Mercurial > repos > iuc > mothur_remove_seqs
comparison remove.seqs.xml @ 0:e59ddb750b65 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author | iuc |
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date | Fri, 19 May 2017 05:58:47 -0400 |
parents | |
children | 0b8ca0026f28 |
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-1:000000000000 | 0:e59ddb750b65 |
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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="stdio"/> | |
8 <expand macro="version_command"/> | |
9 <command><![CDATA[ | |
10 @SHELL_OPTIONS@ | |
11 | |
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) | |
13 #import os | |
14 #if $os.lstat(str($accnos)).st_size == 0: | |
15 echo "accnos file empty, nothing to remove, skipping step" | |
16 #if $fasta_in: | |
17 && cp $fasta_in $fasta_out | |
18 #end if | |
19 #if $fastq_in: | |
20 && cp $fastq_in $fastq_out | |
21 #end if | |
22 #if $count_in: | |
23 && cp $count_in $count_out | |
24 #end if | |
25 #if $qfile_in: | |
26 && cp $qfile_in $qfile_out | |
27 #end if | |
28 #if $name_in: | |
29 && cp $name_in $name_out | |
30 #end if | |
31 #if $group_in: | |
32 && cp $group_in $group_out | |
33 #end if | |
34 #if $alignreport_in: | |
35 && cp $alignreport_in $alignreport_out | |
36 #end if | |
37 #if $list_in: | |
38 && cp $list_in $list_out | |
39 #end if | |
40 #if $taxonomy_in: | |
41 && cp $taxonomy_in $taxonomy_out | |
42 #end if | |
43 #else: | |
44 ## create symlinks to input datasets | |
45 ln -s "$accnos" accnos.dat && | |
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 $dups | |
86 )' | |
87 | sed 's/ //g' ## mothur trips over whitespace | |
88 | mothur | |
89 | tee mothur.out.log | |
90 #end if | |
91 ]]></command> | |
92 <inputs> | |
93 <param name="accnos" type="data" format="mothur.accnos" label="accnos - Accession Names of sequences to be removed"/> | |
94 <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - Fasta Sequences"/> | |
95 <param name="qfile_in" type="data" format="qual" optional="true" label="qfile - Fasta Quality"/> | |
96 <param name="fastq_in" type="data" format="fastq" optional="true" label="fastq"/> | |
97 <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/> | |
98 <param name="group_in" type="data" format="mothur.groups" optional="true" label="group - Sequences Groups"/> | |
99 <param name="alignreport_in" type="data" format="mothur.align.report" optional="true" label="alignreport - Align Report"/> | |
100 <param name="list_in" type="data" format="mothur.list" optional="true" label="list - OTU List"/> | |
101 <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/> | |
102 <param name="count_in" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> | |
103 <param name="dups" type="boolean" truevalue="" falsevalue=",dups=false" checked="true" label="dups - Apply to duplicates"/> | |
104 </inputs> | |
105 <outputs> | |
106 <expand macro="logfile-output"/> | |
107 <data name="fasta_out" format_source="fasta_in" from_work_dir="fasta_in.pick.dat" label="${tool.name} on ${on_string}: pick.fasta"> | |
108 <filter>fasta_in</filter> | |
109 </data> | |
110 <data name="fastq_out" format_source="fastq_in" from_work_dir="fastq_in.pick.dat" label="${tool.name} on ${on_string}: pick.fastq"> | |
111 <filter>fastq_in</filter> | |
112 </data> | |
113 <data name="count_out" format_source="count_in" from_work_dir="count_in.pick.dat" label="${tool.name} on ${on_string}: pick.count"> | |
114 <filter>count_in</filter> | |
115 </data> | |
116 <data name="qfile_out" format_source="qfile_in" from_work_dir="qfile_in.pick.dat" label="${tool.name} on ${on_string}: pick.qfile"> | |
117 <filter>qfile_in</filter> | |
118 </data> | |
119 <data name="name_out" format="mothur.names" from_work_dir="name_in.pick.dat" label="${tool.name} on ${on_string}: pick.names"> | |
120 <filter>name_in</filter> | |
121 </data> | |
122 <data name="group_out" format="mothur.groups" from_work_dir="group_in.pick.dat" label="${tool.name} on ${on_string}: pick.groups"> | |
123 <filter>group_in</filter> | |
124 </data> | |
125 <data name="alignreport_out" format="mothur.align.report" from_work_dir="alignreport_in.pick.dat" label="${tool.name} on ${on_string}: pick.align.report"> | |
126 <filter>alignreport_in</filter> | |
127 </data> | |
128 <data name="list_out" format="mothur.list" from_work_dir="list_in.pick.dat" label="${tool.name} on ${on_string}: pick.list"> | |
129 <filter>list_in</filter> | |
130 </data> | |
131 <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="taxonomy_in.pick.dat" label="${tool.name} on ${on_string}: pick.taxonomy"> | |
132 <filter>taxonomy_in</filter> | |
133 </data> | |
134 </outputs> | |
135 <tests> | |
136 <test> | |
137 <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/> | |
138 <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/> | |
139 <param name="dups" value=""/> | |
140 <expand macro="logfile-test"/> | |
141 <output name="fasta_out" md5="2357e1429647afbe21521a60935919bf"/> | |
142 </test> | |
143 <test> | |
144 <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/> | |
145 <param name="fastq_in" value="Mock_S280_L001_R1_001_small.fastq"/> | |
146 <expand macro="logfile-test"/> | |
147 <output name="fastq_out" md5="1e10d0793f1c5f12388156d5922c0eb8"/> | |
148 </test> | |
149 <test><!-- test two input files --> | |
150 <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/> | |
151 <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/> | |
152 <param name="fastq_in" value="Mock_S280_L001_R1_001_small.fastq"/> | |
153 <param name="dups" value=",dups=false"/> | |
154 <expand macro="logfile-test"/> | |
155 <output name="fasta_out" md5="2357e1429647afbe21521a60935919bf"/> | |
156 <output name="fastq_out" md5="1e10d0793f1c5f12388156d5922c0eb8"/> | |
157 </test> | |
158 <test> | |
159 <param name="accnos" value="amazon.bad.accnos"/> | |
160 <param name="count_in" value="amazon.count_table"/> | |
161 <expand macro="logfile-test"/> | |
162 <output name="count_out" md5="bd1cb7af6f277210c5c11ff7d7c54592"/> | |
163 </test> | |
164 <!-- TODO: make test for empty accnos file --> | |
165 </tests> | |
166 <help> | |
167 <![CDATA[ | |
168 | |
169 @MOTHUR_OVERVIEW@ | |
170 | |
171 **Command Documentation** | |
172 | |
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. | |
174 | |
175 .. _name: https://www.mothur.org/wiki/Name_file | |
176 .. _group: https://www.mothur.org/wiki/Group_file | |
177 .. _list: https://www.mothur.org/wiki/List_file | |
178 .. _align.report: https://www.mothur.org/wiki/Align.seqs | |
179 .. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline | |
180 .. _list.seqs: https://www.mothur.org/wiki/list.seqs | |
181 .. _remove.seqs: https://www.mothur.org/wiki/Remove.seqs | |
182 ]]> | |
183 </help> | |
184 <expand macro="citations"/> | |
185 </tool> |