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comparison screen.seqs.xml @ 0:125a6ae65887 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 05:48:41 -0400
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children 8743aecd26a9
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-1:000000000000 0:125a6ae65887
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="stdio"/>
8 <expand macro="version_command"/>
9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
12 ## create symlinks to input datasets
13 ln -s "$fasta_in" fasta_in.dat &&
14 ln -s "$names_in" names_in.dat &&
15 ln -s "$groups_in" groups_in.dat &&
16 ln -s "$qfile_in" qfile_in.dat &&
17 ln -s "$count_in" count_in.dat &&
18 ln -s "$alignreport_in" alignreport_in.dat &&
19 ln -s "$taxonomy_in" taxonomy_in.dat &&
20 ln -s "$summary" summary.dat &&
21 ln -s "$contigsreport" contigsreport.dat &&
22
23 echo 'screen.seqs(
24 fasta=fasta_in.dat
25 #if int($start) > -1:
26 ,start=$start
27 #end if
28 #if int($end) > -1:
29 ,end=$end
30 #end if
31 #if int($minlength) > -1:
32 ,minlength=$minlength
33 #end if
34 #if int($maxlength) > -1:
35 ,maxlength=$maxlength
36 #end if
37 #if int($maxambig) > -1:
38 ,maxambig=$maxambig
39 #end if
40 #if int($maxhomop) > -1:
41 ,maxhomop=$maxhomop
42 #end if
43 #if int($criteria) > -1:
44 ,criteria=$criteria
45 #end if
46 #if $optimize:
47 ,optimize=$optimize
48 #end if
49 #if $qfile_in:
50 ,qfile=qfile_in.dat
51 #end if
52 #if $names_in:
53 ,name=names_in.dat
54 #end if
55 #if $groups_in:
56 ,group=groups_in.dat
57 #end if
58 #if $alignreport_in:
59 ,alignreport=alignreport_in.dat
60 #end if
61 #if $taxonomy_in:
62 ,taxonomy=taxonomy_in.dat
63 #end if
64 #if $count_in:
65 ,count=count_in.dat
66 #end if
67 #if $summary:
68 ,summary=summary.dat
69 #end if
70 #if $contigsreport:
71 ,contigsreport=contigsreport.dat
72 #end if
73 ,processors='"\${GALAXY_SLOTS:-8}"'
74 )'
75 | sed 's/ //g' ## mothur trips over whitespace
76 | mothur
77 | tee mothur.out.log
78 ]]></command>
79 <inputs>
80 <param name="fasta_in" type="data" format="fasta,mothur.align" label="fasta - Fasta to screen"/>
81 <param name="start" type="integer" value="-1" label="start - Remove sequences that start after position (ignored when negative)"/>
82 <param name="end" type="integer" value="-1" label="end - Remove sequences that end before position (ignored when negative)"/>
83 <param name="minlength" type="integer" value="-1" label="minlength - Remove sequences shorter than (ignored when negative)"/>
84 <param name="maxlength" type="integer" value="-1" label="maxlength - Remove sequences longer than (ignored when negative)"/>
85 <param name="maxambig" type="integer" value="-1" label="maxambig - Remove sequences with ambiguous bases greater than (ignored when negative)"/>
86 <param name="maxhomop" type="integer" value="-1" label="maxhomop - Remove sequences with homopolymers greater than (ignored when negative)"/>
87 <param name="criteria" type="integer" value="-1" label="criteria - Percent of sequences that an optimize value must match to be retained(ignored when negative)"/>
88 <param name="optimize" type="select" multiple="true" display="checkboxes" label="optimize - Optimize selected paramenters">
89 <option value="start">start</option>
90 <option value="end">end</option>
91 <option value="minlength">minlength</option>
92 <option value="maxlength">maxlength</option>
93 <option value="maxambig">maxambig</option>
94 <option value="maxhomop">maxhomop</option>
95 </param>
96 <param name="qfile_in" type="data" format="qual" optional="true" label="qfile - Sequence Quality file to screen"/>
97 <param name="names_in" type="data" format="mothur.names" optional="true" label="name - Sequence Names to screen"/>
98 <param name="groups_in" type="data" format="mothur.groups" optional="true" label="group - Groups to screen"/>
99 <param name="alignreport_in" type="data" format="mothur.align.report" optional="true" label="alignreport - Align Report to screen"/>
100 <param name="summary" type="data" format="mothur.summary" optional="true" label="summary file - as created by summary.seqs" help="saves processing time when screening with parameters in the summary file"/>
101 <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"/>
102 <param name="taxonomy_in" type="data" format="taxonomy" optional="true" label="taxonomy - Taxonomy to screen"/>
103 <param name="count_in" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
104 </inputs>
105 <outputs>
106 <expand macro="logfile-output"/>
107 <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}"/>
108 <data name="bad_accnos" format="mothur.accnos" from_work_dir="fasta_in*.bad.accnos" label="${tool.name} on ${on_string}: bad.accnos"/>
109 <data name="qfile_out" format_source="qfile_in" from_work_dir="qfile_in*.good.dat" label="${tool.name} on ${on_string}: qfile">
110 <filter>qfile_in</filter>
111 </data>
112 <data name="names_out" format="mothur.names" from_work_dir="names_in*.good.dat" label="${tool.name} on ${on_string}: names">
113 <filter>names_in</filter>
114 </data>
115 <data name="groups_out" format="mothur.groups" from_work_dir="groups_in*.good.dat" label="${tool.name} on ${on_string}: groups">
116 <filter>groups_in</filter>
117 </data>
118 <data name="alignreport_out" format="mothur.align.report" from_work_dir="alignreport_in*.good.dat" label="${tool.name} on ${on_string}: align.report">
119 <filter>alignreport_in</filter>
120 </data>
121 <data name="count_out" format="mothur.count_table" from_work_dir="count_in*.good.dat" label="${tool.name} on ${on_string}: count">
122 <filter>count_in</filter>
123 </data>
124 </outputs>
125 <tests>
126 <test>
127 <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta" ftype="fasta"/>
128 <param name="maxambig" value="0"/>
129 <param name="maxlength" value="275"/>
130 <output name="fasta_out" file="Mock_S280_L001_R1_001_small.trim.contigs.good.fasta" ftype="fasta"/>
131 <output name="bad_accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos" ftype="mothur.accnos"/>
132 <expand macro="logfile-test"/>
133 </test>
134 <test>
135 <param name="fasta_in" value="amazon.fasta" ftype="mothur.align"/>
136 <param name="count_in" value="amazon.count_table"/>
137 <param name="maxambig" value="0"/>
138 <param name="maxlength" value="275"/>
139 <output name="fasta_out" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.align"/>
140 <output name="count_out" md5="5f4a08bbf3ec12f954edbcc6b2a2feee" ftype="mothur.count_table"/>
141 <output name="bad_accnos" md5="66acde5349e34fc97be22032ce68eea5" ftype="mothur.accnos"/>
142 <expand macro="logfile-test"/>
143 </test>
144 </tests>
145 <help>
146 <![CDATA[
147
148 @MOTHUR_OVERVIEW@
149
150 **Command Documentation**
151
152 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.
153
154 .. _name: https://www.mothur.org/wiki/Name_file
155 .. _group: https://www.mothur.org/wiki/Group_file
156 .. _align.report: https://www.mothur.org/wiki/Align.seqs
157 .. _screen.seqs: https://www.mothur.org/wiki/Screen.seqs
158
159 ]]>
160 </help>
161 <expand macro="citations"/>
162 </tool>