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comparison seq.error.xml @ 0:3d74b329068b 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 16:49:43 -0400
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-1:000000000000 0:3d74b329068b
1 <tool profile="16.07" id="mothur_seq_error" name="Seq.error" version="@WRAPPER_VERSION@.0">
2 <description>assess error rates in sequencing data</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 "$fasta_in" fasta_in.dat &&
11 ln -s "$name_in" name_in.dat &&
12 ln -s "$count" count.dat &&
13 ln -s "$alignment.template" alignment.template.dat &&
14 #if $qual.use == "yes":
15 ln -s "$qual.qfile_in" qfile_in.dat &&
16 ln -s "$qual.alignreport_in" alignreport_in.dat &&
17 #end if
18
19 echo 'seq.error(
20 fasta=fasta_in.dat,
21 reference=alignment.template.dat,
22 #if $name_in:
23 name=name_in.dat,
24 #end if
25 #if $qual.use == "yes":
26 qfile=qfile_in.dat,
27 report=alignreport_in.dat,
28 #end if
29 #if $threshold:
30 threshold=$threshold,
31 #end if
32 ignorechimeras=$ignorechimeras,
33 #if $count:
34 count=count.dat,
35 #end if
36 processors='\${GALAXY_SLOTS:-8}'
37 )'
38 | sed 's/ //g' ## mothur trips over whitespace
39 | mothur
40 ]]></command>
41 <inputs>
42 <param name="fasta_in" type="data" format="mothur.align" label="fasta - Candidate Sequences" help="sequences must be aligned"/>
43 <conditional name="alignment">
44 <param name="source" type="select" label="Select Reference Template from" help="">
45 <option value="ref">Cached Reference</option>
46 <option value="history">Your History</option>
47 </param>
48 <when value="ref">
49 <param name="template" type="select" label="reference - Select an alignment database" help="">
50 <options from_data_table="mothur_aligndb"/>
51 </param>
52 </when>
53 <when value="history">
54 <param name="template" type="data" format="mothur.align" label="reference - Reference to align with" help=""/>
55 </when>
56 </conditional>
57 <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
58 <conditional name="qual">
59 <param name="use" type="select" label="Include a quality file and an alignment report as inputs" help="">
60 <option value="no">No</option>
61 <option value="yes">Yes</option>
62 </param>
63 <when value="yes">
64 <param name="qfile_in" type="data" format="qual" label="qfile - Fasta Quality"/>
65 <param name="alignreport_in" type="data" format="mothur.align.report" label="alignreport - Align Report"/>
66 </when>
67 <when value="no"/>
68 </conditional>
69 <param name="count" type="data" format="mothur.count_table" optional="true" label="The count parameter allows you to provide a count file associated with your fasta file, so you can include the redundant sequences in your error analysis"/>
70 <param name="threshold" type="float" value="" min="0" max="1" optional="true" label="threshold - error rate at which to report (default 1.)"/>
71 <param name="ignorechimeras" type="boolean" truevalue="true" falsevalue="false" checked="true" label="ignorechimeras - "/>
72 <param name="output_sel" type="select" multiple="true" display="checkboxes" label="Outputs as history datasets">
73 <option value="summary">error.summary</option>
74 <option value="seq">error.seq</option>
75 <option value="seq_forward">error.seq.forward</option>
76 <option value="seq_reverse">error.seq.reverse</option>
77 <option value="chimera">error.chimera</option>
78 <option value="count">error.count</option>
79 <option value="matrix">error.matrix</option>
80 <option value="quality">error.quality</option>
81 <option value="qual_forward">error.qual.forward</option>
82 <option value="qual_reverse">error.qual.reverse</option>
83 <option value="ref_query">error.ref-query</option>
84 </param>
85 </inputs>
86 <outputs>
87 <expand macro="logfile-output"/>
88 <data name="summary_out" format="tabular" from_work_dir="fasta_in*.error.summary" label="${tool.name} on ${on_string}: error.summary">
89 <filter>'summary' in output_sel</filter>
90 </data>
91 <data name="seq_out" format="fasta" from_work_dir="fasta_in*.error.seq" label="${tool.name} on ${on_string}: error.seq">
92 <filter>'seq' in output_sel</filter>
93 </data>
94 <data name="seq_forward_out" format="tabular" from_work_dir="fasta_in*.error.seq.forward" label="${tool.name} on ${on_string}: error.seq.forward">
95 <filter>'seq_forward' in output_sel</filter>
96 </data>
97 <data name="seq_reverse_out" format="tabular" from_work_dir="fasta_in*.error.seq.reverse" label="${tool.name} on ${on_string}: error.seq.reverse">
