Mercurial > repos > iuc > mothur_remove_seqs

comparison remove.seqs.xml @ 0:f9e64904c5dd draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 16:48:28 -0400
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children 87747f00c377
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-1:000000000000 0:f9e64904c5dd
1 <tool profile="16.07" id="mothur_remove_seqs" name="Remove.seqs" version="@WRAPPER_VERSION@.0">
2 <description>Remove sequences by name</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[
9 ## create symlinks to input datasets
10 ln -s "$accnos" accnos.dat &&
11 ln -s "$fasta_in" fasta_in.dat &&
12 ln -s "$fastq_in" fastq_in.dat &&
13 ln -s "$count_in" count_in.dat &&
14 ln -s "$qfile_in" qfile_in.dat &&
15 ln -s "$name_in" name_in.dat &&
16 ln -s "$group_in" group_in.dat &&
17 ln -s "$alignreport_in" alignreport_in.dat &&
18 ln -s "$list_in" list_in.dat &&
19 ln -s "$taxonomy_in" taxonomy_in.dat &&
20
21 echo 'remove.seqs(
22 accnos=accnos.dat
23 #if $fasta_in:
24 ,fasta=fasta_in.dat
25 #end if
26 #if $fastq_in:
27 ,fastq=fastq_in.dat
28 #end if
29 #if $count_in:
30 ,count=count_in.dat
31 #end if
32 #if $qfile_in:
33 ,qfile=qfile_in.dat
34 #end if
35 #if $name_in:
36 ,name=name_in.dat
37 #end if
38 #if $group_in:
39 ,group=group_in.dat
40 #end if
41 #if $alignreport_in:
42 ,alignreport=alignreport_in.dat
43 #end if
44 #if $list_in:
45 ,list=list_in.dat
46 #end if
47 #if $taxonomy_in:
48 ,taxonomy=taxonomy_in.dat
49 #end if
50 $dups
51 )'
52 | sed 's/ //g' ## mothur trips over whitespace
53 | mothur
54 ]]></command>
55 <inputs>
56 <param name="accnos" type="data" format="mothur.accnos" label="accnos - Accession Names of sequences to be removed"/>
57 <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - Fasta Sequences"/>
58 <param name="qfile_in" type="data" format="qual" optional="true" label="qfile - Fasta Quality"/>
59 <param name="fastq_in" type="data" format="fastq" optional="true" label="fastq"/>
60 <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
61 <param name="group_in" type="data" format="mothur.groups" optional="true" label="group - Sequences Groups"/>
62 <param name="alignreport_in" type="data" format="mothur.align.report" optional="true" label="alignreport - Align Report"/>
63 <param name="list_in" type="data" format="mothur.list" optional="true" label="list - OTU List"/>
64 <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/>
65 <param name="count_in" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
66 <param name="dups" type="boolean" truevalue="" falsevalue=",dups=false" checked="true" label="dups - Apply to duplicates"/>
67 </inputs>
68 <outputs>
69 <expand macro="logfile-output"/>
70 <data name="fasta_out" format_source="fasta_in" from_work_dir="fasta_in.pick.dat" label="${tool.name} on ${on_string}: pick.fasta">
71 <filter>fasta_in</filter>
72 </data>
73 <data name="fastq_out" format_source="fastq_in" from_work_dir="fastq_in.pick.dat" label="${tool.name} on ${on_string}: pick.fastq">
74 <filter>fastq_in</filter>
75 </data>
76 <data name="count_out" format_source="count_in" from_work_dir="count_in.pick.dat" label="${tool.name} on ${on_string}: pick.count">
77 <filter>count_in</filter>
78 </data>
79 <data name="qfile_out" format_source="qfile_in" from_work_dir="qfile_in.pick.dat" label="${tool.name} on ${on_string}: pick.qfile">
80 <filter>qfile_in</filter>
81 </data>
82 <data name="name_out" format="mothur.names" from_work_dir="name_in.pick.dat" label="${tool.name} on ${on_string}: pick.names">
83 <filter>name_in</filter>
84 </data>
85 <data name="group_out" format="mothur.groups" from_work_dir="group_in.pick.dat" label="${tool.name} on ${on_string}: pick.groups">
86 <filter>group_in</filter>
87 </data>
88 <data name="alignreport_out" format="mothur.align.report" from_work_dir="alignreport_in.pick.dat" label="${tool.name} on ${on_string}: pick.align.report">
89 <filter>alignreport_in</filter>
90 </data>
91 <data name="list_out" format="mothur.list" from_work_dir="list_in.pick.dat" label="${tool.name} on ${on_string}: pick.list">
92 <filter>list_in</filter>
93 </data>
94 <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="taxonomy_in.pick.dat" label="${tool.name} on ${on_string}: pick.taxonomy">
95 <filter>taxonomy_in</filter>
96 </data>
97 </outputs>
98 <tests>
99 <test>
100 <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/>
101 <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/>
102 <param name="dups" value=""/>
103 <expand macro="logfile-test"/>
104 <output name="fasta_out" md5="2357e1429647afbe21521a60935919bf"/>
105 </test>
106 <test>
107 <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/>
108 <param name="fastq_in" value="Mock_S280_L001_R1_001_small.fastq"/>
109 <expand macro="logfile-test"/>
110 <output name="fastq_out" md5="1e10d0793f1c5f12388156d5922c0eb8"/>
111 </test>
112 <test><!-- test two input files -->
113 <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/>
114 <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/>
115 <param name="fastq_in" value="Mock_S280_L001_R1_001_small.fastq"/>
116 <param name="dups" value=",dups=false"/>
117 <expand macro="logfile-test"/>
118 <output name="fasta_out" md5="2357e1429647afbe21521a60935919bf"/>
119 <output name="fastq_out" md5="1e10d0793f1c5f12388156d5922c0eb8"/>
120 </test>
121 <test>
122 <param name="accnos" value="amazon.bad.accnos"/>
123 <param name="count_in" value="amazon.count_table"/>
124 <expand macro="logfile-test"/>
125 <output name="count_out" md5="bd1cb7af6f277210c5c11ff7d7c54592"/>
126 </test>
127 </tests>
128 <help>
129 <![CDATA[
130
131 @MOTHUR_OVERVIEW@
132
133 **Command Documenation**
134
135 The remove.seqs_ command takes a list of sequence names and either a fasta, name_, group_, list_, align.report_ or taxonomy_ file to generate a new file that does not contain the sequences in the list. This command may be used in conjunction with the list.seqs_ command to help screen a sequence collection.
136
137 .. _name: http://www.mothur.org/wiki/Name_file
138 .. _group: http://www.mothur.org/wiki/Group_file
139 .. _list: http://www.mothur.org/wiki/List_file
140 .. _align.report: http://www.mothur.org/wiki/Align.seqs
141 .. _taxonomy: http://www.mothur.org/wiki/Taxonomy_outline
142 .. _list.seqs: http://www.mothur.org/wiki/list.seqs
143 .. _remove.seqs: http://www.mothur.org/wiki/Remove.seqs
144 ]]>
145 </help>
146 <expand macro="citations"/>
147 </tool>