Mercurial > repos > iuc > mothur_merge_sfffiles
comparison merge.sfffiles.xml @ 2:e0d980518148 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 22:10:34 -0400 |
parents | e7f1da3e0339 |
children |
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1:e7d03df2fc00 | 2:e0d980518148 |
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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 #for $i in $input: | 13 #for $i in $input: |
14 ln -s "$i" input${input.index($i)}.dat && | 14 ln -s '$i' input${input.index($i)}.dat && |
15 #end for | 15 #end for |
16 | 16 |
17 echo 'merge.sfffiles( | 17 echo 'merge.sfffiles( |
18 sff=#for $i in $input#input${input.index($i)}.dat-#end for#, | 18 sff=#for $i in $input#input${input.index($i)}.dat-#end for#, |
19 output=$output | 19 output=$output |
20 )' | 20 )' |
21 | sed 's/ //g' ## mothur trips over whitespace | 21 | sed 's/ //g' ## mothur trips over whitespace |
22 | sed 's/-,/,/g' | 22 | sed 's/-,/,/g' |
23 | mothur | 23 | mothur |
24 | tee mothur.out.log | 24 | tee mothur.out.log |
25 ]]></command> | 25 ]]></command> |
26 <inputs> | 26 <inputs> |
27 <param name="input" type="data" format="sff" multiple="true" label="input - sff files to merge"/> | 27 <param name="input" type="data" format="sff" multiple="true" label="input - sff files to merge"/> |
28 <expand macro="param-savelog"/> | |
28 </inputs> | 29 </inputs> |
29 <outputs> | 30 <outputs> |
30 <expand macro="logfile-output"/> | 31 <expand macro="logfile-output"/> |
31 <data name="output" format="sff" label="${tool.name} on ${on_string}: merged sff"/> | 32 <data name="output" format="sff" label="${tool.name} on ${on_string}: merged sff"/> |
32 </outputs> | 33 </outputs> |
36 <output name="output" ftype="sff"> | 37 <output name="output" ftype="sff"> |
37 <assert_contents> | 38 <assert_contents> |
38 <has_text text="FLP3FBN01ELBSX"/> | 39 <has_text text="FLP3FBN01ELBSX"/> |
39 </assert_contents> | 40 </assert_contents> |
40 </output> | 41 </output> |
42 <param name="savelog" value="true"/> | |
41 <expand macro="logfile-test"/> | 43 <expand macro="logfile-test"/> |
42 </test> | 44 </test> |
43 </tests> | 45 </tests> |
44 <help> | 46 <help><![CDATA[ |
45 <![CDATA[ | |
46 | 47 |
47 @MOTHUR_OVERVIEW@ | 48 @MOTHUR_OVERVIEW@ |
48 | 49 |
49 .. _Mothur: https://www.mothur.org/wiki/Main_Page | 50 .. _Mothur: https://www.mothur.org/wiki/Main_Page |
50 | 51 |
52 | 53 |
53 The merge.sfffiles_ command merge inputs into a single output. | 54 The merge.sfffiles_ command merge inputs into a single output. |
54 | 55 |
55 .. _merge.sfffiles: https://www.mothur.org/wiki/Merge.sfffiles | 56 .. _merge.sfffiles: https://www.mothur.org/wiki/Merge.sfffiles |
56 | 57 |
57 ]]> | 58 ]]></help> |
58 </help> | |
59 <expand macro="citations"/> | 59 <expand macro="citations"/> |
60 </tool> | 60 </tool> |