Mercurial > repos > iuc > mothur_remove_seqs

comparison remove.seqs.xml @ 2:0b8ca0026f28 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 22:12:08 -0400
parents e59ddb750b65
children
comparison
equal deleted inserted replaced
1:008f62670efc 2:0b8ca0026f28
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 ## if accnos file is empty, just output files as-is, mothur errors if accnos empty (e.g. chimera filtering in pipeline but sample had no chimeras) 12 ## if accnos file is empty, just output files as-is, mothur errors if accnos empty (e.g. chimera filtering in pipeline but sample had no chimeras)
13 #import os 13 #import os
14 #if $os.lstat(str($accnos)).st_size == 0: 14 #if $os.lstat(str($accnos)).st_size == 0:
15 echo "accnos file empty, nothing to remove, skipping step" 15 echo "accnos file empty, nothing to remove, skipping step"
16 #if $fasta_in: 16 #if $fasta_in:
17 && cp $fasta_in $fasta_out 17 && cp $fasta_in $fasta_out
18 #end if 18 #end if
19 #if $fastq_in: 19 #if $fastq_in:
20 && cp $fastq_in $fastq_out 20 && cp $fastq_in $fastq_out
21 #end if 21 #end if
22 #if $count_in: 22 #if $count_in:
23 && cp $count_in $count_out 23 && cp $count_in $count_out
24 #end if 24 #end if
25 #if $qfile_in: 25 #if $qfile_in:
26 && cp $qfile_in $qfile_out 26 && cp $qfile_in $qfile_out
27 #end if 27 #end if
28 #if $name_in: 28 #if $name_in:
29 && cp $name_in $name_out 29 && cp $name_in $name_out
30 #end if 30 #end if
31 #if $group_in: 31 #if $group_in:
32 && cp $group_in $group_out 32 && cp $group_in $group_out
33 #end if 33 #end if
34 #if $alignreport_in: 34 #if $alignreport_in:
35 && cp $alignreport_in $alignreport_out 35 && cp $alignreport_in $alignreport_out
36 #end if 36 #end if
37 #if $list_in: 37 #if $list_in:
38 && cp $list_in $list_out 38 && cp $list_in $list_out
39 #end if 39 #end if
40 #if $taxonomy_in: 40 #if $taxonomy_in:
41 && cp $taxonomy_in $taxonomy_out 41 && cp $taxonomy_in $taxonomy_out
42 #end if 42 #end if
43 #else: 43 #else:
44 ## create symlinks to input datasets 44 ## create symlinks to input datasets
45 ln -s "$accnos" accnos.dat && 45 ln -s '$accnos' accnos.dat &&
46 ln -s "$fasta_in" fasta_in.dat && 46 ln -s '$fasta_in' fasta_in.dat &&
47 ln -s "$fastq_in" fastq_in.dat && 47 ln -s '$fastq_in' fastq_in.dat &&
48 ln -s "$count_in" count_in.dat && 48 ln -s '$count_in' count_in.dat &&
49 ln -s "$qfile_in" qfile_in.dat && 49 ln -s '$qfile_in' qfile_in.dat &&
50 ln -s "$name_in" name_in.dat && 50 ln -s '$name_in' name_in.dat &&
51 ln -s "$group_in" group_in.dat && 51 ln -s '$group_in' group_in.dat &&
52 ln -s "$alignreport_in" alignreport_in.dat && 52 ln -s '$alignreport_in' alignreport_in.dat &&
53 ln -s "$list_in" list_in.dat && 53 ln -s '$list_in' list_in.dat &&
54 ln -s "$taxonomy_in" taxonomy_in.dat && 54 ln -s '$taxonomy_in' taxonomy_in.dat &&
55 55
56 echo 'remove.seqs( 56 echo 'remove.seqs(
57 accnos=accnos.dat 57 accnos=accnos.dat
58 #if $fasta_in: 58 #if $fasta_in:
59 ,fasta=fasta_in.dat 59 ,fasta=fasta_in.dat
60 #end if 60 #end if
61 #if $fastq_in: 61 #if $fastq_in:
62 ,fastq=fastq_in.dat 62 ,fastq=fastq_in.dat
63 #end if 63 #end if
64 #if $count_in: 64 #if $count_in:
65 ,count=count_in.dat 65 ,count=count_in.dat
66 #end if 66 #end if
67 #if $qfile_in: 67 #if $qfile_in:
68 ,qfile=qfile_in.dat 68 ,qfile=qfile_in.dat
69 #end if 69 #end if
70 #if $name_in: 70 #if $name_in:
71 ,name=name_in.dat 71 ,name=name_in.dat
72 #end if 72 #end if
73 #if $group_in: 73 #if $group_in:
74 ,group=group_in.dat 74 ,group=group_in.dat
