Mercurial > repos > iuc > mothur_rename_seqs

comparison rename.seqs.xml @ 0:1ac1d3e02088 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 22:01:03 -0400
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children 02a42e3fa758
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-1:000000000000 0:1ac1d3e02088
1 <tool profile="16.07" id="mothur_rename_seqs" name="Rename.seqs" version="@WRAPPER_VERSION@.0">
2 <description>Rename sequences by concatenating the group name</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8 <expand macro="version_command"/>
9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
12 ## create symlinks to input datasets
13 ln -s '$fasta' fasta.dat &&
14 ln -s '$group' group.dat &&
15 ln -s '$name' name.dat &&
16 ln -s '$qfile' qfile.dat &&
17 ln -s '$contigsreport' contigsreport.dat &&
18
19 echo 'rename.seqs(
20 fasta=fasta.dat,
21 group=group.dat,
22 #if $name:
23 name=name.dat,
24 #end if
25 #if $qfile:
26 qfile=qfile.dat,
27 #end if
28 #if $contigsreport:
29 contigsreport=contigsreport.dat,
30 #end if
31 placement=$placement
32 )'
33 | sed 's/ //g' ## mothur trips over whitespace
34 | mothur
35 | tee mothur.out.log
36 ]]></command>
37 <inputs>
38 <param argument="fasta" type="data" format="fasta,mothur.align" label="Fasta file"/>
39 <param argument="group" type="data" format="mothur.groups" label="Group file"/>
40 <param argument="name" type="data" format="mothur.names" optional="true" label="Names file"/>
41 <param argument="qfile" type="data" format="qual454" optional="true" label="quality file"/>
42 <param argument="contigsreport" type="data" format="tabular" optional="true" label="Contigsreport file"/>
43 <param argument="placement" type="select" label="Placement of group name">
44 <option value="back" selected="true">back</option>
45 <option value="front">front</option>
46 </param>
47 <expand macro="param-savelog"/>
48 </inputs>
49 <outputs>
50 <expand macro="logfile-output"/>
51 <data name="group_renamed" format="mothur.groups" from_work_dir="group.renamed.dat" label="${tool.name} on ${on_string}: group_renamed"/>
52 <data name="fasta_renamed" format_source="fasta" from_work_dir="fasta.renamed.dat" label="${tool.name} on ${on_string}: fasta_renamed"/>
53 <data name="map" format="tabular" from_work_dir="fasta.renamed_map" label="${tool.name} on ${on_string}: renaming map"/>
54 <data name="name_renamed" format="mothur.names" from_work_dir="name.renamed.dat" label="${tool.name} on ${on_string}: name_renamed">
55 <filter>name</filter>
56 </data>
57 <data name="qfile_renamed" format="qual454" from_work_dir="qfile.renamed.dat" label="${tool.name} on ${on_string}: qfile_renamed">
58 <filter>qfile</filter>
59 </data>
60 <data name="contigsreport_renamed" format="tabular" from_work_dir="contigsreport.renamed.dat" label="${tool.name} on ${on_string}: contigsreport_renamed">
61 <filter>contigsreport</filter>
62 </data>
63 </outputs>
64 <tests>
65 <test><!-- test with required params -->
66 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
67 <param name="group" value="amazon.groups"/>
68 <param name="name" value="amazon1.names"/>
69 <output name="fasta_renamed" ftype="fasta">
70 <assert_contents>
71 <expand macro="test-fasta-format"/>
72 <has_text text="42_forest"/>
73 <has_text text="42_pasture"/>
74 </assert_contents>
75 </output>
76 <output name="map" ftype="tabular">
77 <assert_contents>
78 <has_n_columns n="2"/>
79 <has_line_matching expression="^42_forest\tU68631$"/>
80 </assert_contents>
81 </output>
82 <output name="group_renamed" ftype="mothur.groups">
83 <assert_contents>
84 <has_n_columns n="2"/>
85 <has_line_matching expression="^42_forest\tforest$"/>
86 </assert_contents>
87 </output>
88 <output name="name_renamed" ftype="mothur.names">
89 <assert_contents>
90 <has_n_columns n="2"/>
91 <has_line_matching expression="^42_forest\t42_forest$"/>
92 </assert_contents>
93 </output>
94 <param name="savelog" value="true"/>
95 <expand macro="logfile-test"/>
96 </test>
97 </tests>
98 <help><![CDATA[
99
100 @MOTHUR_OVERVIEW@
101
102 **Command Documentation**
103
104 The rename.seqs_ command takes fasta-formatted sequence file and group file, and renames
105 the sequences by appending the group name to the sequence number.
106
107 .. _rename.seqs: https://www.mothur.org/wiki/Rename.seqs
108
109 ]]></help>
110 <expand macro="citations"/>
111 </tool>