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comparison screen.seqs.xml @ 0:5a01375eadf0 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 16:49:07 -0400
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children d0190913cb6c
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-1:000000000000 0:5a01375eadf0
1 <tool profile="16.07" id="mothur_screen_seqs" name="Screen.seqs" version="@WRAPPER_VERSION@.0">
2 <description>Screen sequences</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 "$fasta_in" fasta_in.dat &&
11 ln -s "$names_in" names_in.dat &&
12 ln -s "$groups_in" groups_in.dat &&
13 ln -s "$qfile_in" qfile_in.dat &&
14 ln -s "$count_in" count_in.dat &&
15 ln -s "$alignreport_in" alignreport_in.dat &&
16 ln -s "$taxonomy_in" taxonomy_in.dat &&
17 ln -s "$summary" summary.dat &&
18 ln -s "$contigsreport" contigsreport.dat &&
19
20 echo 'screen.seqs(
21 fasta=fasta_in.dat
22 #if $start > -1:
23 ,start=$start
24 #end if
25 #if $end > -1:
26 ,end=$end
27 #end if
28 #if $minlength > -1:
29 ,minlength=$minlength
30 #end if
31 #if $maxlength > -1:
32 ,maxlength=$maxlength
33 #end if
34 #if $maxambig > -1:
35 ,maxambig=$maxambig
36 #end if
37 #if $maxhomop > -1:
38 ,maxhomop=$maxhomop
39 #end if
40 #if $criteria > -1:
41 ,criteria=$criteria
42 #end if
43 #if $optimize:
44 ,optimize=$optimize
45 #end if
46 #if $qfile_in:
47 ,qfile=qfile_in.dat
48 #end if
49 #if $names_in:
50 ,name=names_in.dat
51 #end if
52 #if $groups_in:
53 ,group=groups_in.dat
54 #end if
55 #if $alignreport_in:
56 ,alignreport=alignreport_in.dat
57 #end if
58 #if $taxonomy_in:
59 ,taxonomy=taxonomy_in.dat
60 #end if
61 #if $count_in:
62 ,count=count_in.dat
63 #end if
64 #if $summary:
65 ,summary=summary.dat
66 #end if
67 #if $contigsreport:
68 ,contigsreport=contigsreport.dat
69 #end if
70 ,processors='"\${GALAXY_SLOTS:-8}"'
71 )'
72 | sed 's/ //g' ## mothur trips over whitespace
73 | mothur
74 ]]></command>
75 <inputs>
76 <param name="fasta_in" type="data" format="fasta,mothur.align" label="fasta - Fasta to screen"/>
77 <param name="start" type="integer" value="-1" label="start - Remove sequences that start after position (ignored when negative)"/>
78 <param name="end" type="integer" value="-1" label="end - Remove sequences that end before position (ignored when negative)"/>
79 <param name="minlength" type="integer" value="-1" label="minlength - Remove sequences shorter than (ignored when negative)"/>
80 <param name="maxlength" type="integer" value="-1" label="maxlength - Remove sequences longer than (ignored when negative)"/>
81 <param name="maxambig" type="integer" value="-1" label="maxambig - Remove sequences with ambiguous bases greater than (ignored when negative)"/>
82 <param name="maxhomop" type="integer" value="-1" label="maxhomop - Remove sequences with homopolymers greater than (ignored when negative)"/>
83 <param name="criteria" type="integer" value="-1" label="criteria - Percent of sequences that an optimize value must match to be retained(ignored when negative)"/>
84 <param name="optimize" type="select" multiple="true" display="checkboxes" label="optimize - Optimize selected paramenters">
85 <option value="start">start</option>
86 <option value="end">end</option>
87 <option value="minlength">minlength</option>
88 <option value="maxlength">maxlength</option>
89 <option value="maxambig">maxambig</option>
90 <option value="maxhomop">maxhomop</option>
91 </param>
92 <param name="qfile_in" type="data" format="qual" optional="true" label="qfile - Sequence Quality file to screen"/>
93 <param name="names_in" type="data" format="mothur.names" optional="true" label="name - Sequence Names to screen"/>
