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comparison chimera.ccode.xml @ 0:3eca08ae427b 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 05:14:11 -0400
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-1:000000000000 0:3eca08ae427b
1 <tool profile="16.07" id="mothur_chimera_ccode" name="Chimera.ccode" version="@WRAPPER_VERSION@.0">
2 <description>Find putative chimeras using ccode</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 "$fasta" fasta.dat &&
14 ln -s "$alignment.template" alignment.template.dat &&
15 #if $mask.source2 == "history":
16 ln -s "$mask.input" mask.input.dat &&
17 #end if
18
19 echo 'chimera.ccode(
20 fasta=fasta.dat,
21 reference=alignment.template.dat,
22 filter=$filter,
23 #if $mask.source2 == "default":
24 mask=default,
25 #elif $mask.source2 == "history":
26 mask=mask.input.dat,
27 #end if
28 #if int($window) > 0:
29 window=$window,
30 #end if
31 #if int($numwanted) > 0:
32 numwanted=$numwanted,
33 #end if
34 processors='\${GALAXY_SLOTS:-8}'
35 )'
36 | sed 's/ //g' ## mothur trips over whitespace
37 | mothur
38 | tee mothur.out.log
39 ]]></command>
40 <inputs>
41 <param name="fasta" type="data" format="mothur.align" label="fasta - Candiate Aligned Sequences"/>
42 <conditional name="alignment">
43 <param name="source" type="select" label="Select Reference Template from" help="">
44 <option value="hist">History</option>
45 <option value="ref">Cached Reference</option>
46 </param>
47 <when value="ref">
48 <param name="template" type="select" label="reference - Select an alignment database" help="">
49 <options from_data_table="mothur_aligndb">
50 </options>
51 </param>
52 </when>
53 <when value="hist">
54 <param name="template" type="data" format="fasta" label="reference - Reference to align with" help=""/>
55 </when>
56 </conditional>
57 <param name="filter" type="boolean" falsevalue="False" truevalue="True" checked="false" label="filter - Apply a 50% soft vertical filter"/>
58 <conditional name="mask">
59 <param name="source2" type="select" label="Mask option">
60 <option value="">None</option>
61 <option value="default">default ecoli mask</option>
62 <option value="history">From Your History</option>
63 </param>
64 <when value="history">
65 <param name="input" type="data" format="mothur.filter" label="Mask for the reference file" help=""/>
66 </when>
67 <when value=""/>
68 <when value="default"/>
69 </conditional>
70 <param name="window" type="integer" value="0" label="window - Length of sequence you want in each window analyzed (default if &lt; 1)" help="Recommended window size is between 5 and 20% of your trimmed sequence length. Default is 10% of the sequence length."/>
71 <param name="numwanted" type="integer" value="20" label="numwanted - Number of sequences compared with each query (uses default if set to 0)"/>
72 </inputs>
73 <outputs>
74 <expand macro="logfile-output"/>
75 <data name="out_file" format="txt" from_work_dir="fasta.*ccode.chimeras" label="${tool.name} on ${on_string}: ccode.chimeras"/>
76 <data name="out_accnos" format="mothur.accnos" from_work_dir="fasta.*ccode.accnos" label="${tool.name} on ${on_string}: ccode.accnos"/>
77 <data name="mapinfo" format="tabular" from_work_dir="*.mapinfo" label="${tool.name} on ${on_string}: mapinfo"/>
78 </outputs>
79 <tests>
80 <test>
81 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
82 <param name="source" value="hist"/>
83 <param name="template" value="HMP_MOCK.v35.align"/>
84 <output name="out_file" ftype="txt">
85 <assert_contents>
86 <has_line_matching expression="^Window\tAvgQ\t\(sdQ\)\tAvgR\t\(sdR\)\tRatio\tAnova$"/>
87 </assert_contents>
88 </output>
89 <output name="out_accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.good.ccode.accnos" ftype="mothur.accnos"/>
90 <output name="mapinfo" md5="ef3353b1467fe95a24153513917e6444" ftype="tabular"/>
91 <expand macro="logfile-test"/>
92 </test>
93 <test> <!-- test with default ecoli mask -->
94 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
95 <param name="source" value="hist"/>
96 <param name="template" value="HMP_MOCK.v35.align"/>
97 <param name="source2" value="default"/>
98 <param name="window" value="100"/>
99 <output name="out_file" ftype="txt">
100 <assert_contents>
101 <has_line_matching expression="^Window\tAvgQ\t\(sdQ\)\tAvgR\t\(sdR\)\tRatio\tAnova$"/>
102 </assert_contents>
103 </output>
104 <output name="out_accnos" md5="47ddf86ec36aafd495aa902b3e06ffca" ftype="mothur.accnos"/>
105 <output name="mapinfo" md5="25221b1e109d9c0a939efb319e7a9896" ftype="tabular"/>
106 <expand macro="logfile-test"/>
107 </test>
108 </tests>
109 <help>
110 <![CDATA[
111
112 @MOTHUR_OVERVIEW@
113
114 **Command Documentation**
115
116 The chimera.ccode_ command identifies putative chimeras using the ccode approach (Chimera and Cross-Over Detection and Evaluation). Ccode_ compares differences in distances, for each word, between query sequence and reference sequences, and reference sequences and themselves.
117
118 This method was written using the algorithms described in the paper_ "Evaluating putative chimeric sequences from PCR-amplified products" by Juan M. Gonzalez, Johannes Zimmerman and Cesareo Saiz-Jimenez.
119
120 The program can analyze sequences for any required word length. Generally, values of 5-20% of sequence length appear to deliver accurate results, for example, working on 16S rDNA sequences with a full-length of #1500 nt. It should be noted that the use of fragments either too long or too short might result in a reduction of sensitivity.
121
122 .. _Ccode: http://www.microextreme.net/downloads.html
123 .. _paper: http://bioinformatics.oxfordjournals.org/content/21/3/333.full.pdf
124 .. _chimera.ccode: https://www.mothur.org/wiki/Chimera.ccode
125
126 ]]>
127 </help>
128 <expand macro="citations"/>
129 </tool>