Mercurial > repos > iuc > mothur_sort_seqs

comparison sort.seqs.xml @ 0:a8653fd1ca73 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 05:30:16 -0400
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children 6619e67b064d
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-1:000000000000 0:a8653fd1ca73
1 <tool profile="16.07" id="mothur_sort_seqs" name="Sort.seqs" version="@WRAPPER_VERSION@.0">
2 <description>put sequences in different files in the same order</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 "$fasta_in" fasta_in.dat &&
14 ln -s "$qfile_in" qfile_in.dat &&
15 ln -s "$flow_in" flow_in.dat &&
16 ln -s "$name_in" name_in.dat &&
17 ln -s "$group_in" group_in.dat &&
18 ln -s "$tax_in" tax_in.dat &&
19 ln -s "$accnos" accnos.dat &&
20 ln -s "$count" count.dat &&
21
22 echo 'sort.seqs(
23 #if $fasta_in:
24 fasta=fasta_in.dat,
25 #end if
26 #if $qfile_in:
27 qfile=qfile_in.dat,
28 #end if
29 #if $flow_in:
30 flow=flow_in.dat,
31 #end if
32 #if $name_in:
33 name=name_in.dat,
34 #end if
35 #if $group_in:
36 group=group_in.dat,
37 #end if
38 #if $tax_in:
39 taxonomy=tax_in.dat,
40 #end if
41 #if $accnos:
42 accnos=accnos.dat,
43 #end if
44 #if $count:
45 count=count.dat,
46 #end if
47 large=$large
48 )'
49 | sed 's/ //g' ## mothur trips over whitespace
50 | mothur
51 | tee mothur.out.log
52 ]]></command>
53 <inputs>
54 <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - sequences" help="format must be fasta"/>
55 <param name="qfile_in" type="data" format="qual454" optional="true" label="qfile - sequence quality" help="format must be qual454"/>
56 <param name="flow_in" type="data" format="mothur.sff.flow" optional="true" label="flow - sff flowgram" help="format must be mothur.sff.flow"/>
57 <param name="group_in" type="data" format="mothur.groups" optional="true" label="groups - sequence groupings" help="format must be mothur.groups"/>
58 <param name="name_in" type="data" format="mothur.names" optional="true" label="names - name reference" help="format must be mothur.names"/>
59 <param name="tax_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - taxonomy reference" help="format must be mothur.seq.taxonomy"/>
60 <param name="accnos" type="data" format="mothur.accnos" optional="true" label="accnos - sort" help="format must be mothur.accnos"/>
61 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="format must be mothur.count_table (generated by count.seqs)"/>
62 <param name="large" type="boolean" checked="false" truevalue="true" falsevalue="false" label="large - Datasets are large and may not fit in RAM"/>
63 </inputs>
64 <outputs>
65 <expand macro="logfile-output"/>
66 <data name="fasta_out" format_source="fasta_in" from_work_dir="fasta_in*.sorted.*" label="${tool.name} on ${on_string}: sorted.fasta">
67 <filter>fasta_in</filter>
68 </data>
69 <data name="qfile_out" format_source="qfile_in" from_work_dir="qfile_in*.sorted.*" label="${tool.name} on ${on_string}: sorted.qfile">
70 <filter>qfile_in</filter>
71 </data>
72 <data name="flow_out" format_source="flow_in" from_work_dir="flow_in*.sorted.*" label="${tool.name} on ${on_string}: sorted.flow">
73 <filter>flow_in</filter>
74 </data>
75 <data name="group_out" format_source="group_in" from_work_dir="group_in*.sorted.*" label="${tool.name} on ${on_string}: sorted.group">
76 <filter>group_in</filter>
77 </data>
78 <data name="name_out" format_source="name_in" from_work_dir="name_in*.sorted.*" label="${tool.name} on ${on_string}: sorted.name">
79 <filter>name_in</filter>
80 </data>
81 <data name="taxonomy_out" format_source="tax_in" from_work_dir="tax_in*.sorted.*" label="${tool.name} on ${on_string}: sorted.taxonomy">
82 <filter>tax_in</filter>
83 </data>
84 </outputs>
85 <tests>
86 <test>
87 <param name="fasta_in" value="amazon.fasta" ftype="fasta"/>
88 <output name="fasta_out" md5="0bc9320647234e8367c3b1b654f9302d" ftype="fasta"/>
89 <expand macro="logfile-test"/>
90 </test>
91 <test>
92 <param name="qfile_in" value="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual454"/>
93 <output name="qfile_out" md5="abed9d1811786c810a12fd00a376cee4" ftype="qual454"/>
94 <expand macro="logfile-test"/>
95 </test>
96 <test>
97 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
98 <output name="group_out" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/>
99 <expand macro="logfile-test"/>
100 </test>
101 <test>
102 <param name="fasta_in" value="amazon.fasta" ftype="fasta"/>
103 <param name="count" value="amazon.count_table" ftype="mothur.count_table"/>
104 <output name="fasta_out" md5="0bc9320647234e8367c3b1b654f9302d" ftype="fasta"/>
105 <expand macro="logfile-test"/>
106 </test>
107 <test><!-- test with multiple file types input -->
108 <param name="fasta_in" value="amazon.fasta" ftype="fasta"/>
109 <param name="qfile_in" value="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual454"/>
110 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
111 <output name="fasta_out" md5="0bc9320647234e8367c3b1b654f9302d" ftype="fasta"/>
112 <output name="qfile_out" md5="abed9d1811786c810a12fd00a376cee4" ftype="qual454"/>
113 <output name="group_out" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/>
114 <expand macro="logfile-test"/>
115 </test>
116 </tests>
117 <help>
118 <![CDATA[
119
120 @MOTHUR_OVERVIEW@
121
122 **Command Documentation**
123
124 The sort.seqs_ command puts sequences from a fasta, name, group, quality, flow or taxonomy file in the same order.
125 You can provide an accnos file to indicate the order you want, otherwise mothur will use the order of the first file it reads.
126
127 .. _sort.seqs: https://www.mothur.org/wiki/Sort.seqs
128
129 ]]>
130 </help>
131 <expand macro="citations"/>
132 </tool>