Mercurial > repos > iuc > mothur_merge_sfffiles

comparison merge.sfffiles.xml @ 2:e0d980518148 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 22:10:34 -0400
parents e7f1da3e0339
children
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1:e7d03df2fc00 2:e0d980518148
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>