Mercurial > repos > iuc > vsearch

annotate clustering.xml @ 2:f29e21388219 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
author iuc
date Thu, 17 Dec 2015 12:53:39 -0500
parents 8c4e2933a17a
children 4258854759ba
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f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
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1 <tool id="vsearch_clustering" name="VSearch clustering" version="@VERSION@.2">
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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
2
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14 #if $clustering_mode.clustering_mode_select == 'cluster_fast':
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15 --cluster_fast "$infile"
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16 #else if $clustering_mode.clustering_mode_select == 'cluster_smallmem':
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17 --cluster_smallmem "$infile"
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18 #end if
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19 ##--clusters STRING output each cluster to a separate FASTA file
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20
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21 #if $maxrejects:
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22 --maxrejects "$maxrejects"
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23 #end if
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24 #if $maxaccepts:
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25 --maxaccepts "$maxaccepts"
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26 #end if
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27
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28 $cons_truncate
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29 --id "$id"
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30 --iddef "$iddef"
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31
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32 #if '--msaout' in str($outputs).split( "," ):
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
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33 --msaout "$msaout"
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34 #end if
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35 #if '--consout' in str($outputs).split( "," ):
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36 --consout "$consout"
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37 #end if
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38 #if '--centroids' in str($outputs).split( "," ):
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
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39 --centroids "$centroids"
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40 #end if
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41 #if '--alnout' in str($outputs).split( "," ):
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42 --alnout "$alnout"
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43 #end if
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44 #if '--blast6out' in str($outputs).split( "," ):
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45 --blast6out "$blast6out"
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46 #end if
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47 #if '--notmatched' in str($outputs).split( "," ):
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48 --notmatched "$notmatched"
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49 #end if
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50 #if '--fastapairs' in str($outputs).split( "," ):
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51 --fastapairs "$fastapairs"
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52 #end if
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53 #if '--matched' in str($outputs).split( "," ):
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
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54 --matched "$matched"
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55 #end if
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56 #if str( $qmask ) != 'no':
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57 --qmask "$qmask"
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58 #end if
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59 $sizein
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60 $sizeout
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61 --strand "$strand"
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62 $usersort
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63 #if $uc:
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64 --uc "$uc_outfile"
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65 #end if
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66
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67 ]]>
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68 </command>
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69 <inputs>
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70 <param name="infile" type="data" format="fasta" label="Select your input FASTA file" help="" />
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71 <conditional name="clustering_mode">
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72 <param name="clustering_mode_select" type="select" label="Choose sorting method to use before clustering" help="">
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73 <option value="cluster_fast" default="True">Cluster sequences after sorting by length (--cluster-fast)</option>
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74 <option value="cluster_smallmem">Cluster already sorted sequences (--cluster-smallmem)</option>
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75 </param>
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76 <when value="cluster_fast">
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77 </when>
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78 <when value="cluster_smallmem">
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79 </when>
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80 </conditional>
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81 <param name="usersort" type="boolean" truevalue="--usersort" falsevalue="" checked="False"
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82 label="Indicate that input sequences are not presorted by length" help="(--usersort)"/>
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83 <expand macro="id_and_iddef" />
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84 <param name="cons_truncate" type="boolean" truevalue="--cons_truncate" falsevalue="" checked="False"
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85 label="Do not ignore terminal gaps in MSA for consensus" help="(--cons_truncate)"/>
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86 <expand macro="qmask" />
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87 <expand macro="sizein" />
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88 <expand macro="sizeout" />
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89 <expand macro="strand" />
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90 <expand macro="maxrejects" />
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91 <expand macro="maxaccepts" />
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92 <expand macro="general_output">
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93 <option value="--msaout">Multiple sequence alignments</option>
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94 <option value="--consout">Cluster consensus sequences</option>
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95 <option value="--centroids">Centroid sequences</option>
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96 <option value="--notmatched">Write non-matching query sequences to separate file</option>
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97 <option value="--matched">Write matching query sequences to separate file</option>
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98 </expand>
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99 <expand macro="uclust_like_output" />
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100
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101 </inputs>
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102 <outputs>
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103 <data name="msaout" format="fasta" label="${tool.name} on ${on_string}: Multiple Sequence Alignments">
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104 <filter>'--msaout' in outputs</filter>
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105 </data>
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106 <data name="consout" format="fasta" label="${tool.name} on ${on_string}: Consensus Sequences">
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107 <filter>'--consout' in outputs</filter>
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108 </data>
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109 <data name="centroids" format="fasta" label="${tool.name} on ${on_string}: Cluster centroids">
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110 <filter>'--centroids' in outputs</filter>
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111 </data>
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112 <data name="alnout" format="fasta" label="${tool.name} on ${on_string}: Alignment">
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113 <filter>'--alnout' in outputs</filter>
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114 </data>
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115 <data name="notmatched" format="fasta" label="${tool.name} on ${on_string}: Non-matched queries">
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116 <filter>'--notmatched' in outputs</filter>
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117 </data>
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118 <data name="matched" format="fasta" label="${tool.name} on ${on_string}: Matching query sequences">
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119 <filter>'--matched' in outputs</filter>
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120 </data>
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121 <data name="blast6out" format="tabular" label="${tool.name} on ${on_string}: BLAST like tabular">
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122 <filter>'--blast6out' in outputs</filter>
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123 </data>
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124 <data name="fastapairs" format="fasta" label="${tool.name} on ${on_string}: Query/Target sequences">
