Mercurial > repos > iuc > mothur_merge_sfffiles
diff merge.sfffiles.xml @ 0:e7f1da3e0339 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author | iuc |
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date | Fri, 19 May 2017 05:15:22 -0400 |
parents | |
children | e0d980518148 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/merge.sfffiles.xml Fri May 19 05:15:22 2017 -0400 @@ -0,0 +1,60 @@ +<tool profile="16.07" id="mothur_merge_sfffiles" name="Merge.sfffiles" version="@WRAPPER_VERSION@.0"> + <description>Merge SFF files</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <expand macro="version_command"/> + <command><![CDATA[ + @SHELL_OPTIONS@ + + ## create symlinks to input datasets + #for $i in $input: + ln -s "$i" input${input.index($i)}.dat && + #end for + + echo 'merge.sfffiles( + sff=#for $i in $input#input${input.index($i)}.dat-#end for#, + output=$output + )' + | sed 's/ //g' ## mothur trips over whitespace + | sed 's/-,/,/g' + | mothur + | tee mothur.out.log + ]]></command> + <inputs> + <param name="input" type="data" format="sff" multiple="true" label="input - sff files to merge"/> + </inputs> + <outputs> + <expand macro="logfile-output"/> + <data name="output" format="sff" label="${tool.name} on ${on_string}: merged sff"/> + </outputs> + <tests> + <test> + <param name="input" value="Fasting_Example1.sff,Fasting_Example2.sff"/> + <output name="output" ftype="sff"> + <assert_contents> + <has_text text="FLP3FBN01ELBSX"/> + </assert_contents> + </output> + <expand macro="logfile-test"/> + </test> + </tests> + <help> +<![CDATA[ + +@MOTHUR_OVERVIEW@ + +.. _Mothur: https://www.mothur.org/wiki/Main_Page + +**Command Documentation** + +The merge.sfffiles_ command merge inputs into a single output. + +.. _merge.sfffiles: https://www.mothur.org/wiki/Merge.sfffiles + +]]> + </help> + <expand macro="citations"/> +</tool>