Mercurial > repos > iuc > mothur_get_seqs

comparison get.seqs.xml @ 0:bfd467665e6c 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 05:44:07 -0400
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children 5acd4d7339b9
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-1:000000000000 0:bfd467665e6c
1 <tool profile="16.07" id="mothur_get_seqs" name="Get.seqs" version="@WRAPPER_VERSION@.0">
2 <description>Picks 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 ## create symlinks to input datasets
13 ln -s "$accnos" accnos.dat &&
14 ln -s "$fasta_in" fasta_in.dat &&
15 ln -s "$fastq_in" fastq_in.dat &&
16 ln -s "$count_in" count_in.dat &&
17 ln -s "$qfile_in" qfile_in.dat &&
18 ln -s "$name_in" name_in.dat &&
19 ln -s "$group_in" group_in.dat &&
20 ln -s "$alignreport_in" alignreport_in.dat &&
21 ln -s "$list_in" list_in.dat &&
22 ln -s "$taxonomy_in" taxonomy_in.dat &&
23
24 echo 'get.seqs(
25 accnos=accnos.dat,
26 #if $fasta_in:
27 fasta=fasta_in.dat,
28 #end if
29 #if $fastq_in:
30 fastq=fastq_in.dat,
31 #end if
32 #if $count_in:
33 count=count_in.dat,
34 #end if
35 #if $qfile_in:
36 qfile=qfile_in.dat,
37 #end if
38 #if $name_in:
39 name=name_in.dat,
40 #end if
41 #if $group_in:
42 group=group_in.dat,
43 #end if
44 #if $alignreport_in:
45 alignreport=alignreport_in.dat,
46 #end if
47 #if $list_in:
48 list=list_in.dat,
49 #end if
50 #if $taxonomy_in:
51 taxonomy=taxonomy_in.dat,
52 #end if
53 dups=$dups
54 )'
55 | sed 's/ //g' ## mothur trips over whitespace
56 | mothur
57 | tee mothur.out.log
58 ]]></command>
59 <inputs>
60 <param name="accnos" type="data" format="mothur.accnos" label="accnos - Accession Names"/>
61 <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - Fasta Sequences"/>
62 <param name="qfile_in" type="data" format="qual" optional="true" label="qfile - Fasta Quality"/>
63 <param name="fastq_in" type="data" format="fastq" optional="true" label="count - a count_table" help="fastq - allows you to select sequences from your fastq file"/>
64 <param name="count_in" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
65 <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
66 <param name="group_in" type="data" format="mothur.groups" optional="true" label="group - Sequences Groups"/>
67 <param name="alignreport_in" type="data" format="mothur.align.report" optional="true" label="alignreport - Align Report"/>
68 <param name="list_in" type="data" format="mothur.list" optional="true" label="list - OTU List"/>
69 <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/>
70 <param name="dups" type="boolean" truevalue="dups" falsevalue="false" checked="true" label="dups - Apply to duplicates"/>
71 </inputs>
72 <outputs>
73 <expand macro="logfile-output"/>
74 <data name="fasta_out" format_source="fasta_in" from_work_dir="fasta_in*.pick.*" label="${tool.name} on ${on_string}: pick.fasta">
75 <filter>fasta_in</filter>
76 </data>
77 <data name="fastq_out" format_source="fastq_in" from_work_dir="fastq_in*.pick.*" label="${tool.name} on ${on_string}: pick.fastq">
78 <filter>fastq_in</filter>
79 </data>
80 <data name="count_out" format_source="count_in" from_work_dir="count_in*.pick.*" label="${tool.name} on ${on_string}: pick.count">
81 <filter>count_in</filter>
82 </data>
83 <data name="qfile_out" format_source="qfile_in" from_work_dir="qfile_in*.pick.*" label="${tool.name} on ${on_string}: pick.qfile">
84 <filter>qfile_in</filter>
85 </data>
86 <data name="name_out" format="mothur.names" from_work_dir="name_in*.pick.*" label="${tool.name} on ${on_string}: pick.names">
87 <filter>name_in</filter>
88 </data>
89 <data name="group_out" format="mothur.groups" from_work_dir="group_in*.pick.*" label="${tool.name} on ${on_string}: pick.groups">
90 <filter>group_in</filter>
91 </data>
92 <data name="alignreport_out" format="mothur.align.report" from_work_dir="alignreport_in*.pick.*" label="${tool.name} on ${on_string}: pick.align.report">
93 <filter>alignreport_in</filter>
94 </data>
95 <data name="list_out" format="mothur.list" from_work_dir="list_in*.pick.*" label="${tool.name} on ${on_string}: pick.list">
96 <filter>list_in</filter>
97 </data>
98 <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="taxonomy_in*.pick.*" label="${tool.name} on ${on_string}: pick.taxonomy">
99 <filter>taxonomy_in</filter>
100 </data>
101 </outputs>
102 <tests>
103 <test>
104 <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/>
105 <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/>
106 <param name="dups" value=""/>
107 <output name="fasta_out" md5="f9335b6b70dc639e420d33809e51431d"/>
108 <expand macro="logfile-test"/>
109 </test>
110 <test>
111 <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/>
112 <param name="fastq_in" value="Mock_S280_L001_R1_001_small.fastq"/>
113 <output name="fastq_out" md5="e9aae546bf9c00cb7e884dff267d4ba1"/>
114 <expand macro="logfile-test"/>
115 </test>
116 <test>
117 <!-- test two input files -->
118 <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/>
119 <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/>
120 <param name="fastq_in" value="Mock_S280_L001_R1_001_small.fastq"/>
121 <param name="dups" value="false"/>
122 <output name="fasta_out" md5="f9335b6b70dc639e420d33809e51431d"/>
123 <output name="fastq_out" md5="e9aae546bf9c00cb7e884dff267d4ba1"/>
124 <expand macro="logfile-test"/>
125 </test>
126 <test>
127 <param name="accnos" value="amazon.bad.accnos"/>
128 <param name="count_in" value="amazon.count_table"/>
129 <output name="count_out" md5="6892dd99850ce9e9f8f15e77b28f57e2"/>
130 <expand macro="logfile-test"/>
131 </test>
132 </tests>
133 <help>
134 <![CDATA[
135
136 @MOTHUR_OVERVIEW@
137
138 **Command Documentation**
139
140 The get.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 contains only the sequences in the list. This command may be used in conjunction with the list.seqs_ command to help screen a sequence collection.
141
142 .. _name: https://www.mothur.org/wiki/Name_file
143 .. _group: https://www.mothur.org/wiki/Group_file
144 .. _list: https://www.mothur.org/wiki/List_file
145 .. _align.report: https://www.mothur.org/wiki/Align.seqs
146 .. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline
147 .. _list.seqs: https://www.mothur.org/wiki/list.seqs
148 .. _get.seqs: https://www.mothur.org/wiki/Get.seqs
149
150 v.1.27.0 : Updated to Mothur 1.33, added count and fastq params
151 ]]>
152 </help>
153 <expand macro="citations"/>
154 </tool>