Mercurial > repos > iuc > mothur_screen_seqs

comparison screen.seqs.xml @ 4:2159457a4586 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
author iuc
date Wed, 14 Feb 2018 10:06:49 -0500
parents 7dabd4117ad1
children 921ff33138df
comparison
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3:7dabd4117ad1 4:2159457a4586
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@ 10 @SHELL_OPTIONS@
11 11
12 ## create symlinks to input datasets 12 ## create symlinks to input datasets
13 ln -s "$fasta_in" fasta_in.dat && 13 ln -s '$fasta' fasta.dat &&
14 ln -s "$names_in" names_in.dat && 14 ln -s '$names' names.dat &&
15 ln -s "$groups_in" groups_in.dat && 15 ln -s '$groups' groups.dat &&
16 ln -s "$qfile_in" qfile_in.dat && 16 ln -s '$qfile' qfile.dat &&
17 ln -s "$count_in" count_in.dat && 17 ln -s '$count' count.dat &&
18 ln -s "$alignreport_in" alignreport_in.dat && 18 ln -s '$taxonomy' taxonomy.dat &&
19 ln -s "$taxonomy_in" taxonomy_in.dat && 19 ln -s '$summary' summary.dat &&
20 ln -s "$summary" summary.dat && 20 #if $contigsrep.usecontigs == "yes":
21 ln -s "$contigsreport" contigsreport.dat && 21 ln -s '$contigsrep.contigsreport' contigsreport.dat &&
22 22 #end if
23 echo 'screen.seqs( 23 #if $alignrep.usealign == "yes":
24 fasta=fasta_in.dat 24 ln -s '$alignrep.alignreport' alignreport.dat &&
25 #if int($start) > -1: 25 #end if
26 ,start=$start 26
27 #end if 27 echo 'screen.seqs(
28 #if int($end) > -1: 28 fasta=fasta.dat
29 ,end=$end 29 #if int($start) > -1:
30 #end if 30 ,start=$start
31 #if int($minlength) > -1: 31 #end if
32 ,minlength=$minlength 32 #if int($end) > -1:
33 #end if 33 ,end=$end
34 #if int($maxlength) > -1: 34 #end if
35 ,maxlength=$maxlength 35 #if int($minlength) > -1:
36 #end if 36 ,minlength=$minlength
37 #if int($maxambig) > -1: 37 #end if
38 ,maxambig=$maxambig 38 #if int($maxlength) > -1:
39 #end if 39 ,maxlength=$maxlength
40 #if int($maxhomop) > -1: 40 #end if
41 ,maxhomop=$maxhomop 41 #if int($maxambig) > -1:
42 #end if 42 ,maxambig=$maxambig
43 #if int($criteria) > -1: 43 #end if
44 ,criteria=$criteria 44 #if int($maxhomop) > -1:
45 #end if 45 ,maxhomop=$maxhomop
46 #if $optimize: 46 #end if
47 ,optimize=$optimize 47 #if int($criteria) > -1:
48 #end if 48 ,criteria=$criteria
49 #if $qfile_in: 49 #end if
50 ,qfile=qfile_in.dat 50 #if $optimize:
51 #end if 51 ,optimize=$optimize
52 #if $names_in: 52 #end if
53 ,name=names_in.dat 53 #if $qfile:
54 #end if 54 ,qfile=qfile.dat
55 #if $groups_in: 55 #end if
56 ,group=groups_in.dat 56 #if $names:
57 #end if 57 ,name=names.dat
58 #if $alignreport_in: 58 #end if
59 ,alignreport=alignreport_in.dat 59 #if $groups:
60 #end if 60 ,group=groups.dat
61 #if $taxonomy_in: 61 #end if
62 ,taxonomy=taxonomy_in.dat 62 #if $taxonomy:
63 #end if 63 ,taxonomy=taxonomy.dat
64 #if $count_in: 64 #end if
65 ,count=count_in.dat 65 #if $count:
66 #end if 66 ,count=count.dat
67 #if $summary: 67 #end if
68 ,summary=summary.dat 68 #if $summary:
69 #end if 69 ,summary=summary.dat
70 #if $contigsreport: 70 #end if
71 ,contigsreport=contigsreport.dat 71 #if $contigsrep.usecontigs == "yes":
72 #end if 72 ,contigsreport=contigsreport.dat
73 ,processors='"\${GALAXY_SLOTS:-8}"' 73 ,minoverlap=$contigsrep.minoverlap
74 )' 74 ,ostart=$contigsrep.ostart
75 | sed 's/ //g' ## mothur trips over whitespace 75 ,oend=$contigsrep.oend
76 | mothur 76 ,mismatches=$contigsrep.mismatches
77 | tee mothur.out.log 77 #end if
78 #if $alignrep.usealign == "yes":
79 ,alignreport=alignreport.dat
80 ,minsim=$alignrep.minsim
81 ,minscore=$alignrep.minscore
82 ,maxinsert=$alignrep.maxinsert
83 #end if
84 ,processors='"\${GALAXY_SLOTS:-8}"'
85 )'
86 | sed 's/ //g' ## mothur trips over whitespace
87 | mothur
88 | tee mothur.out.log
78 ]]></command> 89 ]]></command>
79 <inputs> 90 <inputs>
