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comparison obiannotate.xml @ 0:6ddfa9d9653b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
author iuc
date Wed, 12 Apr 2017 17:37:37 -0400
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children 3d21aa00d575
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-1:000000000000 0:6ddfa9d9653b
1 <tool id="obi_annotate" name="obiannotate" version="@WRAPPER_VERSION@">
2 <description>Adds/Edits sequence record annotations</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8 <command>
9
10 <![CDATA[
11 obiannotate
12 ${seqrank}
13
14 #if $rename_tag.old_name and $rename_tag.new_name
15 -R '$rename_tag.old_name':'$rename_tag.new_name'
16 #end if
17
18 #if $deletetag_key
19 --delete-tag='$deletetag_key'
20 #end if
21
22 #if $set_tag.key and $set_tag.pythonexpression
23 -S '$set_tag.key':'$set_tag.pythonexpression'
24 #end if
25
26 #if $taglist
27 --tag-list='$taglist'
28 #end if
29
30 #if $setid_pythonexpression
31 --set-identifier='$setid_pythonexpression'
32 #end if
33
34 #if $pythonexpression
35 --run='$pythonexpression'
36 #end if
37
38 #if $setsequence_pythonexpression
39 --set-sequence='$setsequence_pythonexpression'
40 #end if
41
42 #if $setdefinition_pythonexpression
43 --set-definition='$setdefinition_pythonexpression'
44 #end if
45
46 #if $key_selector.key
47 --keep='$key_selector.key'
48 #end if
49 #if $key_selector.key2
50 --keep='$key_selector.key2'
51 #end if
52 #if $key_selector.key3
53 --keep='$key_selector.key3'
54 #end if
55 #if $key_selector.key4
56 --keep='$key_selector.key4'
57 #end if
58 #if $key_selector.key5
59 --keep='$key_selector.key5'
60 #end if
61
62 ${length}
63 ${clearbool}
64 ${uniqid}
65
66 #if $rankname
67 --with-taxon-at-rank='$rankname'
68 #end if
69
70 #if $mclfile
71 --mcl='$mclfile'
72 #end if
73
74 '$inputseq' > '$output'
75 ]]>
76
77 </command>
78
79 <inputs>
80 <param name="inputseq" type="data" format="fastq,fasta" label="Input sequences file" />
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" />
82 <section name="rename_tag" title="Rename attribute" expanded="False">
83 <param name="old_name" type="text" label="old name" optional="true"/>
84 <param name="new_name" type="text" label="new name" optional="true"/>
85 </section>
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"/>
87
88 <section name="set_tag" title="Create a new attribute" expanded="False">
89 <param name="key" type="text" label="key" optional="true"/>
90 <param name="pythonexpression" type="text" label="python expression" optional="true"/>
91 </section>
92
93 <param name="taglist" type="data" optional="true" format="txt,tabular" label="Use a tag list" help="file containing identifiers of sequences to select" />
94
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" />
96
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"/>
98
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"/>
100
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"/>
102
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" />
104
105 <section name="key_selector" title="Keep only attribute with key" expanded="False">
106 <param name="key" type="text" label="key" optional="true" />
107 <param name="key2" type="text" label="if you want to specify a second key" optional="true" />
108 <param name="key3" type="text" label="if you want to specify a third key" optional="true" />
109 <param name="key4" type="text" label="if you want to specify a fourth key" optional="true" />
110 <param name="key5" type="text" label="if you want to specify a fifth key" optional="true" />
111 </section>
112
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" />
114
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"/>
116
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" />
118
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" />
120
121 </inputs>
122 <outputs>
123 <data format="fasta" name="output" label="output.fasta with ${tool.name} on ${on_string}" />
124 </outputs>
125
126 <tests>
127 <test>
128 <param name="inputseq" value="output_obiuniq.fasta" />
129 <section name="key_selector">
130 <param name="key" value="count" />
131 <param name="key2" value="merged_sample" />
132 </section>
133 <param name="uniqid" value="true" />
134 <param name="clearbool" value="true" />
135 <param name="length" value="true" />
136 <param name="seqrank" value="true" />
137
138 <output name="output" file="output_obiannotate.fasta" ftype="fasta"/>
139 </test>
140 </tests>
141
142 <help><![CDATA[
143
144 .. class:: infomark
145
146 **What it does**
147
148 `obiannotate` is the command that allows adding/modifying/removing annotation attributes attached to sequence records.
149
150 Once such attributes are added, they can be used by the other OBITools commands for filtering purposes or for statistics computing.
151
152 @OBITOOLS_LINK@
153
154 ]]>
155
156 </help>
157 <expand macro="citation" />
158 </tool>