Mercurial > repos > iuc > mothur_sffinfo

annotate sffinfo.xml @ 5:12507ed33710 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7f7605c2c8d8e92f3369dfdc290e5d8d06fa409a
author iuc
date Fri, 03 Aug 2018 14:42:10 -0400
parents 13d1e5e44a91
children 51d7c2486a68
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5ada2d00e874 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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1 <tool profile="16.07" id="mothur_sffinfo" name="Sffinfo" version="@WRAPPER_VERSION@.0">
5ada2d00e874 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 <description>Summarize the quality of sequences</description>
5ada2d00e874 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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3 <macros>
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4 <import>macros.xml</import>
5ada2d00e874 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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5 </macros>
5ada2d00e874 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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6 <expand macro="requirements"/>
5ada2d00e874 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
2
13d1e5e44a91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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10 @SHELL_OPTIONS@
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11
2
13d1e5e44a91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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12 ## create symlinks to input datasets
13d1e5e44a91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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13 ln -s '$sff' sff.dat &&
13d1e5e44a91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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14 ln -s '$accnos' accnos.dat &&
13d1e5e44a91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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15 #if $oligo.add == "yes":
13d1e5e44a91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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16 ln -s '$oligo.oligos' oligo.oligos.dat &&
13d1e5e44a91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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17 #end if
0
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18
2
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19 echo 'sffinfo(
13d1e5e44a91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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20 sff=sff.dat,
13d1e5e44a91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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21 fasta=$fasta,
13d1e5e44a91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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22 qfile=$qfile,
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23 $sfftxt
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24 flow=$flow,
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25 trim=$trim
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26 #if $accnos:
13d1e5e44a91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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27 ,accnos=accnos.dat
13d1e5e44a91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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28 #end if
13d1e5e44a91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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29 #if $oligo.add == "yes":
13d1e5e44a91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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30 ,oligos=oligo.oligos.dat
13d1e5e44a91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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31 ,bdiffs=$oligo.bdiffs
13d1e5e44a91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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32 ,pdiffs=$oligo.pdiffs
13d1e5e44a91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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33 ,tdiffs=$oligo.tdiffs
13d1e5e44a91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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34 ,ldiffs=$oligo.ldiffs
13d1e5e44a91 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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35 ,sdiffs=$oligo.sdiffs
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36 #end if
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37 )'
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38 | sed 's/ //g' ## mothur trips over whitespace
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39 | mothur
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40 | tee mothur.out.log
0
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41 ]]></command>
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42 <inputs>
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43 <param name="sff" type="data" format="sff" label="sff - Sff data"/>
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44 <conditional name="oligo">
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45 <param name="add" type="select" label="Trim with an oligos file?" help="a file that can contain the sequences of the forward and reverse primers and barcodes and their sample identifier. Each line of the oligos file can start with the key words &quot;forward&quot;, &quot;reverse&quot;, and &quot;barcode&quot; or it can start with a &quot;#&quot; to tell mothur to ignore that line of the oligos file.">
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46 <option value="no" selected="true">no</option>
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47 <option value="yes">yes</option>
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48 </param>
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49 <when value="no"/>
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50 <when value="yes">
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51 <param name="oligos" type="data" format="mothur.oligos" label="oligos - barcodes and primers"/>
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52 <param name="bdiffs" type="integer" value="0" min="0" label="bdiffs - number of differences to allow in the barcode (default 0)"/>
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53 <param name="pdiffs" type="integer" value="0" min="0" label="pdiffs - number of differences to allow in the primer (default 0)"/>
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54 <param name="tdiffs" type="integer" value="0" min="0" label="tdiffs - total number of differences to allow in primer and barcode (default 0)"/>
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55 <param name="ldiffs" type="integer" value="0" min="0" label="ldiffs - total number of differences to allow in linker sequence (default 0)"/>