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125 <filter>'--fastapairs' in outputs</filter>
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126 </data>
1
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127 <data name="uc_outfile" format="tabular" label="${tool.name} on ${on_string}: UCLUST like output">
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128 <filter>uc is True</filter>
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129 </data>
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130 </outputs>
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131 <tests>
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132 <test>
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133 <param name="infile" value="BioMarKs5k.fsa.bz2" ftype="fasta" />
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134 <param name="id" value="0.99"/>
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135 <param name="maxaccepts" value="1"/>
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136 <param name="maxrejects" value="2"/>
1
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137 <param name="sizeout" value=""/>
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138 <param name="outputs" value="--centroids,--alnout,--blast6out,--notmatched" />
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139 <output name="centroids" file="clustering_centroids_result1.fasta" ftype="fasta" />
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140 <output name="blast6out" file="clustering_blast6out_result1.tab" ftype="tabular" />
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141 <output name="notmatched" file="clustering_notmatched_result1.fasta" ftype="fasta" />
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142 <!-- The result following result files would be too big -->
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143 <!--output name="matched" file="clustering_matched_result1.fasta" ftype="fasta" /-->
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144 <!--output name="alnout" file="clustering_alnout_result1.fasta" lines_diff="2" ftype="fasta" /-->
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145 <!--output name="fastapairs" file="clustering_fastapairs_result1.fasta" ftype="fasta" /-->
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146 <!--output name="msaout" file="clustering_msaout_result1.fasta" ftype="fasta" /-->
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147 </test>
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148 <test>
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149 <param name="infile" value="BioMarKs5k.fsa.bz2" ftype="fasta" />
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150 <param name="clustering_mode_select" value="cluster_smallmem"/>
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151 <param name="usersort" value="--usersort"/>
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152 <param name="id" value="0.99"/>
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153 <param name="maxaccepts" value="1"/>
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154 <param name="maxrejects" value="2"/>
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155 <param name="sizeout" value="--sizeout"/>
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156 <param name="outputs" value="--centroids,--blast6out,--notmatched" />
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157 <output name="centroids" file="clustering_centroids_result2.fasta" ftype="fasta" />
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158 <output name="blast6out" file="clustering_blast6out_result2.tab" ftype="tabular" />
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159 <output name="notmatched" file="clustering_notmatched_result2.fasta" ftype="fasta" />
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160 </test>
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161 <test>
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162 <param name="infile" value="BioMarKs5k.fsa.bz2" ftype="fasta" />
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163 <param name="clustering_mode_select" value="cluster_smallmem"/>
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164 <param name="usersort" value="--usersort"/>
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165 <param name="id" value="0.99"/>
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166 <param name="maxaccepts" value="1"/>
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167 <param name="maxrejects" value="2"/>
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168 <param name="sizeout" value="--sizeout"/>
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169 <param name="outputs" value="--centroids" />
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170 <param name="uc" value="--uc"/>
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171 <output name="centroids" file="clustering_centroids_result2.fasta" ftype="fasta" />
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172 <output name="uc_outfile" file="clustering_uc_result3.uc" ftype="tabular" />
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173 </test>
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174 <test>
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175 <param name="infile" value="BioMarKs5k.fsa.bz2" ftype="fasta" />
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176 <param name="clustering_mode_select" value="cluster_smallmem"/>
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177 <param name="usersort" value="--usersort"/>
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178 <param name="id" value="0.99"/>
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179 <param name="maxaccepts" value="1"/>
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180 <param name="maxrejects" value="2"/>
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181 <param name="sizeout" value="--sizeout"/>
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182 <param name="outputs" value="--centroids" />
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183 <param name="iddef" value="0"/>
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184 <output name="centroids" file="clustering_centroids_result4.fasta" ftype="fasta" />
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185 </test>
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186 <test>
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187 <param name="infile" value="BioMarKs5k.fsa.bz2" ftype="fasta" />
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188 <param name="clustering_mode_select" value="cluster_fast"/>
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189 <param name="usersort" value="--usersort"/>
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190 <param name="id" value="0.99"/>
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191 <param name="maxaccepts" value="1"/>
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192 <param name="maxrejects" value="2"/>
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193 <param name="sizeout" value=""/>
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194 <param name="outputs" value="--centroids" />
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195 <param name="qmask" value="none"/>
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196 <output name="centroids" file="clustering_centroids_result1.fasta" ftype="fasta" />
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197 </test>
0
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198 </tests>
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199 <help>
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200 <![CDATA[
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201 **What it does**
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202
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203 vsearch implements a single-pass, greedy star-clustering algorithm, similar to the algorithms
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204 implemented in usearch, DNAclust and sumaclust for example.
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205
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206
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207 Clustering options (most searching options also apply)
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208 --centroids FILENAME output centroid sequences to FASTA file
1
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209 --cluster_fast FILENAME cluster sequences after sorting by length
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210 --cluster_size FILENAME cluster sequences after sorting by abundance
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211 --cluster_smallmem FILENAME cluster already sorted sequences (see -usersort)
0
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212 --clusters STRING output each cluster to a separate FASTA file
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213 --consout FILENAME output cluster consensus sequences to FASTA file
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214 --cons_truncate do not ignore terminal gaps in MSA for consensus
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215 --id REAL reject if identity lower
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216 --iddef INT id definition, 0-4=CD-HIT,all,int,MBL,BLAST (2)
1
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217 --msaout FILENAME output multiple seq. alignments to FASTA file
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218 --qmask seqs with dust, soft or no method (dust)
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219 --sizein propagate abundance annotation from input
0
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220 --sizeout write cluster abundances to centroid file
1
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221 --strand cluster using plus or both strands (plus)
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222 --uc FILENAME filename for UCLUST-like output
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223 --usersort indicate sequences not presorted by length
0
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224
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225
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226 @EXTERNAL_DOCUMENTATION@
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227
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228
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229 ]]>
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230 </help>
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231 <expand macro="citations" />
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232 </tool>