Mercurial > repos > erasmus-medical-center > mycrobiota
changeset 1:e93e39c121b1 draft default tip
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit aadbfac9c48191cac625f10590082a6d1a0bfd09
| author | erasmus-medical-center |
|---|---|
| date | Tue, 29 Jan 2019 12:13:23 -0500 |
| parents | 607c5e7e0a64 |
| children | |
| files | recover_samples_discarded_by_subsample.xml |
| diffstat | 1 files changed, 17 insertions(+), 8 deletions(-) [+] |
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--- a/recover_samples_discarded_by_subsample.xml Wed Dec 13 10:09:50 2017 -0500 +++ b/recover_samples_discarded_by_subsample.xml Tue Jan 29 12:13:23 2019 -0500 @@ -19,17 +19,17 @@ && if [ -z "\$samples"]; then - touch fasta.pick.dat; - touch group.pick.dat; + cp fasta2.dat final_fasta; + cp group2.dat final_group; else echo "get.groups(fasta=fasta.dat, group=group.dat, groups=\$samples)" | sed 's/ //g' | mothur; - fi + + ## merge selected reads (fasta.pick.dat) with the fasta file from after sub.sample + echo "merge.files(input=fasta2.dat-fasta.pick.dat, output=final_fasta)" | sed 's/ //g' | mothur; - ## merge selected reads (fasta.pick.dat) with the fasta file from after sub.sample - && echo "merge.files(input=fasta2.dat-fasta.pick.dat, output=final_fasta)" | sed 's/ //g' | mothur - - ## merge group files - && echo "merge.files(input=group2.dat-group.pick.dat, output=final_group)" | sed 's/ //g' | mothur + ## merge group files + echo "merge.files(input=group2.dat-group.pick.dat, output=final_group)" | sed 's/ //g' | mothur; + fi ]]></command> <inputs> @@ -53,6 +53,15 @@ <output name="out_fasta" file="recovered.fasta"/> <output name="out_group" file="recovered.groups"/> </test> + <test><!-- test case where nothing was discarded --> + <param name="in_fasta" value="fasta_before_subsample_small.fasta" ftype="fasta"/> + <param name="in_fasta_subsampled" value="fasta_after_subsample_small.fasta" ftype="fasta"/> + <param name="in_group" value="groups_before_subsample_small.groups" ftype="mothur.groups"/> + <param name="in_group_subsampled" value="groups_after_subsample_small.groups" ftype="mothur.groups"/> + <param name="threshold" value="1"/> + <output name="out_fasta" file="fasta_after_subsample_small.fasta"/> + <output name="out_group" file="groups_after_subsample_small.groups"/> + </test> </tests> <help><![CDATA[ **What it does**