Mercurial > repos > iuc > mothur_merge_sfffiles
comparison merge.sfffiles.xml @ 0:e7f1da3e0339 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author | iuc |
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date | Fri, 19 May 2017 05:15:22 -0400 |
parents | |
children | e0d980518148 |
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-1:000000000000 | 0:e7f1da3e0339 |
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1 <tool profile="16.07" id="mothur_merge_sfffiles" name="Merge.sfffiles" version="@WRAPPER_VERSION@.0"> | |
2 <description>Merge SFF files</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 #for $i in $input: | |
14 ln -s "$i" input${input.index($i)}.dat && | |
15 #end for | |
16 | |
17 echo 'merge.sfffiles( | |
18 sff=#for $i in $input#input${input.index($i)}.dat-#end for#, | |
19 output=$output | |
20 )' | |
21 | sed 's/ //g' ## mothur trips over whitespace | |
22 | sed 's/-,/,/g' | |
23 | mothur | |
24 | tee mothur.out.log | |
25 ]]></command> | |
26 <inputs> | |
27 <param name="input" type="data" format="sff" multiple="true" label="input - sff files to merge"/> | |
28 </inputs> | |
29 <outputs> | |
30 <expand macro="logfile-output"/> | |
31 <data name="output" format="sff" label="${tool.name} on ${on_string}: merged sff"/> | |
32 </outputs> | |
33 <tests> | |
34 <test> | |
35 <param name="input" value="Fasting_Example1.sff,Fasting_Example2.sff"/> | |
36 <output name="output" ftype="sff"> | |
37 <assert_contents> | |
38 <has_text text="FLP3FBN01ELBSX"/> | |
39 </assert_contents> | |
40 </output> | |
41 <expand macro="logfile-test"/> | |
42 </test> | |
43 </tests> | |
44 <help> | |
45 <![CDATA[ | |
46 | |
47 @MOTHUR_OVERVIEW@ | |
48 | |
49 .. _Mothur: https://www.mothur.org/wiki/Main_Page | |
50 | |
51 **Command Documentation** | |
52 | |
53 The merge.sfffiles_ command merge inputs into a single output. | |
54 | |
55 .. _merge.sfffiles: https://www.mothur.org/wiki/Merge.sfffiles | |
56 | |
57 ]]> | |
58 </help> | |
59 <expand macro="citations"/> | |
60 </tool> |