Mercurial > repos > iuc > mothur_merge_files
diff merge.files.xml @ 2:669032cdc951 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
| author | iuc |
|---|---|
| date | Tue, 20 Mar 2018 22:18:51 -0400 |
| parents | 28a135978ed0 |
| children | bc20680d28d5 |
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--- a/merge.files.xml Tue Sep 05 16:58:03 2017 -0400 +++ b/merge.files.xml Tue Mar 20 22:18:51 2018 -0400 @@ -7,21 +7,21 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - ## create symlinks to input datasets - #for $i in $merge.inputs: - ln -s "$i" input${merge.inputs.index($i)}.dat && - #end for +## create symlinks to input datasets +#for $i in $merge.inputs: + ln -s '$i' input${merge.inputs.index($i)}.dat && +#end for - echo 'merge.files( - input=#for $i in $merge.inputs#input${merge.inputs.index($i)}.dat-#end for#, - output=$output - )' - | sed 's/ //g' ## mothur trips over whitespace - | sed 's/-,/,/g' - | mothur - | tee mothur.out.log +echo 'merge.files( + input=#for $i in $merge.inputs#input${merge.inputs.index($i)}.dat-#end for#, + output=$output +)' +| sed 's/ //g' ## mothur trips over whitespace +| sed 's/-,/,/g' +| mothur +| tee mothur.out.log ]]></command> <inputs> <conditional name="merge"> @@ -48,6 +48,7 @@ <param name="inputs" type="data" format="mothur.accnos" multiple="true" label="inputs - accnos"/> </when> <!-- fasta --> </conditional> <!-- merge --> + <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> @@ -58,10 +59,11 @@ <param name="type" value="fasta"/> <param name="inputs" value="sample1.fa,sample2.fa,sample3.fa" ftype="fasta"/> <output name="output" file="output.fa" ftype="fasta"/> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> </tests> - <help> + <help><![CDATA[ @MOTHUR_OVERVIEW@ **Command Documentation** @@ -71,6 +73,6 @@ .. _merge.files: https://www.mothur.org/wiki/Merge.files - </help> - <expand macro="citations"/> + ]]></help> + <expand macro="citations"/> </tool>