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56 <param name="sdiffs" type="integer" value="0" min="0" label="sdiffs - total number of differences to allow in spacer sequence (default 0)"/>
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57 </when>
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58 </conditional>
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59 <param name="fasta" type="boolean" truevalue="true" falsevalue="false" checked="true" label="fasta - Add fasta to your history"/>
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60 <param name="qfile" type="boolean" truevalue="true" falsevalue="false" checked="true" label="qfile - Add qfile to your history"/>
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61 <param name="sfftxt" type="boolean" truevalue="sfftxt=true," falsevalue="" checked="false" label="sfftxt - Add sfftxt to your history"/>
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62 <param name="flow" type="boolean" truevalue="true" falsevalue="false" checked="true" label="flow - Add flow to your history"/>
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63 <param name="trim" type="boolean" truevalue="true" falsevalue="false" checked="true" label="trim - Trim sequences and quality scores"/>
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64 <param name="accnos" type="data" format="mothur.accnos" optional="true" label="accnos - Limit output to named Accessions"/>
2
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65 <expand macro="param-savelog"/>
0
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66 </inputs>
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67 <outputs>
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68 <expand macro="logfile-output"/>
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69 <data name="out_fasta" format="fasta" from_work_dir="sff*.fasta" label="${tool.name} on ${on_string}: fasta">
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70 <filter>fasta</filter>
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71 </data>
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72 <data name="out_qfile" format="qual454" from_work_dir="sff*.qual" label="${tool.name} on ${on_string}: qual">
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73 <filter>qfile</filter>
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74 </data>
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75 <data name="out_sfftxt" format="txt" from_work_dir="sff*.sff.txt" label="${tool.name} on ${on_string}: sff.txt">
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76 <filter>sfftxt</filter>
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77 </data>
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78 <data name="out_flow" format="mothur.sff.flow" from_work_dir="sff*.flow" label="${tool.name} on ${on_string}: flowgram">
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79 <filter>flow</filter>
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80 </data>
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81 <data name="out_scrap" format="sff" from_work_dir="sff*.scrap.sff" label="${tool.name} on ${on_string}: scrap.sff">
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82 <filter>oligo['add'] == 'yes'</filter>
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83 </data>
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84 </outputs>
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85 <tests>
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86 <test><!-- test without oligos -->
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87 <param name="sff" value="Fasting_Example1.sff"/>
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88 <param name="sfftxt" value="true"/>
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89 <output name="out_fasta" md5="fbe6f4d51959d4723a8417636476d0e0" ftype="fasta"/>
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90 <output name="out_qfile" md5="ffcc4831369139055e1b8e9add9a59c0" ftype="qual454"/>
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91 <output name="out_sfftxt" md5="fdc80c8e476016632d317cfd7893713c" ftype="txt"/>
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92 <output name="out_flow" md5="34b17477f98ab19c1ff755a61848d968" ftype="mothur.sff.flow"/>
2
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93 <param name="savelog" value="true"/>
0
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94 <expand macro="logfile-test"/>
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95 </test>
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96 <test><!-- test with oligos file -->
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97 <param name="sff" value="Fasting_Example1.sff"/>
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98 <param name="add" value="yes"/>
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99 <param name="oligos" value="GQY1XT001.oligos"/>
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100 <output name="out_fasta" md5="212fa15e1ed077cecb65ee87f17ef2e1" ftype="fasta"/>
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101 <output name="out_qfile" md5="ffcc4831369139055e1b8e9add9a59c0" ftype="qual454"/>
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102 <output name="out_flow" md5="34b17477f98ab19c1ff755a61848d968" ftype="mothur.sff.flow"/>
2
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103 <output name="out_scrap" file="Fasting_Example1.scrap.sff" ftype="sff" compare="sim_size"/>
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104 <param name="savelog" value="true"/>
0
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105 <expand macro="logfile-test"/>
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106 </test>
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107 </tests>
2
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108 <help><![CDATA[
0
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109
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110 @MOTHUR_OVERVIEW@
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111
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112 **Command Documentation**
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113
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114 The sffinfo_ command will summarize the quality of sequences in an unaligned or aligned fasta-formatted sequence file.
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115
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116
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117 .. _sffinfo: https://www.mothur.org/wiki/Sffinfo
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118
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119 ]]></help>
0
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120 <expand macro="citations"/>
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121 </tool>