Mercurial > repos > iuc > mothur_remove_seqs

comparison remove.seqs.xml @ 1:87747f00c377 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:26:56 -0400
parents f9e64904c5dd
children cfab052e5e8a
comparison
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0:f9e64904c5dd 1:87747f00c377
2 <description>Remove sequences by name</description> 2 <description>Remove sequences by name</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
7 <expand macro="version_command"/> 8 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[ 9 <command><![CDATA[
9 ## create symlinks to input datasets 10 @SHELL_OPTIONS@
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 11
21 echo 'remove.seqs( 12 ## if accnos file is empty, just output files as-is, mothur errors if accnos empty (e.g. chimera filtering in pipeline but sample had no chimeras)
22 accnos=accnos.dat 13 #import os
14 #if $os.lstat(str($accnos)).st_size == 0:
15 echo "accnos file empty, nothing to remove, skipping step"
23 #if $fasta_in: 16 #if $fasta_in:
24 ,fasta=fasta_in.dat 17 && cp $fasta_in $fasta_out
25 #end if 18 #end if
26 #if $fastq_in: 19 #if $fastq_in:
27 ,fastq=fastq_in.dat 20 && cp $fastq_in $fastq_out
28 #end if 21 #end if
29 #if $count_in: 22 #if $count_in:
30 ,count=count_in.dat 23 && cp $count_in $count_out
31 #end if 24 #end if
32 #if $qfile_in: 25 #if $qfile_in:
33 ,qfile=qfile_in.dat 26 && cp $qfile_in $qfile_out
34 #end if 27 #end if
35 #if $name_in: 28 #if $name_in:
36 ,name=name_in.dat 29 && cp $name_in $name_out
37 #end if 30 #end if
38 #if $group_in: 31 #if $group_in:
39 ,group=group_in.dat 32 && cp $group_in $group_out
40 #end if 33 #end if
41 #if $alignreport_in: 34 #if $alignreport_in:
42 ,alignreport=alignreport_in.dat 35 && cp $alignreport_in $alignreport_out
43 #end if 36 #end if
44 #if $list_in: 37 #if $list_in:
45 ,list=list_in.dat 38 && cp $list_in $list_out
46 #end if 39 #end if
47 #if $taxonomy_in: 40 #if $taxonomy_in:
48 ,taxonomy=taxonomy_in.dat 41 && cp $taxonomy_in $taxonomy_out
49 #end if 42 #end if
50 $dups 43 #else:
51 )' 44 ## create symlinks to input datasets
52 | sed 's/ //g' ## mothur trips over whitespace 45 ln -s "$accnos" accnos.dat &&
53 | mothur 46 ln -s "$fasta_in" fasta_in.dat &&
47 ln -s "$fastq_in" fastq_in.dat &&
48 ln -s "$count_in" count_in.dat &&
49 ln -s "$qfile_in" qfile_in.dat &&
50 ln -s "$name_in" name_in.dat &&
51 ln -s "$group_in" group_in.dat &&
52 ln -s "$alignreport_in" alignreport_in.dat &&
53 ln -s "$list_in" list_in.dat &&
54 ln -s "$taxonomy_in" taxonomy_in.dat &&
55
56 echo 'remove.seqs(
57 accnos=accnos.dat
58 #if $fasta_in:
59 ,fasta=fasta_in.dat
60 #end if
61 #if $fastq_in:
62 ,fastq=fastq_in.dat
63 #end if
64 #if $count_in:
65 ,count=count_in.dat
66 #end if
67 #if $qfile_in:
68 ,qfile=qfile_in.dat
69 #end if
70 #if $name_in:
71 ,name=name_in.dat
72 #end if
73 #if $group_in:
74 ,group=group_in.dat
75 #end if
76 #if $alignreport_in:
77 ,alignreport=alignreport_in.dat
78 #end if
79 #if $list_in:
80 ,list=list_in.dat
81 #end if
82 #if $taxonomy_in:
83 ,taxonomy=taxonomy_in.dat
84 #end if
85 $dups
86 )'
87 | sed 's/ //g' ## mothur trips over whitespace
88 | mothur
89 | tee mothur.out.log
90 #end if
54 ]]></command> 91 ]]></command>
55 <inputs> 92 <inputs>
56 <param name="accnos" type="data" format="mothur.accnos" label="accnos - Accession Names of sequences to be removed"/> 93 <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"/> 94 <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"/> 95 <param name="qfile_in" type="data" format="qual" optional="true" label="qfile - Fasta Quality"/>
122 <param name="accnos" value="amazon.bad.accnos"/> 159 <param name="accnos" value="amazon.bad.accnos"/>
123 <param name="count_in" value="amazon.count_table"/> 160 <param name="count_in" value="amazon.count_table"/>
124 <expand macro="logfile-test"/> 161 <expand macro="logfile-test"/>
125 <output name="count_out" md5="bd1cb7af6f277210c5c11ff7d7c54592"/> 162 <output name="count_out" md5="bd1cb7af6f277210c5c11ff7d7c54592"/>
126 </test> 163 </test>
164 <!-- TODO: make test for empty accnos file -->
127 </tests> 165 </tests>
128 <help> 166 <help>
129 <![CDATA[ 167 <![CDATA[
130 168
131 @MOTHUR_OVERVIEW@ 169 @MOTHUR_OVERVIEW@
132 170
133 **Command Documenation** 171 **Command Documentation**
134 172
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. 173 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.
136 174
137 .. _name: http://www.mothur.org/wiki/Name_file 175 .. _name: https://www.mothur.org/wiki/Name_file
138 .. _group: http://www.mothur.org/wiki/Group_file 176 .. _group: https://www.mothur.org/wiki/Group_file
139 .. _list: http://www.mothur.org/wiki/List_file 177 .. _list: https://www.mothur.org/wiki/List_file
140 .. _align.report: http://www.mothur.org/wiki/Align.seqs 178 .. _align.report: https://www.mothur.org/wiki/Align.seqs
141 .. _taxonomy: http://www.mothur.org/wiki/Taxonomy_outline 179 .. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline
142 .. _list.seqs: http://www.mothur.org/wiki/list.seqs 180 .. _list.seqs: https://www.mothur.org/wiki/list.seqs
143 .. _remove.seqs: http://www.mothur.org/wiki/Remove.seqs 181 .. _remove.seqs: https://www.mothur.org/wiki/Remove.seqs
144 ]]> 182 ]]>
145 </help> 183 </help>
146 <expand macro="citations"/> 184 <expand macro="citations"/>
147 </tool> 185 </tool>