Mercurial > repos > iuc > mothur_trim_flows
diff trim.flows.xml @ 1:054074503e50 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
| author | iuc |
|---|---|
| date | Thu, 18 May 2017 18:33:52 -0400 |
| parents | f60bc63d84cf |
| children | 5c31047be933 |
line wrap: on
line diff
--- a/trim.flows.xml Fri Jun 24 16:53:21 2016 -0400 +++ b/trim.flows.xml Thu May 18 18:33:52 2017 -0400 @@ -4,8 +4,11 @@ <import>macros.xml</import> </macros> <expand macro="requirements"/> + <expand macro="stdio"/> <expand macro="version_command"/> - <command detect_errors="aggressive"><![CDATA[ + <command><![CDATA[ + @SHELL_OPTIONS@ + ## create symlinks to input datasets ln -s "$flow" flow.dat && #if $oligo.add == "yes": @@ -35,6 +38,7 @@ )' | sed 's/ //g' ## mothur trips over whitespace | mothur + | tee mothur.out.log ## prevent these two files from being gathered into collection && mv flow.trim.flow flow.trim && mv flow.scrap.flow flow.scrap @@ -84,8 +88,8 @@ <tests> <test><!-- test with defaults --> <param name="flow" value="mock.flow" ftype="mothur.sff.flow"/> - <output name="trim_flow" md5="91e44b2c4f00156cf6d816aa2ecb9bf8" ftype="mothur.sff.flow"/> - <output name="scrap_flow" md5="a0f5c3112195c69621d2e8db856cafb2" ftype="mothur.sff.flow"/> + <output name="trim_flow" md5="6850bb59570822aec6cd7aa7ce4675c4" ftype="mothur.sff.flow"/> + <output name="scrap_flow" md5="e5d39459c28f5e7245bae7c509f05cba" ftype="mothur.sff.flow"/> <output name="flow_files" ftype="tabular"> <assert_contents> <has_text text="flow"/> @@ -120,11 +124,11 @@ @MOTHUR_OVERVIEW@ -**Command Documenation** +**Command Documentation** The trim.flows_ command is analogous to the trim.seqs command, except that it uses the flowgram data that comes bundled in the sff file that is generated by 454 sequencing. It's primary usage is as a preliminary step to running shhh.seqs. Chris Quince has a series of perl scripts that fulfill a similar role [1]. This command will allow you to partition your flowgram data by sample based on the barcode, trim the flows to a specified length range, and cull sequences that are too short or have too many mismatches to barcodes and primers. -.. _trim.flows: http://www.mothur.org/wiki/Trim.flows +.. _trim.flows: https://www.mothur.org/wiki/Trim.flows ]]> </help>