75 #end if 75 #end if
76 #if $alignreport_in: 76 #if $alignreport_in:
77 ,alignreport=alignreport_in.dat 77 ,alignreport=alignreport_in.dat
78 #end if 78 #end if
79 #if $list_in: 79 #if $list_in:
80 ,list=list_in.dat 80 ,list=list_in.dat
81 #end if 81 #end if
82 #if $taxonomy_in: 82 #if $taxonomy_in:
83 ,taxonomy=taxonomy_in.dat 83 ,taxonomy=taxonomy_in.dat
84 #end if 84 #end if
85 $dups 85 $dups
86 )' 86 )'
87 | sed 's/ //g' ## mothur trips over whitespace 87 | sed 's/ //g' ## mothur trips over whitespace
88 | mothur 88 | mothur
89 | tee mothur.out.log 89 | tee mothur.out.log
90 #end if 90 #end if
91 ]]></command> 91 ]]></command>
92 <inputs> 92 <inputs>
93 <param name="accnos" type="data" format="mothur.accnos" label="accnos - Accession Names of sequences to be removed"/> 93 <param name="accnos" type="data" format="mothur.accnos" label="accnos - Accession Names of sequences to be removed"/>
94 <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - Fasta Sequences"/> 94 <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - Fasta Sequences"/>
95 <param name="qfile_in" type="data" format="qual" optional="true" label="qfile - Fasta Quality"/> 95 <param name="qfile_in" type="data" format="qual" optional="true" label="qfile - Fasta Quality"/>
99 <param name="alignreport_in" type="data" format="mothur.align.report" optional="true" label="alignreport - Align Report"/> 99 <param name="alignreport_in" type="data" format="mothur.align.report" optional="true" label="alignreport - Align Report"/>
100 <param name="list_in" type="data" format="mothur.list" optional="true" label="list - OTU List"/> 100 <param name="list_in" type="data" format="mothur.list" optional="true" label="list - OTU List"/>
101 <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/> 101 <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/>
102 <param name="count_in" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> 102 <param name="count_in" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
103 <param name="dups" type="boolean" truevalue="" falsevalue=",dups=false" checked="true" label="dups - Apply to duplicates"/> 103 <param name="dups" type="boolean" truevalue="" falsevalue=",dups=false" checked="true" label="dups - Apply to duplicates"/>
104 <expand macro="param-savelog"/>
104 </inputs> 105 </inputs>
105 <outputs> 106 <outputs>
106 <expand macro="logfile-output"/> 107 <expand macro="logfile-output"/>
107 <data name="fasta_out" format_source="fasta_in" from_work_dir="fasta_in.pick.dat" label="${tool.name} on ${on_string}: pick.fasta"> 108 <data name="fasta_out" format_source="fasta_in" from_work_dir="fasta_in.pick.dat" label="${tool.name} on ${on_string}: pick.fasta">
108 <filter>fasta_in</filter> 109 <filter>fasta_in</filter>
135 <tests> 136 <tests>
136 <test> 137 <test>
137 <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/> 138 <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/>
138 <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/> 139 <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/>
139 <param name="dups" value=""/> 140 <param name="dups" value=""/>
140 <expand macro="logfile-test"/> 141 <param name="savelog" value="true"/>
141 <output name="fasta_out" md5="2357e1429647afbe21521a60935919bf"/> 142 <expand macro="logfile-test"/>
143 <output name="fasta_out">
144 <assert_contents>
145 <expand macro="test-fasta-format"/>
146 <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/>
147 </assert_contents>
148 </output>
142 </test> 149 </test>
