Mercurial > repos > iuc > mothur_reverse_seqs
comparison reverse.seqs.xml @ 2:503898f17f42 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author | iuc |
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date | Tue, 20 Mar 2018 21:55:28 -0400 |
parents | a8a1a7c5ab14 |
children |
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1:c7cde36b331a | 2:503898f17f42 |
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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 "$fasta" fasta.dat && | 13 ln -s '$fasta' fasta.dat && |
14 | 14 |
15 echo 'reverse.seqs( | 15 echo 'reverse.seqs( |
16 fasta=fasta.dat | 16 fasta=fasta.dat |
17 )' | 17 )' |
18 | sed 's/ //g' ## mothur trips over whitespace | 18 | sed 's/ //g' ## mothur trips over whitespace |
19 | mothur | 19 | mothur |
20 | tee mothur.out.log | 20 | tee mothur.out.log |
21 ]]></command> | 21 ]]></command> |
22 <inputs> | 22 <inputs> |
23 <param name="fasta" type="data" format="fasta,mothur.align" label="fasta - Sequences to reverse complement"/> | 23 <param name="fasta" type="data" format="fasta,mothur.align" label="fasta - Sequences to reverse complement"/> |
24 <expand macro="param-savelog"/> | |
24 </inputs> | 25 </inputs> |
25 <outputs> | 26 <outputs> |
26 <expand macro="logfile-output"/> | 27 <expand macro="logfile-output"/> |
27 <data name="out_fasta" format_source="fasta" from_work_dir="fasta*.rc.*" label="${tool.name} on ${on_string}: rc.fasta"/> | 28 <data name="out_fasta" format_source="fasta" from_work_dir="fasta*.rc.*" label="${tool.name} on ${on_string}: rc.fasta"/> |
28 </outputs> | 29 </outputs> |
29 <tests> | 30 <tests> |
30 <test> | 31 <test> |
31 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/> | 32 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/> |
32 <output name="out_fasta" file="Mock_S280_L001_R1_001_small.trim.contigs.good.rc.align_head"/> | 33 <output name="out_fasta" file="Mock_S280_L001_R1_001_small.trim.contigs.good.rc.align_head"/> |
34 <param name="savelog" value="true"/> | |
33 <expand macro="logfile-test"/> | 35 <expand macro="logfile-test"/> |
34 </test> | 36 </test> |
35 </tests> | 37 </tests> |
36 <help> | 38 <help><![CDATA[ |
37 <![CDATA[ | |
38 | 39 |
39 @MOTHUR_OVERVIEW@ | 40 @MOTHUR_OVERVIEW@ |
40 | 41 |
41 **Command Documentation** | 42 **Command Documentation** |
42 | 43 |
43 The reverse.seqs_ command will generate a fasta containing the reverse complement of each sequence in the input fasta. | 44 The reverse.seqs_ command will generate a fasta containing the reverse complement of each sequence in the input fasta. |
44 | 45 |
45 .. _reverse.seqs: https://www.mothur.org/wiki/Reverse.seqs | 46 .. _reverse.seqs: https://www.mothur.org/wiki/Reverse.seqs |
46 ]]> | 47 |
47 </help> | 48 ]]></help> |
48 <expand macro="citations"/> | 49 <expand macro="citations"/> |
49 </tool> | 50 </tool> |