Mercurial > repos > mbernt > maxbin2
changeset 3:cfd50144a871 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit fe30b00aa09587876f4c8be2a1494ca5ef6b8bac"
| author | iuc |
|---|---|
| date | Sun, 01 Dec 2019 09:42:33 -0500 |
| parents | 6a638de7915c |
| children | 4ef88f9a195d |
| files | maxbin2.xml |
| diffstat | 1 files changed, 9 insertions(+), 8 deletions(-) [+] |
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--- a/maxbin2.xml Tue Oct 29 08:45:20 2019 -0400 +++ b/maxbin2.xml Sun Dec 01 09:42:33 2019 -0500 @@ -1,4 +1,4 @@ -<tool id="maxbin2" name="MaxBin2" version="@MAXBIN_VERSION@+galaxy1"> +<tool id="maxbin2" name="MaxBin2" version="@MAXBIN_VERSION@+galaxy2"> <description>clusters metagenomic contigs into bins</description> <macros> <token name="@MAXBIN_VERSION@">2.2.7</token> @@ -49,16 +49,16 @@ #end if -thread \${GALAXY_SLOTS:-1} - && tar -xf out.marker_of_each_bin.tar.gz + && gzip -cd out.marker_of_each_bin.tar.gz | tar -xf - - ## redirect the idba out and err file content to stdout and err - ## since this is also wanted in case the error case ';' is used here to - ## separate commands + ## redirect the idba out and err file content to stdout and err + ## since this is also wanted in case the error case ';' is used here to + ## separate commands #if $intype_cond.intype_select == 'rds' and $intype_cond.reassembly != "" ; echo "==== IDBA stdout ====" - && cat out.idba.out + && if [[ -f out.idba.out ]]; then cat out.idba.out; fi && echo "==== IDBA stderr ====" 1>&2 - && cat out.idba.err 1>&2 + && if [[ -f out.idba.err ]]; then cat out.idba.err 1>&2; fi #end if ]]></command> <inputs> @@ -142,7 +142,8 @@ </data> </outputs> <tests> - <test expect_num_outputs="4"><!-- test w contigs and reads as input --> + <!-- test w contigs and reads as input --> + <test expect_num_outputs="4"> <param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" /> <conditional name="intype_cond"> <param name="intype_select" value="rds"/>