143 <test> 150 <test>
144 <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/> 151 <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/>
145 <param name="fastq_in" value="Mock_S280_L001_R1_001_small.fastq"/> 152 <param name="fastq_in" value="Mock_S280_L001_R1_001_small.fastq"/>
146 <expand macro="logfile-test"/> 153 <param name="savelog" value="true"/>
147 <output name="fastq_out" md5="1e10d0793f1c5f12388156d5922c0eb8"/> 154 <expand macro="logfile-test"/>
155 <output name="fastq_out">
156 <assert_contents>
157 <expand macro="test-fastq-format"/>
158 <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/>
159 </assert_contents>
160 </output>
148 </test> 161 </test>
149 <test><!-- test two input files --> 162 <test><!-- test two input files -->
150 <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/> 163 <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/>
151 <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/> 164 <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/>
152 <param name="fastq_in" value="Mock_S280_L001_R1_001_small.fastq"/> 165 <param name="fastq_in" value="Mock_S280_L001_R1_001_small.fastq"/>
153 <param name="dups" value=",dups=false"/> 166 <param name="dups" value=",dups=false"/>
154 <expand macro="logfile-test"/> 167 <param name="savelog" value="true"/>
155 <output name="fasta_out" md5="2357e1429647afbe21521a60935919bf"/> 168 <expand macro="logfile-test"/>
156 <output name="fastq_out" md5="1e10d0793f1c5f12388156d5922c0eb8"/> 169 <output name="fasta_out">
170 <assert_contents>
171 <expand macro="test-fasta-format"/>
172 <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/>
173 </assert_contents>
174 </output>
175 <output name="fastq_out">
176 <assert_contents>
177 <expand macro="test-fastq-format"/>
178 <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/>
179 </assert_contents>
180 </output>
157 </test> 181 </test>
158 <test> 182 <test>
159 <param name="accnos" value="amazon.bad.accnos"/> 183 <param name="accnos" value="amazon.bad.accnos"/>
160 <param name="count_in" value="amazon.count_table"/> 184 <param name="count_in" value="amazon.count_table"/>
161 <expand macro="logfile-test"/> 185 <param name="savelog" value="true"/>
162 <output name="count_out" md5="bd1cb7af6f277210c5c11ff7d7c54592"/> 186 <expand macro="logfile-test"/>
187 <output name="count_out">
188 <assert_contents>
189 <expand macro="test-count-format"/>
190 <has_text text="U68595"/>
191 </assert_contents>
192 </output>
163 </test> 193 </test>
164 <!-- TODO: make test for empty accnos file --> 194 <!-- TODO: make test for empty accnos file -->
165 </tests> 195 </tests>
166 <help> 196 <help><![CDATA[
167 <![CDATA[
168 197
169 @MOTHUR_OVERVIEW@ 198 @MOTHUR_OVERVIEW@
170 199
171 **Command Documentation** 200 **Command Documentation**
172 201
177 .. _list: https://www.mothur.org/wiki/List_file 206 .. _list: https://www.mothur.org/wiki/List_file
178 .. _align.report: https://www.mothur.org/wiki/Align.seqs 207 .. _align.report: https://www.mothur.org/wiki/Align.seqs
179 .. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline 208 .. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline
180 .. _list.seqs: https://www.mothur.org/wiki/list.seqs 209 .. _list.seqs: https://www.mothur.org/wiki/list.seqs
181 .. _remove.seqs: https://www.mothur.org/wiki/Remove.seqs 210 .. _remove.seqs: https://www.mothur.org/wiki/Remove.seqs
182 ]]> 211
183 </help> 212 ]]></help>
184 <expand macro="citations"/> 213 <expand macro="citations"/>
185 </tool> 214 </tool>