Mercurial > repos > iuc > obi_annotate

annotate obiannotate.xml @ 2:3021b9f5809f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
author iuc
date Thu, 28 Nov 2019 15:50:43 -0500
parents 3d21aa00d575
children f82cefbbcea5
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3d21aa00d575 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
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1 <tool id="obi_annotate" name="obiannotate" version="@TOOL_VERSION@">
0
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2 <description>Adds/Edits sequence record annotations</description>
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3 <macros>
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4 <import>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 <command>
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10 <![CDATA[
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11 obiannotate
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12 ${seqrank}
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14 #if $rename_tag.old_name and $rename_tag.new_name
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15 -R '$rename_tag.old_name':'$rename_tag.new_name'
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16 #end if
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18 #if $deletetag_key
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19 --delete-tag='$deletetag_key'
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20 #end if
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22 #if $set_tag.key and $set_tag.pythonexpression
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23 -S '$set_tag.key':'$set_tag.pythonexpression'
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24 #end if
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26 #if $taglist
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27 --tag-list='$taglist'
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28 #end if
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30 #if $setid_pythonexpression
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31 --set-identifier='$setid_pythonexpression'
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32 #end if
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34 #if $pythonexpression
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35 --run='$pythonexpression'
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36 #end if
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38 #if $setsequence_pythonexpression
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39 --set-sequence='$setsequence_pythonexpression'
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40 #end if
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42 #if $setdefinition_pythonexpression
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43 --set-definition='$setdefinition_pythonexpression'
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44 #end if
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46 #if $key_selector.key
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47 --keep='$key_selector.key'
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48 #end if
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49 #if $key_selector.key2
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50 --keep='$key_selector.key2'
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51 #end if
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52 #if $key_selector.key3
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53 --keep='$key_selector.key3'
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54 #end if
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55 #if $key_selector.key4
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56 --keep='$key_selector.key4'
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57 #end if
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58 #if $key_selector.key5
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59 --keep='$key_selector.key5'
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60 #end if
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61
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62 ${length}
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63 ${clearbool}
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64 ${uniqid}
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65
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66 #if $rankname
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67 --with-taxon-at-rank='$rankname'
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68 #end if
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69
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70 #if $mclfile
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71 --mcl='$mclfile'
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72 #end if
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73
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74 '$inputseq' > '$output'
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75 ]]>
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76
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77 </command>
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78
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79 <inputs>
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80 <param name="inputseq" type="data" format="fastq,fasta" label="Input sequences file" />
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81 <param name="seqrank" type="boolean" label="Add a new attribute seq_rank" truevalue="--seq-rank" falsevalue="" help="Use this option if you want to add a new attribute named seq_rank to the sequence record indicating its entry number in the sequence file" />
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82 <section name="rename_tag" title="Rename attribute" expanded="False">
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83 <param name="old_name" type="text" label="old name" optional="true"/>
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84 <param name="new_name" type="text" label="new name" optional="true"/>
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85 </section>
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86 <param name="deletetag_key" type="text" label="Delete attribute" optional="true" help="Use this option if you want to delete attribute named ATTRIBUTE_NAME.When this attribute is missing, the sequence record is skipped and the next one is examined"/>
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87
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88 <section name="set_tag" title="Create a new attribute" expanded="False">
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89 <param name="key" type="text" label="key" optional="true"/>
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90 <param name="pythonexpression" type="text" label="python expression" optional="true"/>
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91 </section>
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92
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93 <param name="taglist" type="data" optional="true" format="txt,tabular" label="Use a tag list" help="file containing identifiers of sequences to select" />
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94
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95 <param name="setid_pythonexpression" type="text" label="Set sequence record identifier with a value" help="Use this option if you want to set sequence record identifier with a value computed from PYTHON_EXPRESSION" />
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96
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97 <param name="pythonexpression" type="text" label="Run a PYTHON_EXPRESSION on each selected sequence" optional="true" help="Use this option if you want to run a PYTHON_EXPRESSION on each selected sequence"/>
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98
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99 <param name="setsequence_pythonexpression" type="text" label="Change the sequence itself with a value" help="Use this option if you want to change the sequence itself with a value computed from PYTHON_EXPRESSION"/>
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100
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101 <param name="setdefinition_pythonexpression" type="text" label="Set sequence definition with a value computed" help="Use this option if you want to set sequence definition with a value computed from PYTHON_EXPRESSION"/>
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102
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103 <param name="clearbool" type="boolean" label="Clear all attributes associated to the sequence records" truevalue="--clear" falsevalue="" help="Use this option if you want to clear all attributes associated to the sequence records" />
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104
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105 <section name="key_selector" title="Keep only attribute with key" expanded="False">
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106 <param name="key" type="text" label="key" optional="true" />
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107 <param name="key2" type="text" label="if you want to specify a second key" optional="true" />
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108 <param name="key3" type="text" label="if you want to specify a third key" optional="true" />
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109 <param name="key4" type="text" label="if you want to specify a fourth key" optional="true" />
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110 <param name="key5" type="text" label="if you want to specify a fifth key" optional="true" />
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111 </section>
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112
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113 <param name="length" type="boolean" label="Use the length option?" truevalue="--length" falsevalue="" help="Use this option if you want to add attribute with seq_length as a key and sequence length as a value" />
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114
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115 <param name="rankname" type="text" label="Add taxonomic annotation" help="Use this option if you want to add taxonomic annotation at taxonomic rank RANK_NAME"/>
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116
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117 <param name="mclfile" optional="true" type="data" format="txt,tabular" label="mcl file" help="use this option if you want to add a new attribute containing the number of the cluster the sequence record was assigned to, as indicated in file MCLFILE" />
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118
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119 <param name="uniqid" type="boolean" label="Force sequence record ids to be unique" truevalue="--uniq-id" falsevalue="" help="Use this option if you want to force sequence record ids to be unique" />
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120
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121 </inputs>
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122 <outputs>
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123 <data format="fasta" name="output" label="output.fasta with ${tool.name} on ${on_string}" />
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124 </outputs>
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125
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126 <tests>
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127 <test>
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128 <param name="inputseq" value="output_obiuniq.fasta" />
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129 <section name="key_selector">
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130 <param name="key" value="count" />
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131 <param name="key2" value="merged_sample" />
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132 </section>
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133 <param name="uniqid" value="true" />
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134 <param name="clearbool" value="true" />
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135 <param name="length" value="true" />
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136 <param name="seqrank" value="true" />
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137
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138 <output name="output" file="output_obiannotate.fasta" ftype="fasta"/>
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139 </test>
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140 </tests>
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141
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142 <help><![CDATA[
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143
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144 .. class:: infomark
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145
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146 **What it does**
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147
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148 `obiannotate` is the command that allows adding/modifying/removing annotation attributes attached to sequence records.
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149
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150 Once such attributes are added, they can be used by the other OBITools commands for filtering purposes or for statistics computing.
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151
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152 @OBITOOLS_LINK@
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153
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154 ]]>
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155
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156 </help>
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157 <expand macro="citation" />
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158 </tool>