80 <param name="fasta_in" type="data" format="fasta,mothur.align" label="fasta - Fasta to screen"/> 91 <param argument="fasta" 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)"/> 92 <param argument="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)"/> 93 <param argument="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)"/> 94 <param argument="minlength" type="integer" value="10" 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)"/> 95 <param argument="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)"/> 96 <param argument="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)"/> 97 <param argument="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)"/> 98 <param argument="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"> 99 <param argument="optimize" type="select" multiple="true" display="checkboxes" label="optimize - Optimize selected paramenters">
89 <option value="start">start</option> 100 <option value="start">start</option>
90 <option value="end">end</option> 101 <option value="end">end</option>
91 <option value="minlength">minlength</option> 102 <option value="minlength">minlength</option>
92 <option value="maxlength">maxlength</option> 103 <option value="maxlength">maxlength</option>
93 <option value="maxambig">maxambig</option> 104 <option value="maxambig">maxambig</option>
94 <option value="maxhomop">maxhomop</option> 105 <option value="maxhomop">maxhomop</option>
95 </param> 106 </param>
96 <param name="qfile_in" type="data" format="qual" optional="true" label="qfile - Sequence Quality file to screen"/> 107 <param argument="qfile" 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"/> 108 <param argument="names" 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"/> 109 <param argument="groups" 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"/> 110 <param argument="summary" type="data" format="mothur.summary" optional="true" label="summary file - as created by summary.seqs"
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"/> 111 help="saves processing time when screening with parameters in the summary file"/>
101 <param name="contigsreport" type="data" format="tabular" 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"/> 112 <param argument="taxonomy" type="data" format="taxonomy" optional="true" label="taxonomy - Taxonomy to screen"/>
102 <param name="taxonomy_in" type="data" format="taxonomy" optional="true" label="taxonomy - Taxonomy to screen"/> 113 <param argument="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
103 <param name="count_in" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> 114 <conditional name="alignrep">
115 <param name="usealign" type="select" label="Perform screening using an alignment report?" help="An alignment report is created by the align.seqs tool.
116 If you provide the alignment report file you can screen your sequences using the following parameters: minsim, minscore, and maxinsert">
117 <option value="yes">Yes</option>
118 <option value="no" selected="true">No</option>
119 </param>
120 <when value="yes">
121 <param argument="alignreport" type="data" format="mothur.align.report" label="alignreport - Align Report to screen with"/>
122 <param argument="minsim" type="integer" value="-1" min="-1" label="minsim - Minimum similarity to template sequences during alignment"/>
123 <param argument="minscore" type="integer" value="-1" min="-1" label="minscore - Minimum search score during alignment (ignored when negative)"/>
124 <param argument="maxinsert" type="integer" value="-1" min="-1" label="maxinsert - Maximum number of insertions during alignment (ignored when negative)"/>
125 </when>
126 <when value="no"/>
127 </conditional>
128 <conditional name="contigsrep">
129 <param name="usecontigs" type="select" label="Perform screening using a contigsreport?" help="A contigsreport is created by the make.contigs tool.
