Mercurial > repos > iuc > mothur_make_lefse
comparison make.lefse.xml @ 2:5e4ee2031e00 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
| author | iuc |
|---|---|
| date | Tue, 20 Mar 2018 21:54:05 -0400 |
| parents | d58287720f30 |
| children | 678c90b43e17 |
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| 1:1db7c73264b3 | 2:5e4ee2031e00 |
|---|---|
| 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 "$otu" otu.dat && | 13 ln -s '$otu' otu.dat && |
| 14 ln -s "$design" design.dat && | 14 ln -s '$design' design.dat && |
| 15 ln -s "$constaxonomy" constaxonomy.dat && | 15 ln -s '$constaxonomy' constaxonomy.dat && |
| 16 | 16 |
| 17 echo 'make.lefse( | 17 echo 'make.lefse( |
| 18 #if $otu.is_of_type("mothur.relabund"): | 18 #if $otu.is_of_type("mothur.relabund"): |
| 19 relabund=otu.dat, | 19 relabund=otu.dat, |
| 20 #else | 20 #else |
| 21 shared=otu.dat, | 21 shared=otu.dat, |
| 22 #end if | 22 #end if |
| 23 #if $design: | 23 #if $design: |
| 24 design=design.dat, | 24 design=design.dat, |
| 25 #end if | 25 #end if |
| 26 #if $constaxonomy: | 26 #if $constaxonomy: |
| 27 constaxonomy=constaxonomy.dat, | 27 constaxonomy=constaxonomy.dat, |
| 28 #end if | 28 #end if |
| 29 #if $label: | 29 #if $label: |
| 30 label=${ str($label).replace(",","-") }, | 30 label=${ str($label).replace(",","-") }, |
| 31 #end if | 31 #end if |
| 32 scale=$scale | 32 scale=$scale |
| 33 )' | 33 )' |
| 34 | sed 's/ //g' ## mothur trips over whitespace | 34 | sed 's/ //g' ## mothur trips over whitespace |
| 35 | mothur | 35 | mothur |
| 36 | tee mothur.out.log | 36 | tee mothur.out.log |
| 37 ]]></command> | 37 ]]></command> |
| 38 <inputs> | 38 <inputs> |
| 39 <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared or relabund - provide a shared or relabund file"/> | 39 <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared or relabund - provide a shared or relabund file"/> |
| 40 <param name="label" type="select" optional="true" label="label - OTU Labels" help="If none selected, the first label in your file will be used"> | 40 <param name="label" type="select" optional="true" label="label - OTU Labels" help="If none selected, the first label in your file will be used"> |
| 41 <expand macro="labeloptions"/> | 41 <expand macro="labeloptions"/> |
| 46 <option value="totalgroup" selected="true">totalgroup</option> | 46 <option value="totalgroup" selected="true">totalgroup</option> |
| 47 <option value="totalotu">totalotu</option> | 47 <option value="totalotu">totalotu</option> |
| 48 <option value="averagegroup">averagegroup</option> | 48 <option value="averagegroup">averagegroup</option> |
| 49 <option value="averageotu">averageotu</option> | 49 <option value="averageotu">averageotu</option> |
| 50 </param> | 50 </param> |
| 51 <expand macro="param-savelog"/> | |
| 51 </inputs> | 52 </inputs> |
| 52 <outputs> | 53 <outputs> |
| 53 <expand macro="logfile-output"/> | 54 <expand macro="logfile-output"/> |
| 54 <data name="lefse_out" format="tabular" from_work_dir="otu*.lefse" label="${tool.name} on ${on_string}: lefse"/> | 55 <data name="lefse_out" format="tabular" from_work_dir="otu*.lefse" label="${tool.name} on ${on_string}: lefse"/> |
| 55 </outputs> | 56 </outputs> |
| 56 <tests> | 57 <tests> |
| 57 <test><!-- test with shared file and defaults --> | 58 <test><!-- test with shared file and defaults --> |
| 58 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> | 59 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> |
| 59 <output name="lefse_out" md5="295633107cd983be73389e8b92164686" ftype="tabular"/> | 60 <output name="lefse_out" md5="295633107cd983be73389e8b92164686" ftype="tabular"/> |
| 61 <param name="savelog" value="true"/> | |
| 60 <expand macro="logfile-test"/> | 62 <expand macro="logfile-test"/> |
| 61 </test> | 63 </test> |
| 62 <test><!-- test with relabund file --> | 64 <test><!-- test with relabund file --> |
| 63 <param name="otu" value="amazon.an.relabund" ftype="mothur.relabund"/> | 65 <param name="otu" value="amazon.an.relabund" ftype="mothur.relabund"/> |
| 64 <param name="design" value="toymothur.design2" ftype="tabular"/> | 66 <param name="design" value="toymothur.design2" ftype="tabular"/> |
| 65 <param name="label" value="0.18"/> | 67 <param name="label" value="0.18"/> |
| 66 <output name="lefse_out" md5="c1e88702c6db198080c09f3b9c404c63" ftype="tabular"/> | 68 <output name="lefse_out" md5="c1e88702c6db198080c09f3b9c404c63" ftype="tabular"/> |
| 69 <param name="savelog" value="true"/> | |
| 67 <expand macro="logfile-test"/> | 70 <expand macro="logfile-test"/> |
| 68 </test> | 71 </test> |
| 69 </tests> | 72 </tests> |
| 70 <help> | 73 <help><![CDATA[ |
| 71 <![CDATA[ | |
| 72 | 74 |
| 73 @MOTHUR_OVERVIEW@ | 75 @MOTHUR_OVERVIEW@ |
| 74 | 76 |
| 75 **Command Documentation** | 77 **Command Documentation** |
| 76 | 78 |
| 77 The make.lefse_ allows you to create a lefse formatted input file from mothur's output files. | 79 The make.lefse_ allows you to create a lefse formatted input file from mothur's output files. |
| 78 | 80 |
| 79 .. _make.lefse: https://www.mothur.org/wiki/Make.lefse | 81 .. _make.lefse: https://www.mothur.org/wiki/Make.lefse |
| 80 | 82 |
| 81 ]]> | 83 ]]></help> |
| 82 </help> | |
| 83 <citations> | 84 <citations> |
| 84 <citation type="doi">10.1128/AEM.01541-09</citation> | 85 <citation type="doi">10.1128/AEM.01541-09</citation> |
| 85 </citations> | 86 </citations> |
| 86 </tool> | 87 </tool> |