Mercurial > repos > iuc > mothur_sort_seqs

comparison sort.seqs.xml @ 0:60c599375cad 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 16:50:30 -0400
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children 9900cd702dcf
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-1:000000000000 0:60c599375cad
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="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[
9 ## create symlinks to input datasets
10 ln -s "$fasta_in" fasta_in.dat &&
11 ln -s "$qfile_in" qfile_in.dat &&
12 ln -s "$flow_in" flow_in.dat &&
13 ln -s "$name_in" name_in.dat &&
14 ln -s "$group_in" group_in.dat &&
15 ln -s "$tax_in" tax_in.dat &&
16 ln -s "$accnos" accnos.dat &&
17 ln -s "$count" count.dat &&
18
19 echo 'sort.seqs(
20 #if $fasta_in:
21 fasta=fasta_in.dat,
22 #end if
23 #if $qfile_in:
24 qfile=qfile_in.dat,
25 #end if
26 #if $flow_in:
27 flow=flow_in.dat,
28 #end if
29 #if $name_in:
30 name=name_in.dat,
31 #end if
32 #if $group_in:
33 group=group_in.dat,
34 #end if
35 #if $tax_in:
36 taxonomy=tax_in.dat,
37 #end if
38 #if $accnos:
39 accnos=accnos.dat,
40 #end if
41 #if $count:
42 count=count.dat,
43 #end if
44 large=$large
45 )'
46 | sed 's/ //g' ## mothur trips over whitespace
47 | mothur
48 ]]></command>
49 <inputs>
50 <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - sequences" help="format must be fasta"/>
51 <param name="qfile_in" type="data" format="qual454" optional="true" label="qfile - sequence quality" help="format must be qual454"/>
52 <param name="flow_in" type="data" format="mothur.sff.flow" optional="true" label="flow - sff flowgram" help="format must be mothur.sff.flow"/>
53 <param name="group_in" type="data" format="mothur.groups" optional="true" label="groups - sequence groupings" help="format must be mothur.groups"/>
54 <param name="name_in" type="data" format="mothur.names" optional="true" label="names - name reference" help="format must be mothur.names"/>
55 <param name="tax_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - taxonomy reference" help="format must be mothur.seq.taxonomy"/>
56 <param name="accnos" type="data" format="mothur.accnos" optional="true" label="accnos - sort" help="format must be mothur.accnos"/>
57 <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)"/>
58 <param name="large" type="boolean" checked="false" truevalue="true" falsevalue="false" label="large - Datasets are large and may not fit in RAM"/>
59 </inputs>
60 <outputs>
61 <expand macro="logfile-output"/>
62 <data name="fasta_out" format_source="fasta_in" from_work_dir="fasta_in*.sorted.*" label="${tool.name} on ${on_string}: sorted.fasta">
63 <filter>fasta_in</filter>
64 </data>
65 <data name="qfile_out" format_source="qfile_in" from_work_dir="qfile_in*.sorted.*" label="${tool.name} on ${on_string}: sorted.qfile">
66 <filter>qfile_in</filter>
67 </data>
68 <data name="flow_out" format_source="flow_in" from_work_dir="flow_in*.sorted.*" label="${tool.name} on ${on_string}: sorted.flow">
69 <filter>flow_in</filter>
70 </data>
71 <data name="group_out" format_source="group_in" from_work_dir="group_in*.sorted.*" label="${tool.name} on ${on_string}: sorted.group">
72 <filter>group_in</filter>
73 </data>
74 <data name="name_out" format_source="name_in" from_work_dir="name_in*.sorted.*" label="${tool.name} on ${on_string}: sorted.name">
75 <filter>name_in</filter>
76 </data>
77 <data name="taxonomy_out" format_source="tax_in" from_work_dir="tax_in*.sorted.*" label="${tool.name} on ${on_string}: sorted.taxonomy">
78 <filter>tax_in</filter>
79 </data>
80 </outputs>
81 <tests>
82 <test>
83 <param name="fasta_in" value="amazon.fasta" ftype="fasta"/>
84 <output name="fasta_out" md5="0bc9320647234e8367c3b1b654f9302d" ftype="fasta"/>
85 <expand macro="logfile-test"/>
86 </test>
87 <test>
88 <param name="qfile_in" value="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual454"/>
89 <output name="qfile_out" md5="abed9d1811786c810a12fd00a376cee4" ftype="qual454"/>
90 <expand macro="logfile-test"/>
91 </test>
92 <test>
93 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
94 <output name="group_out" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/>
95 <expand macro="logfile-test"/>
96 </test>
97 <test>
98 <param name="fasta_in" value="amazon.fasta" ftype="fasta"/>
99 <param name="count" value="amazon.count_table" ftype="mothur.count_table"/>
100 <output name="fasta_out" md5="0bc9320647234e8367c3b1b654f9302d" ftype="fasta"/>
101 <expand macro="logfile-test"/>
102 </test>
103 <test><!-- test with multiple file types input -->
104 <param name="fasta_in" value="amazon.fasta" ftype="fasta"/>
105 <param name="qfile_in" value="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual454"/>
106 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
107 <output name="fasta_out" md5="0bc9320647234e8367c3b1b654f9302d" ftype="fasta"/>
108 <output name="qfile_out" md5="abed9d1811786c810a12fd00a376cee4" ftype="qual454"/>
109 <output name="group_out" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/>
110 <expand macro="logfile-test"/>
111 </test>
112 </tests>
113 <help>
114 <![CDATA[
115
116 @MOTHUR_OVERVIEW@
117
118 **Command Documenation**
119
120 The sort.seqs_ command puts sequences from a fasta, name, group, quality, flow or taxonomy file in the same order.
121 You can provide an accnos file to indicate the order you want, otherwise mothur will use the order of the first file it reads.
122
123 .. _sort.seqs: http://www.mothur.org/wiki/Sort.seqs
124
125 ]]>
126 </help>
127 <expand macro="citations"/>
128 </tool>