130 If you provide the contigs report file you can screen your sequences using the following parameters: minoverlap, ostart, oend and mismatches">
131 <option value="yes">Yes</option>
132 <option value="no" selected="true">No</option>
133 </param>
134 <when value="yes">
135 <param argument="contigsreport" type="data" format="tabular" label="contigsreport - Contigs Report to screen with"
136 help="this file is created by the make.contigs command"/>
137 <param argument="minoverlap" type="integer" value="-1" min="-1" label="minoverlap - Minimum overlap length (ignored when negative)"/>
138 <param argument="ostart" type="integer" value="-1" min="-1" label="ostart - Position the overlap must start by (ignored when negative)"/>
139 <param argument="oend" type="integer" value="-1" min="-1" label="oend - Position the overlap must end after (ignored when negative)"/>
140 <param argument="mismatches" type="integer" value="-1" min="-1" label="mismatches - Maximum number of mismatches (ignored when negative)"/>
141 </when>
142 <when value="no"/>
143 </conditional>
104 </inputs> 144 </inputs>
105 <outputs> 145 <outputs>
106 <expand macro="logfile-output"/> 146 <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}"/> 147 <data name="fasta_out" format_source="fasta" from_work_dir="fasta*.good.dat" label="${tool.name} on ${on_string}: good.${fasta.datatype.file_ext}"/>
108 <data name="bad_accnos" format="mothur.accnos" from_work_dir="fasta_in*.bad.accnos" label="${tool.name} on ${on_string}: bad.accnos"/> 148 <data name="bad_accnos" format="mothur.accnos" from_work_dir="fasta*.bad.accnos" label="${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 ${on_string}: qfile"> 149 <data name="qfile_out" format_source="qfile" from_work_dir="qfile*.good.dat" label="${tool.name} on ${on_string}: qfile">
110 <filter>qfile_in</filter> 150 <filter>qfile</filter>
111 </data> 151 </data>
112 <data name="names_out" format="mothur.names" from_work_dir="names_in*.good.dat" label="${tool.name} on ${on_string}: names"> 152 <data name="names_out" format="mothur.names" from_work_dir="names*.good.dat" label="${tool.name} on ${on_string}: names">
113 <filter>names_in</filter> 153 <filter>names</filter>
114 </data> 154 </data>
115 <data name="groups_out" format="mothur.groups" from_work_dir="groups_in*.good.dat" label="${tool.name} on ${on_string}: groups"> 155 <data name="groups_out" format="mothur.groups" from_work_dir="groups*.good.dat" label="${tool.name} on ${on_string}: groups">
116 <filter>groups_in</filter> 156 <filter>groups</filter>
117 </data> 157 </data>
118 <data name="alignreport_out" format="mothur.align.report" from_work_dir="alignreport_in*.good.dat" label="${tool.name} on ${on_string}: align.report"> 158 <data name="alignreport_out" format="mothur.align.report" from_work_dir="alignreport.good.align.report" label="${tool.name} on ${on_string}: align.report">
119 <filter>alignreport_in</filter> 159 <filter>alignrep.alignreport</filter>
120 </data> 160 </data>
121 <data name="count_out" format="mothur.count_table" from_work_dir="count_in*.good.dat" label="${tool.name} on ${on_string}: count"> 161 <data name="contigsreport_out" format="tabular" from_work_dir="contigsreport.good.contigs.report" label="${tool.name} on ${on_string}: contigs.report">
122 <filter>count_in</filter> 162 <filter>contigsrep.contigsreport</filter>
163 </data>
164 <data name="count_out" format="mothur.count_table" from_work_dir="count*.good.dat" label="${tool.name} on ${on_string}: count">
165 <filter>count</filter>
123 </data> 166 </data>
124 </outputs> 167 </outputs>
125 <tests> 168 <tests>
126 <test> 169 <test>
127 <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta" ftype="fasta"/> 170 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta" ftype="fasta"/>
128 <param name="maxambig" value="0"/> 171 <param name="maxambig" value="0"/>
129 <param name="maxlength" value="275"/> 172 <param name="maxlength" value="275"/>
130 <output name="fasta_out" file="Mock_S280_L001_R1_001_small.trim.contigs.good.fasta" ftype="fasta"/> 173 <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"/> 174 <output name="bad_accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos" ftype="mothur.accnos"/>
132 <expand macro="logfile-test"/> 175 <expand macro="logfile-test"/>
133 </test> 176 </test>
134 <test> 177 <test><!-- test with count table -->
135 <param name="fasta_in" value="amazon.fasta" ftype="mothur.align"/> 178 <param name="fasta" value="amazon.fasta" ftype="mothur.align"/>
