Mercurial > repos > iuc > mothur_merge_taxsummary

comparison merge.taxsummary.xml @ 0:8eebcd1d81b0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:28:18 -0400
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children 297f3f6ad488
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-1:000000000000 0:8eebcd1d81b0
1 <tool profile="16.07" id="mothur_merge_taxsummary" name="Merge.taxsummary" version="@WRAPPER_VERSION@.0">
2 <description>Merge tax.summary 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.taxsummary(
18 input=#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="mothur.tax.summary" multiple="true" label="input - tax.summary files"/>
28 </inputs>
29 <outputs>
30 <expand macro="logfile-output"/>
31 <data name="output" format="mothur.tax.summary" label="${tool.name} on ${on_string}: merged sff"/>
32 </outputs>
33 <tests>
34 <test>
35 <param name="input" value="amazon.wang.knn.tax.summary,amazon.silva.wang.tax.summary"/>
36 <output name="output" md5="6e1276cc740b03d5407a3707322e1ee3" ftype="mothur.tax.summary"/>
37 <expand macro="logfile-test"/>
38 </test>
39 </tests>
40 <help>
41 <![CDATA[
42
43 @MOTHUR_OVERVIEW@
44
45 .. _Mothur: https://www.mothur.org/wiki/Main_Page
46
47 **Command Documentation**
48
49 The merge.taxsummary command takes a list of tax.summary files separated by dashes and merges them into one file.
50
51 .. _merge.taxsummary: https://www.mothur.org/wiki/Merge.taxsummary
52
53 ]]>
54 </help>
55 <expand macro="citations"/>
56 </tool>