a298 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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33 ]]></command>
8e874c18a298 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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34 <inputs>
2
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35 <param argument="fasta" type="data" format="mothur.align" label="fasta - Candiate Aligned Sequences"/>
0
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36 <conditional name="alignment">
2
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37 <param name="source" type="select" label="Select Reference Template from">
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38 <option value="hist">History</option>
8e874c18a298 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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39 <option value="ref">Cached Reference</option>
8e874c18a298 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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40 </param>
8e874c18a298 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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41 <when value="ref">
2
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42 <param argument="reference" type="select" label="reference - Select an alignment database">
37bd32018025 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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43 <options from_data_table="mothur_aligndb"/>
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44 </param>
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45 </when>
8e874c18a298 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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46 <when value="hist">
2
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47 <param argument="reference" type="data" format="fasta" label="reference - Reference to align with"/>
0
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48 </when>
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49 </conditional>
2
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50 <param argument="ksize" type="integer" value="7" label="ksize - kmer length to determine differences between sequence fragments"
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51 help="uses default if &lt; 1"/>
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52 <param argument="increment" type="integer" value="10" label="increment - Increment for window slide on each iteration"
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53 help="Default is 10, but you may set it up to sequence length minus twice the window."/>
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54 <conditional name="svg_cond">
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55 <param argument="svg" type="select" label="svg - Generate a SVG plot for each query sequence">
0
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56 <option value="no" selected="true">No</option>
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57 <option value="yes">Yes</option>
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58 </param>
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59 <when value="no"/>
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60 <when value="yes">
2
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61 <param argument="name" type="data" format="mothur.names" optional="true" label="name - Names of queries for which to generate SVG plot"/>
0
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62 </when>
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63 </conditional>
2
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64 <expand macro="param-savelog"/>
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65 </inputs>
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66 <outputs>
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67 <expand macro="logfile-output"/>
2
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68 <data name="chimeracheck.chimeras" format="txt" from_work_dir="fasta.chimeracheck.chimeras" label="${tool.name} on ${on_string}: chimeracheck.chimeras"/>
0
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69 <collection name="images" type="list" label="${tool.name} on ${on_string}: SVG images">
8e874c18a298 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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70 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.chimeracheck\.svg"/>
8e874c18a298 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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71 <filter>svg['gen'] == 'yes'</filter>
8e874c18a298 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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72 </collection>
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73 </outputs>
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74 <tests>
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75 <test>
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76 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
8e874c18a298 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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77 <param name="source" value="hist"/>
2
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78 <param name="reference" value="HMP_MOCK.v35.align"/>
37bd32018025 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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79 <output name="chimeracheck.chimeras" file="Mock_S280_L001_R1_001_small.trim.contigs.good.chimeracheck.chimeras" ftype="txt"/>
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80 <param name="savelog" value="true"/>
0
8e874c18a298 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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81 <expand macro="logfile-test"/>
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82 </test>
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83 <test>
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84 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
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85 <param name="source" value="hist"/>
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86 <param name="reference" value="HMP_MOCK.v35.align"/>
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87 <param name="svg" value="yes"/>
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88 <param name="name" value="Mock_S280_L001_R1_001_small.trim.contigs.good.names_tiny"/>
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89 <output name="chimeracheck.chimeras" file="Mock_S280_L001_R1_001_small.trim.contigs.good.chimeracheck.chimeras" ftype="txt"/>
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90 <output_collection name="images" count="2">
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91 <element name="M00967_43_000000000-A3JHG_1_1101_14010_4122" file="M00967_43_000000000-A3JHG_1_1101_14010_4122.chimeracheck.svg"/>
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92 <element name="M00967_43_000000000-A3JHG_1_1101_13293_4703" md5="0d99dc17c183dab4efc75c697060a9a5"/>
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93 </output_collection>
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94 <param name="savelog" value="true"/>
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95 <expand macro="logfile-test"/>
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96 </test>
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97 </tests>
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98 <help><![CDATA[
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99
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100 @MOTHUR_OVERVIEW@
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101
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102 **Command Documentation**
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103
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104 The chimera.check_ command identifies putative chimeras using the chimeraCheck approach. It looks at distance of left side of query to it's closest match + distance of right side of query to it's closest match - distance of whole query and its closest match over several windows.
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105
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106 Note: following the RDP model this method does not determine whether or not a sequence is chimeric, but allows you to determine that based on the IS values produced.
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107
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108 .. _chimera.check: https://www.mothur.org/wiki/Chimera.check
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109
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110 ]]></help>
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111 <expand macro="citations"/>
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112 </tool>