136 <param name="count_in" value="amazon.count_table"/> 179 <param name="count" value="amazon1.count_table"/>
180 <param name="maxambig" value="0"/>
181 <param name="maxlength" value="500"/>
182 <output name="fasta_out" ftype="mothur.align">
183 <assert_contents>
184 <expand macro="test-fasta-format"/>
185 <has_text text="U68638"/>
186 <not_has_text text="U68589"/>
187 </assert_contents>
188 </output>
189 <output name="count_out" ftype="mothur.count_table">
190 <assert_contents>
191 <expand macro="test-count-format"/>
192 <has_text text="U68638"/>
193 <not_has_text text="U68589"/>
194 </assert_contents>
195 </output>
196 <output name="bad_accnos" ftype="mothur.accnos">
197 <assert_contents>
198 <expand macro="test-accnos-format"/>
199 <not_has_text text="U68638"/>
200 <has_text text="U68589"/>
201 <has_text text="ambig"/>
202 <has_text text="length"/>
203 </assert_contents>
204 </output>
205 <expand macro="logfile-test"/>
206 </test>
207 <test><!-- test screening with contigsreport -->
208 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta" ftype="fasta"/>
137 <param name="maxambig" value="0"/> 209 <param name="maxambig" value="0"/>
138 <param name="maxlength" value="275"/> 210 <param name="maxlength" value="275"/>
139 <output name="fasta_out" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.align"/> 211 <param name="usecontigs" value="yes"/>
140 <output name="count_out" md5="5f4a08bbf3ec12f954edbcc6b2a2feee" ftype="mothur.count_table"/> 212 <param name="contigsreport" value="Mock_S280_L001_R1_001_small.contigs.report"/>
141 <output name="bad_accnos" md5="66acde5349e34fc97be22032ce68eea5" ftype="mothur.accnos"/> 213 <param name="mismatches" value="18"/>
214 <output name="fasta_out" file="Mock_S280_L001_R1_001_small.trim.contigs.good.fasta" ftype="fasta"/>
215 <output name="bad_accnos" ftype="mothur.accnos">
216 <assert_contents>
217 <expand macro="test-accnos-format"/>
218 <has_text text="mismatches"/>
219 <has_text text="ambig"/>
220 </assert_contents>
221 </output>
222 <output name="contigsreport_out" ftype="tabular">
223 <assert_contents>
224 <expand macro="test-contigsreport-format"/>
225 <not_has_text text="M00967_43_000000000-A3JHG_1_1101_22487_4260"/>
226 <has_text text="M00967_43_000000000-A3JHG_1_1101_15923_3823"/>
227 </assert_contents>
228 </output>
229 <expand macro="logfile-test"/>
230 </test>
231 <test><!-- test screening with alignment report -->
232 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.fasta" ftype="fasta"/>
233 <param name="maxambig" value="0"/>
234 <param name="maxlength" value="275"/>
235 <param name="usealign" value="yes"/>
236 <param name="alignreport" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align.report"/>
237 <param name="minscore" value="100"/>
238 <output name="fasta_out" ftype="fasta">
239 <assert_contents>
240 <expand macro="test-fasta-format"/>
241 <not_has_text text="M00967_43_000000000-A3JHG_1_1101_14010_4122"/>
242 <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/>
243 </assert_contents>
244 </output>
245 <output name="bad_accnos" ftype="mothur.accnos">
246 <assert_contents>
247 <expand macro="test-accnos-format"/>
248 <has_text text="score"/>
249 </assert_contents>
250 </output>
251 <output name="alignreport_out" ftype="mothur.align.report">
252 <assert_contents>
253 <expand macro="test-alignreport-format"/>
254 <not_has_text text="M00967_43_000000000-A3JHG_1_1101_14010_4122"/>
255 <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/>
256 </assert_contents>
257 </output>
142 <expand macro="logfile-test"/> 258 <expand macro="logfile-test"/>
143 </test> 259 </test>
144 </tests> 260 </tests>
145 <help> 261 <help><![CDATA[
146 <![CDATA[
147 262
148 @MOTHUR_OVERVIEW@ 263 @MOTHUR_OVERVIEW@
149 264
150 **Command Documentation** 265 **Command Documentation**
151 266
154 .. _name: https://www.mothur.org/wiki/Name_file 269 .. _name: https://www.mothur.org/wiki/Name_file
155 .. _group: https://www.mothur.org/wiki/Group_file 270 .. _group: https://www.mothur.org/wiki/Group_file
156 .. _align.report: https://www.mothur.org/wiki/Align.seqs 271 .. _align.report: https://www.mothur.org/wiki/Align.seqs
157 .. _screen.seqs: https://www.mothur.org/wiki/Screen.seqs 272 .. _screen.seqs: https://www.mothur.org/wiki/Screen.seqs
158 273
159 ]]> 274 ]]></help>
160 </help>
161 <expand macro="citations"/> 275 <expand macro="citations"/>
162 </tool> 276 </tool>