Mercurial > repos > iuc > mothur_chimera_bellerophon

comparison chimera.bellerophon.xml @ 2:d8fdd5448cda 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 22:07:34 -0400
parents 2146e981bc7f
children ad0df6ad0499
comparison
equal deleted inserted replaced
1:c2c9c2078a0f 2:d8fdd5448cda
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 'chimera.bellerophon( 15 echo 'chimera.bellerophon(
16 fasta=fasta.dat, 16 fasta=fasta.dat,
17 filter=$filter, 17 filter=$filter,
18 correction=$correction, 18 correction=$correction,
19 #if int($window) > 0: 19 #if int($window) > 0:
20 window=$window, 20 window=$window,
21 #end if 21 #end if
22 #if $increment: 22 #if $increment:
23 increment=$increment, 23 increment=$increment,
24 #end if 24 #end if
25 processors='\${GALAXY_SLOTS:-8}' 25 processors='\${GALAXY_SLOTS:-8}'
26 )' 26 )'
27 | sed 's/ //g' ## mothur trips over whitespace 27 | sed 's/ //g' ## mothur trips over whitespace
28 | mothur 28 | mothur
29 | tee mothur.out.log 29 | tee mothur.out.log
30 ]]></command> 30 ]]></command>
31 <inputs> 31 <inputs>
32 <param name="fasta" type="data" format="fasta" label="fasta - Candiate Sequences"/> 32 <param argument="fasta" type="data" format="fasta" label="fasta - Candiate Sequences"/>
33 <param name="filter" type="boolean" falsevalue="False" truevalue="True" checked="false" label="filter - Apply a 50% soft vertical filter"/> 33 <param argument="filter" type="boolean" falsevalue="False" truevalue="True" checked="false" label="filter - Apply a 50% soft vertical filter"/>
34 <param name="correction" type="boolean" falsevalue="False" truevalue="True" checked="true" label="correction - Use the square root of the distances instead of the distance value"/> 34 <param argument="correction" type="boolean" falsevalue="False" truevalue="True" checked="true" label="correction - Use the square root of the distances instead of the distance value"/>
35 <param name="window" type="integer" value="0" label="window - Length of sequence you want in each window analyzed (uses default if &lt; 1)" help="Default is 25% of the sequence length."/> 35 <param argument="window" type="integer" value="0" label="window - Length of sequence you want in each window analyzed"
36 <param name="increment" type="integer" value="25" min="0" label="increment - Increment for window slide on each iteration" help="Default is 25, but you may set it up to sequence length minus twice the window."/> 36 help="Default is 25% of the sequence length. Uses default if &lt; 1"/>
37 <param argument="increment" type="integer" value="25" min="0" label="increment - Increment for window slide on each iteration"
38 help="Default is 25, but you may set it up to sequence length minus twice the window."/>
39 <expand macro="param-savelog"/>
37 </inputs> 40 </inputs>
38 <outputs> 41 <outputs>
39 <expand macro="logfile-output"/> 42 <expand macro="logfile-output"/>
40 <data name="out_file" format="txt" from_work_dir="fasta.bellerophon.chimeras" label="${tool.name} on ${on_string}: bellerophon.chimeras"/> 43 <data name="bellerophon.chimeras" format="txt" from_work_dir="fasta.bellerophon.chimeras" label="${tool.name} on ${on_string}: bellerophon.chimeras"/>
41 <data name="out_accnos" format="mothur.accnos" from_work_dir="fasta.bellerophon.accnos" label="${tool.name} on ${on_string}: bellerophon.accnos"/> 44 <data name="bellerophon.accnos" format="mothur.accnos" from_work_dir="fasta.bellerophon.accnos" label="${tool.name} on ${on_string}: bellerophon.accnos"/>
42 </outputs> 45 </outputs>
43 <tests> 46 <tests>
44 <test> 47 <test>
45 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.fasta"/> 48 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.fasta"/>
46 <param name="window" value="-1"/> <!-- don't use window if negative --> 49 <param name="window" value="-1"/> <!-- don't use window if negative -->
47 <output name="out_file" md5="435ff11d15d6c117e29747ab8ac36c75" ftype="txt"/> 50 <output name="bellerophon.chimeras" md5="435ff11d15d6c117e29747ab8ac36c75" ftype="txt"/>
48 <output name="out_accnos" ftype="mothur.accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.good.bellerophon.accnos"/> 51 <output name="bellerophon.accnos" ftype="mothur.accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.good.bellerophon.accnos"/>
49 <output name="logfile" ftype="txt"> <!-- outputs some results to the log file --> 52 <output name="logfile" ftype="txt"> <!-- outputs some results to the log file -->
50 <assert_contents> 53 <assert_contents>
51 <has_text text="Minimum"/> 54 <has_text text="Minimum"/>
52 <has_text text="Median"/> 55 <has_text text="Median"/>
53 <has_text text="Maximum"/> 56 <has_text text="Maximum"/>
54 </assert_contents> 57 </assert_contents>
55 </output> 58 </output>
59 <param name="savelog" value="true"/>
56 <expand macro="logfile-test"/> 60 <expand macro="logfile-test"/>
57 </test> 61 </test>
58 </tests> 62 </tests>
59 <help> 63 <help><![CDATA[
60 <![CDATA[
61 64
62 @MOTHUR_OVERVIEW@ 65 @MOTHUR_OVERVIEW@
63 66
64 **Command Documentation** 67 **Command Documentation**
65 68
82 85
83 86
84 .. _bellerophon: http://comp-bio.anu.edu.au/Bellerophon/doc/doc.html 87 .. _bellerophon: http://comp-bio.anu.edu.au/Bellerophon/doc/doc.html
85 .. _chimera.bellerophon: https://www.mothur.org/wiki/Chimera.bellerophon 88 .. _chimera.bellerophon: https://www.mothur.org/wiki/Chimera.bellerophon
86 89
87 ]]> 90 ]]></help>
88 </help>
89 <expand macro="citations"/> 91 <expand macro="citations"/>
90 </tool> 92 </tool>