98 <filter>'seq_reverse' in output_sel</filter>
99 </data>
100 <data name="chimera_out" format="tabular" from_work_dir="fasta_in*.error.chimera" label="${tool.name} on ${on_string}: error.chimera">
101 <filter>'chimera' in output_sel</filter>
102 </data>
103 <data name="count_out" format="tabular" from_work_dir="fasta_in*.error.count" label="${tool.name} on ${on_string}: error.count">
104 <filter>'count' in output_sel</filter>
105 </data>
106 <data name="matrix_out" format="tabular" from_work_dir="fasta_in*.error.matrix" label="${tool.name} on ${on_string}: error.matrix">
107 <filter>'matrix' in output_sel</filter>
108 </data>
109 <data name="quality_out" format="tabular" from_work_dir="fasta_in*.error.quality" label="${tool.name} on ${on_string}: error.quality">
110 <filter>qual['use'] == 'yes' and 'quality' in output_sel</filter>
111 </data>
112 <data name="qual_forward_out" format="tabular" from_work_dir="fasta_in*.error.qual.forward" label="${tool.name} on ${on_string}: error.qual.forward">
113 <filter>qual['use'] == 'yes' and 'qual_forward' in output_sel</filter>
114 </data>
115 <data name="qual_reverse_out" format="tabular" from_work_dir="fasta_in*.error.qual.reverse" label="${tool.name} on ${on_string}: error.qual.reverse">
116 <filter>qual['use'] == 'yes' and 'qual_reverse' in output_sel</filter>
117 </data>
118 <data name="ref_query_out" format="mothur.align" from_work_dir="fasta_in*.error.ref" label="${tool.name} on ${on_string}: error.ref-query">
119 <filter>'ref_query' in output_sel</filter>
120 </data>
121 </outputs>
122 <tests>
123 <test><!--test with all outputs and no qual file-->
124 <param name="fasta_in" value="amazon.align_head" ftype="mothur.align"/>
125 <param name="template" value="HMP_MOCK.v35.align" ftype="mothur.align"/>
126 <param name="source" value="history"/>
127 <param name="output_sel" value="summary,seq,seq_forward,seq_reverse,chimera,count,matrix,ref_query"/>
128 <output name="chimera_out" md5="9faf0da7d724a1db5e0d8f5fcb72b486"/>
129 <output name="count_out" md5="9aea787346ad6a1c496aa1d77262a487"/>
130 <output name="matrix_out" md5="b7d9bbf3cdf363b41551e31c0b460a47"/>
131 <output name="ref_query_out" md5="42b42eb4c6bc2705ded2c697a757106f"/>
132 <output name="seq_out" md5="5a884846a8d94b8482c2935d2e7e43e6"/>
133 <output name="seq_forward_out" md5="92a24ef3155bc050ae4fd31bab43cf92"/>
134 <output name="seq_reverse_out" md5="92a24ef3155bc050ae4fd31bab43cf92"/>
135 <output name="summary_out" md5="04abbbd6aa82f084e4a3bd51c4ce98e6"/>
136 <expand macro="logfile-test"/>
137 </test>
138 <test><!--test with qual file and all outputs -->
139 <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head" ftype="mothur.align"/>
140 <param name="template" value="HMP_MOCK.v35.align" ftype="mothur.align"/>
141 <param name="source" value="history"/>
142 <param name="output_sel" value="summary,seq,seq_forward,seq_reverse,chimera,count,matrix,ref_query,quality,qual_forward,qual_reverse"/>
143 <param name="use" value="yes"/>
144 <param name="qfile_in" value="Mock_S280_L001_R1_001_small.trim.contigs.qual"/>
145 <param name="alignreport_in" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align.report"/>
146 <output name="chimera_out" md5="78e586f1a1362fd98808d7725d786caa"/>
147 <output name="count_out" md5="ee987c7b5dc90d4d3a0ef55d817cc540"/>
148 <output name="matrix_out" md5="6b9310b4acd95c560cd062b620b35826"/>
149 <output name="ref_query_out" md5="dd569264c5a4628079de3ef828766e90"/>
150 <output name="quality_out" md5="844b50d6642381a7f434b8182b9307da"/>
151 <output name="qual_forward_out" md5="371fc760fc51b5adf10044fc26c1bbb8"/>
152 <output name="qual_reverse_out" md5="81f17617ba99cac5807e454a626eb006"/>
153 <output name="seq_out" md5="69a8ec131df0b1d4d95eaeb04e057941"/>
154 <output name="seq_forward_out" md5="dbcbbefdc83c2a7c045e3930850cdbd9"/>
155 <output name="seq_reverse_out" md5="5618b1e431306ec1275f1572d6c0c2fc"/>
156 <output name="summary_out" md5="d33bddf9b112f2f3a80b38cf7ac50e6a"/>
157 <expand macro="logfile-test"/>
158 </test>
159 </tests>
160 <help>
161 <![CDATA[
162
163 @MOTHUR_OVERVIEW@
164
165 **Command Documenation**
166
167 The seq.error_ command evaluates error rate for sequences by comparing to the fasta-formatted template_alignment_.
168 This is demonstrated in http://www.mothur.org/wiki/Schloss_SOP#Error_analysis
169
170 .. _template_alignment: http://www.mothur.org/wiki/Alignment_database
171 .. _seq.error: http://www.mothur.org/wiki/Seq.error
172
173 ]]>
174 </help>
175 <expand macro="citations"/>
176 </tool>