/
summary.seqs.xml
77 lines (69 loc) · 2.87 KB
/
summary.seqs.xml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
<tool profile="16.07" id="mothur_summary_seqs" name="Summary.seqs" version="@WRAPPER_VERSION@.0">
<description>Summarize the quality of sequences</description>
<macros>
<import>macros.xml</import>
</macros>
<expand macro="biotools"/>
<expand macro="requirements"/>
<expand macro="stdio"/>
<expand macro="version_command"/>
<command><![CDATA[
@SHELL_OPTIONS@
## create symlinks to input datasets
ln -s '$fasta' fasta.dat &&
ln -s '$name' name.dat &&
ln -s '$count' count.dat &&
echo 'summary.seqs(
fasta=fasta.dat,
#if $name:
name=name.dat,
#end if
#if $count:
count=count.dat,
#end if
processors='\${GALAXY_SLOTS:-8}'
)'
| sed 's/ //g' ## mothur trips over whitespace
| mothur
| tee mothur.out.log
]]></command>
<inputs>
<param name="fasta" type="data" format="fasta,mothur.align" label="fasta - Dataset"/>
<param name="name" type="data" format="mothur.names" label="name - Names" optional="true"/>
<param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence. "/>
<expand macro="param-savelog"/>
</inputs>
<outputs>
<expand macro="logfile-output"/>
<data name="out_summary" format="mothur.summary" from_work_dir="fasta*.summary" label="${tool.name} on ${on_string}: summary"/>
</outputs>
<tests>
<test>
<param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/>
<output name="out_summary" file="Mock_S280_L001_R1_001_small.trim.contigs.summary" ftype="mothur.summary"/>
<param name="savelog" value="true"/>
<expand macro="logfile-test"/>
</test>
<test><!-- test names input -->
<param name="fasta" value="amazon.unique.fasta"/>
<param name="name" value="amazon.names"/>
<output name="out_summary" md5="b8a53926f64434291d232d2736da8293" ftype="mothur.summary"/>
<param name="savelog" value="true"/>
<expand macro="logfile-test"/>
</test>
<test><!-- test count input -->
<param name="fasta" value="amazon.unique.fasta"/>
<param name="count" value="amazon.count_table"/>
<output name="out_summary" md5="b8a53926f64434291d232d2736da8293" ftype="mothur.summary"/>
<param name="savelog" value="true"/>
<expand macro="logfile-test"/>
</test>
</tests>
<help><![CDATA[
@MOTHUR_OVERVIEW@
**Command Documentation**
The summary.seqs_ command will summarize the quality of sequences in an unaligned or aligned fasta-formatted sequence file.
.. _summary.seqs: https://www.mothur.org/wiki/Summary.seqs
]]></help>
<expand macro="citations"/>
</tool>