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annotate sorting.xml @ 3:4258854759ba draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 29f6e6424a37947adbe1eba92f0e7d3c83efc042-dirty
author iuc
date Tue, 01 Mar 2016 07:07:03 -0500
parents f29e21388219
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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4258854759ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 29f6e6424a37947adbe1eba92f0e7d3c83efc042-dirty
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1 <tool id="vsearch_sorting" name="VSearch sorting" version="@VERSION@.0">
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2 <description></description>
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3 <macros>
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4 <import>vsearch_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="stdio" />
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8 <expand macro="version_command" />
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9 <command>
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10 <![CDATA[
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11 vsearch
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12 @GENERAL@
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13 #if $sorting_mode.sorting_mode_select == 'sortbylength':
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14 --sortbylength "$sorting_mode.infile"
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15 #else:
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16 --sortbysize "$sorting_mode.infile"
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17 #if str( $sorting_mode.minsize ):
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18 --minsize "$sorting_mode.minsize"
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19 #end if
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20 #if str( $sorting_mode.maxsize ):
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21 --maxsize "$sorting_mode.maxsize"
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22 #end if
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23 #end if
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24 --output "$outfile"
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25 #if $relabel:
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26 --relabel "$relabel"
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27 #end if
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28 $sizeout
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29 #if str( $topn ):
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30 --topn "$topn"
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31 #end if
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32
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33 ]]>
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34 </command>
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35 <inputs>
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36 <conditional name="sorting_mode">
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37 <param name="sorting_mode_select" type="select" label="Sorting by" help="">
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38 <option value="sortbylength">sequence length</option>
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39 <option value="sortbyabundance">by abundance</option>
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40 </param>
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41 <when value="sortbylength">
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42 <param name="infile" type="data" format="fasta" label="Select your FASTA file" help="(--sortbylength)" />
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43 </when>
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44 <when value="sortbyabundance">
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45 <param name="infile" type="data" format="fasta" label="Select your FASTA file" help="(--sortbysize)" />
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46 <param name="minsize" type="integer" value="" optional="True" label="Minimum abundance"
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47 help="(--minsize)"/>
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48 <param name="maxsize" type="integer" value="" optional="True" label="Maximum abundance"
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49 help="(--maxsize)"/>
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50 </when>
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51 </conditional>
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52 <expand macro="topn" />
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53 <param name="relabel" type="text" value=""
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54 label="Relabel with this prefix string after sorting" help="(--relabel)"/>
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55 <param name="sizeout" type="boolean" truevalue="--sizeout" falsevalue="" checked="False"
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56 label="Add abundance annotation to output" help="(--sizeout)"/>
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57 </inputs>
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58 <outputs>
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59 <data name="outfile" format="fasta" label="${tool.name} on ${on_string}" />
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60 </outputs>
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61 <tests>
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62 <test>
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63 <param name="sorting_mode_select" value="sortbyabundance"/>
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64 <param name="infile" value="db.fasta" ftype="fasta" />
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65 <output name="outfile" file="sorting_result1.fasta" ftype="fasta" />
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66 </test>
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67 <test>
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68 <param name="sorting_mode_select" value="sortbylength"/>
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69 <param name="infile" value="db.fasta" ftype="fasta" />
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70 <output name="outfile" file="sorting_result2.fasta" ftype="fasta" />
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71 </test>
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72 <test>
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73 <param name="sorting_mode_select" value="sortbylength"/>
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74 <param name="infile" value="db.fasta" ftype="fasta" />
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75 <param name="relabel" value="TEST" />
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76 <output name="outfile" file="sorting_result3.fasta" ftype="fasta" />
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77 </test>
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78 <test>
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79 <param name="sorting_mode_select" value="sortbylength"/>
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80 <param name="infile" value="db.fasta" ftype="fasta" />
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81 <param name="sizeout" value="--sizeout" />
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82 <output name="outfile" file="sorting_result4.fasta" ftype="fasta" />
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83 </test>
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84 <test>
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85 <param name="sorting_mode_select" value="sortbylength"/>
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86 <param name="infile" value="db.fasta" ftype="fasta" />
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87 <param name="relabel" value="With spaces" />
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88 <output name="outfile" file="sorting_result5.fasta" ftype="fasta" />
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89 </test>
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90 </tests>
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91 <help>
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92 <![CDATA[
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93 **What it does**
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94
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95 Fasta entries are sorted by decreasing abundance (−−sortbysize) or sequence length (−−sort-
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96 bylength). To obtain a stable sorting order, ties are sorted by decreasing abundance and label
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97 increasing alpha-numerical order (−−sortbylength), or just by label increasing alpha-numerical
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98 order (−−sortbysize). Label sorting assumes that all sequences have unique labels. The same
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99 applies to the automatic sorting performed during chimera checking (−−uchime_denovo), derepli-
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100 cation (−−derep_fulllength), and clustering (−−cluster_fast and −−cluster_size).
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101
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102 Sorting options
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103 --maxsize INT maximum abundance for sortbysize
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104 --minsize INT minimum abundance for sortbysize
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105 --output FILENAME output FASTA file
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106 --relabel STRING relabel with this prefix string after sorting
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107 --sizeout add abundance annotation to output
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108 --sortbylength FILENAME sort sequences by length in given FASTA file
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109 --sortbysize FILENAME abundance sort sequences in given FASTA file
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110 --topn INT output just top n seqs after sorting
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111
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112
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113 @EXTERNAL_DOCUMENTATION@
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114
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115
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116 ]]>
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117 </help>
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118 <expand macro="citations" />
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119 </tool>