94 <param name="groups_in" type="data" format="mothur.groups" optional="true" label="group - Groups to screen"/>
95 <param name="alignreport_in" type="data" format="mothur.align.report" optional="true" label="alignreport - Align Report to screen"/>
96 <param name="summary" type="data" format="mothur.summary" optional="true" label="summary - allows you to enter the summary file created by summary.seqs to save processing time when screening with parameters in the summary file"/>
97 <param name="contigsreport" type="data" format="contigs.report" optional="true" label="contigsreport - Contigs Report to screen with" help="this file is created by the make.contigs command. If you provide the contigs report file you can screen your sequences using the following parameters: minoverlap, ostart, oend and mismatches"/>
98 <param name="taxonomy_in" type="data" format="taxonomy" optional="true" label="taxonomy - Taxonomy to screen"/>
99 <param name="count_in" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
100 </inputs>
101 <outputs>
102 <expand macro="logfile-output"/>
103 <data name="fasta_out" format_source="fasta_in" from_work_dir="fasta_in*.good.dat" label="${tool.name} on ${on_string}: good.${fasta_in.datatype.file_ext}"/>
104 <data name="bad_accnos" format="mothur.accnos" from_work_dir="fasta_in*.bad.accnos" label="${tool.name} on ${on_string}: bad.accnos"/>
105 <data name="qfile_out" format_source="qfile_in" from_work_dir="qfile_in*.good.dat" label="${tool.name} on ${on_string}: qfile">
106 <filter>qfile_in</filter>
107 </data>
108 <data name="names_out" format="mothur.names" from_work_dir="names_in*.good.dat" label="${tool.name} on ${on_string}: names">
109 <filter>names_in</filter>
110 </data>
111 <data name="groups_out" format="mothur.groups" from_work_dir="groups_in*.good.dat" label="${tool.name} on ${on_string}: groups">
112 <filter>groups_in</filter>
113 </data>
114 <data name="alignreport_out" format="mothur.align.report" from_work_dir="alignreport_in*.good.dat" label="${tool.name} on ${on_string}: align.report">
115 <filter>alignreport_in</filter>
116 </data>
117 <data name="count_out" format="count" from_work_dir="count_in*.good.dat" label="${tool.name} on ${on_string}: count">
118 <filter>count_in</filter>
119 </data>
120 </outputs>
121 <tests>
122 <test>
123 <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/>
124 <param name="maxambig" value="0"/>
125 <param name="maxlength" value="275"/>
126 <output name="fasta_out" file="Mock_S280_L001_R1_001_small.trim.contigs.good.fasta"/>
127 <output name="bad_accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/>
128 <expand macro="logfile-test"/>
129 </test>
130 <test>
131 <param name="fasta_in" value="amazon.fasta"/>
132 <param name="count_in" value="amazon.count_table"/>
133 <param name="maxambig" value="0"/>
134 <param name="maxlength" value="275"/>
135 <output name="fasta_out" md5="d41d8cd98f00b204e9800998ecf8427e"/>
136 <output name="count_out" md5="5f4a08bbf3ec12f954edbcc6b2a2feee"/>
137 <output name="bad_accnos" md5="66acde5349e34fc97be22032ce68eea5"/>
138 <expand macro="logfile-test"/>
139 </test>
140 </tests>
141 <help>
142 <![CDATA[
143
144 @MOTHUR_OVERVIEW@
145
146 **Command Documenation**
147
148 The screen.seqs_ command enables you to keep sequences that fulfill certain user defined criteria. Furthermore, it enables you to cull those sequences not meeting the criteria from a name_, group_, or align.report_ file.
149
150 .. _name: http://www.mothur.org/wiki/Name_file
151 .. _group: http://www.mothur.org/wiki/Group_file
152 .. _align.report: http://www.mothur.org/wiki/Align.seqs
153 .. _screen.seqs: http://www.mothur.org/wiki/Screen.seqs
154
155 ]]>
156 </help>
157 <expand macro="citations"/>
158 </tool>